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X-ray Crystallography - Science method

Explore the latest questions and answers in X-ray Crystallography, and find X-ray Crystallography experts.
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Apart from X ray crystallography.
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CryoEM
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I divided two compounds and found that when their absolute configuration at the 7-position is(R), the C-7 carbon spectrum data is 38.6, and the C-8 carbon spectrum data is 26.7; when the absolute configuration of the 7-position is(S), the C-7 carbon spectrum data is 37.4, and the C-8 carbon spectrum data is 27.1. The absolute configuration of C-7 was determined from single-crystal X-ray crystallography.
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You have two ionizable hydroxy groups in your enantiomers. Your compounds can also exist in a keto- and an enolic forms. Provided that you really have two pure enantiomers 1 and 2, the chemical shift of C7 and C8 must depend on the state of your compounds in solution and hence on the specific conditions used. Small variations in concentration of an acid or a base may change either the predominant form or the state of equilibrium in which your compounds exist. It should be very important to use the same purification procedure for each of the enantiomers and the same lot of solvent for NMR. One simple test you can do is to record an NMR from 1:1 mixture of 1 and 2. If your compounds are enantiomers, you should see only one peak for each C7 and C8. If the spectrum of the mixture shows two peaks for each C7 and C8, then your compounds are unlikely to be enantiomers.
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Greetings all scientist!!
I would like to know, which is the best software for Rietveld refinement among FullProf vs Rietan FP.
Thank you all for Your wonderful opinions in advance.
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First thing you definitely need is the best quality of xrd data. Both refinement tools you mentioned will always produce reliable outcomes, only if you thoroughly understand how refinement works.
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Hello all, this is a 2Fo - Fc and Fo - Fc map of my protein - ligand complex (the R-free is 0.4464), and I can't find out what the hollow electron density map in the center is.
Since the Fo - Fc in that area is 0, I assume that there is no ligand.
However the 2Fo - Fc is still positive with no structure inside!
Is that a noise? Or is it a consequence of a low R-free value?
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before trying to help you, there are some important questions that one needs from you.
Firstly, what's the resolution of te data, how did you solve the phase problem, and in what stage of the refinement are you? All of these are very important issues because an Rfree of 44% is way to high.
Secondly, regarding the screenshot itself, at what sigma level did you got it? The map seems very noisy, and any information at a very low sigma level, together with an Rfree of 44%, is not worth interpretation from the crystallographer.
Thirdly, I apologise but I cannot see any FoFc density in the screenshot. There is a very small green blob at the lower right corner but apart from that I cannot see anything.
I hope you can solve your problem and I apologise if I was not very helpful. Please contact me in private (or by e-mail: jbrito@itqb.unl.pt), if you need further assistance (or don't want to publicly divulge any details.
Best regards,
Jose
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I have a dataset from x-ray crystallography that is has poor statistics from processing (high Rmerge) and does not refine particularly well. I ran the merged reflections through Xtriage (Phenix) and the program tells me that my space group may be incorrect and suggests that I try merging in lower symmetry.
I have done very little manipulation of the files that go in to scaling and processing before, so I'm not sure how I can use XDS to merge in lower symmetry. Usually, I use the processed file from XDS coming off the beamline with no problem, but not this time!
Any help in figuring out how to do this would be much appreciated.
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Dear Gabby,
if I recall correctly, SG 16 is P222 and SG 19 is P212121. So basically, what is happening is that the program is indexing and integrating in the Laue group primitive orthorhombic P222, but then, looking at systematic absences, it outputs space group P212121. Nothing wrong or cumbersome here.
If you want to process with XDS in lower symmetry, here's what you should change in your XDS.INP file:
SPACE_GROUP_NUMBER= 16 UNIT_CELL_CONSTANTS= a b c alpha delta gamma
Anyway, I take this opportunity to make a shameless advertisement (although I am not part of the team or have any interest in this advertisement whatsoever): try to process your data with autoPROC (https://www.globalphasing.com/autoproc/). autoPROC is a pipeline of programs that uses XDS, POINTLESS, AIMLESS and STARANISO for data reduction, space group assignment and iso/aniso scaling, respectively.
The program is quite visual and intuitive, and it will tell (you will see it!), what is happening with your data and what you can do to test different space groups or try different protocols to improve statistics.
Anyway, coming back to the beginning, if you are phasing by molecular replacement, you can use your P222-reduced dataset, and ask the MR program (usually PHASER), to try "all possible in same point group). This way you will know for sure if it's P222 or any of the subgroups of it.
Please contact me in private if you need further assistance.
Best regards,
Jose
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Hello All,
I'm now synthesizing some ruthenium(II) tris(heteroleptic) complexes with the anion hexafluorophosphate.
However, when I'm trying to grow crystals for my complexes, several common solvent pairs (ACN/ether, MeOH/ether, THF/ether ......) does not provide me fine crystals.
Recently, I've found that some research use the solvent pairs Acetone/H2O or MeOH/H2O, and I would like to try the solvent pairs.
Therefore, I'm wondering how I can grow crystals from these solvent pairs? Since water does not evaperate easily for the slow diffusion method, and the density of water is too large for the bilayer method.
Do anyone have experiences using these solvent pairs? Or can anyone give me some suggestions in recrystallization? Thanks!
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Dear Cheng Yun Wu many thanks for sharing this very interesting technical question with the RG community. It might be worth a try using acetonitrile to recrystallize your ionic ruthenium complexes. Often such compounds show a good solubilty in hot acetonitrile and form nice crystals upon cooling of the solution to room temperature. Hot water alone might also be worth a try. If your compounds are very soluble in acetone, you could also try a vapor diffusion technique in which you let diethyl ether diffuse into the actone solution. For more potentially useful suggestions please also have a look at the attached guides to growing single crystals.
Good luck with your experiments and best wishes, Frank Edelmann
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I am contemplating purchasing this software and would like people's opinion.
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Crystalmaker X is compatible with mac OS and macbooks with the Apple chip.
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Can anyone please explain which type of structure is preferred for a ligand-Receptor docking study? When both the NMR based and X ray crystallography based structures both are available in PDB?
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X-ray-based structures are preferred because of their higher resolutions
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When solving the phase problem in x-ray crystallography using the heavy atom isomorphic replacement method, we cannot calculate the patterson function for the protein structure factor and instead calculate it for the heavy atom structure factor. However, why is it that we can calculate the patterson function for the protein structure factor without problems in the molecular replacement method?
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Dear Jane, as a synthetic chemist I'm not an expert enough to give you a qualified answer to your interesting technical question. However, I just came across the following potentially useful article which might help you in your analysis:
An introduction to molecular replacement
Fortunately this article has been posted by the authors as public full text on RG. Thus you can freely download the pdf file.
Good luck with your research and best wishes!
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After the synthesis of a compound at the mono Crystal form I process by structural determination. I ground the product and passed in XRD powder, when I calculated the distance and the lattice planes with HKLgen (using the cell parameters found for the single crystal), I cannot index my spectrum powder? (I did the same for three other hybrid compounds is always the same).
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At present I am working on low valent metal complexes. I am intended to determine their structures by X- ray crystallography. Therefore it would be helpful for me if you answer me the most appropriate methods of crystallization of low valent metal complexes to grow single crystals suitable for XRD.
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Dear Shafikul, many thanks for asking this very interesting and important technical question. Growing single-crystals suitable for X-ray diffraction is often a more difficult task than preparing the respective compounds. I assume that you are equipped to handle air-sensitive compounds. The most common crystallization method is cooling of saturated solutions in organic solvents in the refrigerator or carefully layering such solutions with a non-polar solvent. Vapor diffusion techniques can also be tried within a glovebox. You can find a number of very useful crystallization guides in the internet. For example, please have a look at the attached articles.
Good luck with your work and best wishes!
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Can someone explain to me the phasing problem with X-ray crystallography? How do you get around this?
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Dear Ranjuna,
You may also find useful to read some example from Teaching and Education Section of JAC:
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I am depositing indium oxide thin film (30 nm) and nano wire (200 nm) on p-type Si substrate using E-beam evaporator. I took the XRD Measurement so i want to know how to calculate d-spacing and lattice constant and what information we will get from d-spacing and lattice constant about the structure. Even i want to know through XRD peak how we can analyse whether it is bcc- cubic or simple cubic (Manually, without comparing withJCPDS File, is there any manual way). I am attaching XRD Measurement file. The XRD peaks are 211/ at 21 (degree) , 222/ 33(deg) ,622 / 62(deg) , 032/ 69 (deg).
Please suggest.
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In this video tutorial, I have explained in detail the d-spacing (interplanar spacing) and how to calculate it from the XRD data using OriginLab software. In the case you want to further ask about it, please do comment on the specific video, I'll respond to it shortly. I have provided the practice as well as calculations files here. Thanks
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I am not sure whether crystalexplorer is corrupted or not? I have tried to open .cif file downloaded the Crystallography Open Database, but still can't open it ? I hereby attach this file and please do check it. if it works well, please advise how I can perform hirshfeld surface analysis?
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Probably the latest version does not match with the hardware of your system.
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Hi,
I have some molecules with known crystallography data (cif file) I wanted to calculate the EXANES and XANES for the material.
please suggest me the best way ?
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The problem for all kinds of EXAFS / XANES simulation is a correct and physically valid structural model. This not only includes the positions of the atoms, but also disorder parameters, site occupancies, and potential models. Here, in particular for XANES calculations, small changes may have a big influence on the calculated spectra. For EXAFS, the situation is more safe, as those type of calculations are much more straightforward ... see e.g. the review by John Rehr (Rev. Mod. Phys. 72 (2000) 621, DOI 10.1103/RevModPhys.72.621). Hope this helps, Dirk
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I have tried every combination of parameter changes and after that i have a poor chi square value. I can't get it lower any further. I know there have been a lot of discussion about Rietveld refinement but i can not find any solution for my case. Any insight will be appreciated.
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Should I retake XRD data?
No, it is not necessary. However, any mismatch in the experimental and theoretical calculated point in the fitting will generate a significant influence on chiˆ2.
What conditions should I follow if my data is not perfect for refinement?
It looks ok for refinement; as you can see, there is no peak between, let say, 5 and 22 or 23; that part could be eliminated in a new experiment or just put as a restriction to not be fitted during the fitting process. Only that procedure will decrease the Chiˆ2 that will not consider those background points 5 - 20 2theta.
I am not familiar with the incorporation of vacancies.
You may try it releasing the occupation of the metal sites. Firstly, it will give some insight into cation vacancies; you may check the anion vacancy in the same way. Be aware that doing the procedure you may allow distortion in the structure needs critical evaluation after the fitting.
How would I take oxidation state in fullprof?
Usually, when you define the cation, in the PCR, the Ca atom is in sequence written as Ca2+; this will tell the program how many electrons must be taken.
I have tried Pseudo-Vogit axial digvergent as well. It did not improve much.
In principle, it tells you there is no stacking fault problem or high distortion into your sample's peak profile. Use this information with care, probing other possibilities.
To adequately use FullProf, it is necessary to do it with a known structure first, feel how the fitting undergoes after that expend some time in your real sample.
Best regards
WNM
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i synthesized aromatic schiff base from 3-aryl-5-amino 1,2,4-triazol. How can i know it is E or Z using another tool than X ray crystallography.
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AF2 may most strongly impact experimental determination of protein structure by multiple methods with possible benefits and negative impacts over time.
Some areas may need to quickly pivot or become obsolescent, whereas other may thrive.
Structures of large macromolecular machines should be enabled by having accurate computational structures for subunits and components.
The already great value of sequence data (which is doubling every 8 months) is likely to become far greater by being more directly connected to spatial information.
Overall the pace of biology and biophysical advances can be expected in increase by the ability to better harness the flood of sequence data.
What do you think?
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X-ray people might be impacted more than NMR and cryo-EM people by AF2. It may replace all biophysical techniques for structural determination someday, IMHO, they advertise much better than academic groups for the things they've achieved and still a long way to go (like when Rosetta first introduced). Not to mention the missing pieces like non-natural amino acids, binding partners, dynamics, different circumstances in the cell, more or less scientists would like to validate the prediction experimentally. However, it is hard to argue with its valuable inputs and insights before wet bench works that cost a lot.
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An interstitial atom (such as H, N, O) sitting not on their regular place, but between other atoms in the metals structure.
How to detect where is their location on that structure (in crystallographic viewpoints) with instrument analysis rather than assumed.
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For BCC matrix and interstitials mechanical loss spectra can be measured to quantify amount of interstices. More info you can find in the paper:
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The current state of the art is exploring the three-dimensional structure of RNA by x-ray crystallography.
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I am going with the same answer response of @Adron.
Good luck in your research @Dr.Ibrahim
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there are a number of textbooks available for studying x-ray crystallography by targeting Structural Biology and some of them are definitely excellent. I just want to pick one single textbook which will cover all of the aspects of the x-ray crystallography. As a novice which one will be perfect or at least suitable for me? Please give me your suggestion.
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I Agree With Piotr Zabierowski
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I am refining the crystal structure of a protein that is around 20 kDa. I am getting towards the point where most of the validation statistics and residual look nice: resolution 1.85Å, Rfree=19.5% Rwork=15.5%, Angle and bonds RMS below 0.01Å respectively 1.1˚, mol probity score < 1.1, No Ramachandran outliers and over 98% of Ramachandran favoured, no C-beta outliers, very low clashscore. There are a few rotamer that still need a little bit of attention. After correcting them manually with Coot I usually follow with a short round of refinement (3 macro cycles) with Phenix.refine using the following parameters:
Real space position (XYZ), TLS, individual B-factors and both X-ray /stereochemistry and X-ray ADP weight optimisation. Unfortunately The R-stats always get worse (e.g. +1% for R-free) while the geometry (angle and bond) marginally improves if at all. The rotamers that I have just corrected are often back to the wrong position. Basically my model gets worse. I have played around with the different parameters but I always end up with the same problem. What is the best refinement strategy in this kind of situation? I was wondering if there is a way to tell phenix to make minimal changes to most of the structure and only focus on the area that I have recently modified. I would be keen to learn how to play with Phenix a little more efficiently.
Your help is much appreciated.
Best regards
Guillaume
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If your previous refinement strategy worked better then stick to it. Just rerun the original refinement strategy with the corrected rotamers as input and see in phenix.refine maintains them better without fitting the weight terms.
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I have been trying to synthesize Grephene Quantum dots using graphite using microwave assisted disintegration.
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Agnishwar Girigoswami very interesting article, I will this into my research, Thanks for sharing.
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Basically I want to know what Bragg reflexes I can access with my goniometer.
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I know that x-ray crystallography can be used, and various applications of electron microscopy. however are there any others. I was thinking maybe immunoprecipitation followed by western blotting?
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Yes, you can do any test related to the capsid's antibody, If the antibody is available; or If Capsid protein is immunogenic, which helps to produce antibodies in the mammalian system. You can get antibodies after expression, purification of this protein (immunogenic) through any compatible or recommendable system.
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I want to determine micro strain of tin oxide samples prepared via different mechanism. Kindly suggest me how to determine W-H plot of these samples using XRD pattern.
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Williamson-Hall plot is a method for determination of "mean values" of crystallite size and strain. If a high quality program for Rietveld analysis or for whole powder pattern decomposition supporting microstruce analysis is available this might be better than evaluation by a Williamson-Hall plot.
To provide a Williamson-Hall plot you need a scan covering a large 2theta range and a method for determination of the full width at half maximum B (fwhm) of many peaks of the phase you are interested in. The fwhms must be corrected for instrumental broadening. The easiest would be to substract the line width b of a distinct peak of a well crystalline refernce sample yielding Bcor = B - b. More relialable methods for correcting exist.
The Bcor values (fwhm in degree) are transformed to arc values Bkor', Bcor'(arc) = Bcor(degree) / 180° * pi. Then a plot of Bcor'*cos(theta) versus sin(theta) will be produced. The value of the slope provides the "mean" strain epsilon. Ref. e.g. . http:/pd.chem.ucl.ac.uk/pdnn/peaks/sezedet.htm.
Anisotropic line broadening, correct values of instrumental broadening and shapes of the peaks of your sample may make things more difficult. Please also check
Regards
Robert
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I have a protein crystal structure at 1.83 angstroms with 2 molecules in the asymmetric unit. But the B factor of the second molecule is almost twice as large as the first. After running ARP/wARP , the first protein molecule is built in but only 50% of the second molecule is built into the electron density. It appears that I somehow have weak or missing reflections for the second protein molecule. How can this be?
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Unfortunately I have run out of time for further experimental work. But thanks a lot for the insight and suggestions, they have been very helpful !! :)
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Dear all,
I have a good quality x-ray powder diffraction pattern. For indexing, I tried different software, However, I am sure it can also be done more easily with TOPAS academic version. I know how to search peak with Le bail but I could not apply any indexing algorithms such as ITO etc. in TOPAS. I also use Jedit interface.
I could not find any good material or example on internet. I would be really appreciate if any one can help me or send me a tutorial link.
#XRD #Indexing #TOPAS #crystallography #mineralogy
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Hi Mehdi,
Why don't you look up the textbook "Rietveld Refinement: Practical Powder Diffraction Pattern Analysis using TOPAS" by R. Dinnebier, A. Leineweber, and J.S.O. Evans? There are also somee tutorials on the internet.
Good luck,
Andrzej
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If i repeat a sample at different scanning rate on same instrument, then is there any chance that there will be a shift in peak positions or change in Intensity?
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If you are recording XRD pattern of same materials using same diffractometer of same mounting, peak positions will not change with changing scan rate. Intensity of the XRD data shoes inverse behaviour to the scan rate.
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1) It’s known that x-ray crystallography is better than NMR or homology modeling;
2) Also, it’s known that adaptable resolution (<2 A) is better;
3) And the target should not have missing residues; [how can I know about this criteria?]
BUT
By searching PDB, many of the results (in my case, all of them) are x-ray diffraction, and many of them are in adaptable resolution.
In my case, searching «phosphodiesterase-5» resulted in 30 items in humans.
How can I select the best one for docking?
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"3) And the target should not have missing residues; [how can I know about this criteria?]"
Compare the sequence downloaded from the pdb (SEQRES records) to the sequence extracted from the coordinates.
"How can I select the best one for docking?"
Do a 3D alignment of the potential template structures and look at it carefully - it gives you an idea of which parts of the structure are flexible.
If there is a lot of flexibility in the vicinity of the putative ligand binding site, you might consider using several different structures representing different conformational states.
By comparing free to liganded structures, you can assess whether there are conformational changes associated with ligand binding. If so, a liganded structure (with the ligand removed) is better for docking.
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Please aid with software as well as strategies in order to get X-ray structure in a similar fashion to single crystal X-ray refinement. We have D2 Phaser-Bruker XRD instrument to obtain PXRD data available. Thanks in advance
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EXPO2014 (http://www.ba.ic.cnr.it/softwareic/expo/) is good software for structural determination and rietveld refinement. It is easy to use and has a good manual.
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In several screens, I saw some crystals that look like protein crystals, but they redissolved and became unapparent during checking them under light microscopy after a few seconds.
For example, in a buffer screen containing 30%v/v PEG400,100mM Tris/HCl and 200mM Li2SO4, a rather big (~0.1mm) triangular star-like crystal became unapparent after about 1 minute.
It is really possible for protein or salt crystals? In the reservoir buffer of this screen, there were several plate-like crystals seeming to be Li2SO4 crystals or PEG400! These were different from the crystals in drop.
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To me, this type of crystals is caused from lithium. You can incubate your protein buffer without protein to the same reservoir and see what's going on.
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I am wondering whether the PEG prepared from powder is suitable for crystallisation purpose. As I read from the product speciation of PEG produced by Hampton Research, it mentioned that it is produced for crystallisation uses and it is monodisperse. Hence, I am wondering whether the PEG prepared by ourselves from powder is carrying the same properties.
Thank you.
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Certainly you can use PEG powder to prepare crystallization solutions. I did that back in graduate school and could reproduce crystals initially grown from commercial PEG solutions. The thing is home-made PEG solutions are often not as reproducible as commercial ones due to their high viscosity, so it might be difficult to optimize/reproduce crystals that are picky.
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If the N-terminal region of a protein is known to be very flexible because it doesn't have a good electron density when doing X-ray crystallography, will a His6-tag be expected to affect its activity?
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Dear Gabriela,
Your question is quite interesting despite a very wide use of His-tags and common acceptance of multiple results obtained with tagged proteins. There are at least three considerations that you should take into account and follow the advice of George (doing experiments with and without).
1) Location of the His-tag (including the linker) can influence folding.
2) Mobility of the tag can influence the dynamics of the protein, the dynamics of the substrates and dynamics of the products, therefore overall activity.
3) His-tag can influence metal ion load by spurious chelation.
You may ask how I got this prompts?
As a careful crystallographer I refined many His-tags in my own as well as many deposited in PDB proteins. They are routinely unrefined by a common assumption that they are mobile and not important. But that is a usual error of a confirmation bias. We get what we expect, by not doing the job properly.
The experience shows that 30-50% of the His-tags, I refined, were clearly visible with comparable ED (electron density) level to the protein. In almost all the cases the His-tags influenced the conformation of the protein in some small but sometimes very substantial manner. In several cases they were responsible for aggregation and the form of a crystal. In two cases (because of the closeness to the active site) they clearly influenced the activity.
Good Luck.
Bog
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How to determine the relative content of phases from diffraction patterns? (for example, through integrated intensity)
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Generally speaking; (I) the peak height or the maximum intensity in XRD spectra represents an approximation for the peak intensity, (II) the peak area a.k.a. the integral intensity can be considered as the real measure for the peak intensity that is related to the crystal structure that is commonly used to determine the amount of a particular phase, while (III) peak width or Full Width at Half Max (FWHM) aka half width represent crystallite size, and defects in form of strain and disorder (with line asymmetry associated with particle size). More detail description could be find at: http://www.fhi-berlin.mpg.de/acnew/department/pages/teaching/pages/teaching__wintersemester__2015_2016/frank_girgsdies__peak_profile_fitting_in_xrd__151106.pdf
Also, an example for the application of Rietveld method used in application of XRD in phase analysis can be seen at: http://www.icdd.com/resources/axa/vol47/v47_40.pdf
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Given the different quality metrics for protein models based on XRD and NMR data, I want to know your opinon.
In particular, how good is the agreement between NMR and XRD-derived structures? In case of disagreement, which method would your trust better (assuming both were reasonably conducted)?
When facing the solution of a structure de novo, how is the method chosen? How much does it cost to solve a structure by X-ray compared to NMR?
Thank you very much for your insights!
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The two methods of structure determination are based on completely different properties of proteins. An NMR structure is calculated from magnetic properties of several nuclei while an X-ray structure is derived from electron density of non hydrogen atoms.
Structures of both methods have a high confidence, the determination of secondary structure elements, their relation and loops playing role in catalytic activity is reassuring. The possibility of some catalytic reactions in the circumstances of measurement reinforces the confidence of 3D structures. Regions, weakly defined by NMR or possibly affected by crystal packing, are determined less confidently. These are usually longer surface loops, chain terminals or domain interconnecting loops that have flexible conformation in natural circumstances as well. Pockets with catalytic activity and the framework of secondary structures that is responsible to fix the pocket are usually stabile enough not to be affected by the changes of circumstances.
The nature of the two methods results in the fact that NMR structures are never so concrete as X-ray ones, they allow larger freedom for motions of loops and terminals. It is probable that this freedom is related to dynamism of these regions in solution, however the modelling character of molecular dynamic calculations reminds to carefully handle such comparison.
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Minor lab has recently published this article covering practical aspects or crystallographic model refinement ( ). This tutorial review offers guidelines for choosing the best settings for the reciprocal-space refinement of macromolecular models and provides practical tips for manual model correction. It also gives practical tips for manual model correction in Coot, modelling of side-chains with poor or missing density, and ligand identification, fitting, and refinement. While we hope that this set of the guidelines will help aspiring protein crystallographers, we also acknowledge that this set is by no means complete or fully applicable to all cases.
Our own rules, guidelines, and tips have changed over time due to increased experience and the perpetual evolution of crystallographic software. Moreover, we understand that some crystallographers might disagree with certain suggestions presented in the article. We are always open to discussion on best practices, and I would love to hear feedback, comments, and further suggestions.
If you don’t have an institutional access, please use this link https://www.tandfonline.com/eprint/3UyYh3iNGfhTSJGXyz9K/full (it has a limited number of free copies).
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Very useful, thanks!
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I am working on two proteins of the UPS, that have been shown to interact with each other in vivo. The ultimate goal is to study the complex using X-ray crystallography. I would also like to study if this interaction is direct or mediated by other protein partners.
So far I have not been successful in establishing the interaction in vitro. If I purify the proteins separately and put them together for crystallization, will this help in anyway?
I have also tried performing Co-immunoprecipitation experiments in vivo and check for potential interaction partners using MS analysis, but this has not panned out either.
I would be grateful if anyone has inputs or suggestions as to how i can take this ahead. Thanks in advance!
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With the availability of the purified proteins, you can consider various biophysical approaches, depending on what equipment is available, including surface plasmon resonance and isothermal titration calorimetry. Chemical crosslinking can also be a useful technique.
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As per the underlying concept of this new theory, when X-rays are scattered from tiny crystals or crystallites of any size and shape distributed throughout space, the diffraction pattern will contain enhanced scattering at angles of exactly equal to 2θB, whatever the orientation of the crystal. Thus it is claimed that scattering from a randomly oriented crystal powder with gives rise to Bragg scattering peaks even if the Bragg condition of individual crystallite is not satisfied.
Do you agree ?
What is your opinion?
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Dear Aga Shahee
I think the theory annunced buy Fewster’s is based on the misleading of the effect of solid surface structure which controls the basically the structure forms in the nanoscale sizes of crystals and may be appears clearly in the crystalline powder form. I had a quick looking to the article and he denoted to particles less than 10 microns for his hypothesis. In this size surface effetc will be significantly appears on the X-ray diffraction data for the powder form crystalline, for more details on nanosize crystaline state I suggest to see the following power point
"Solid Surface and Nanoscale materials Structure" M. S. Omar Presentation · July 2016 with 156 Reads DOI: 10.13140/RG.2.2.31947.59684 Charmo, University of Charmo, University of Salahaddin, DOI:10.13140/RG.2.2.31947.596
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i have the XRD data of a rock sample. i want to know the % of its constituent minerals and percentage of clay it contain....how can i do this using Xpert high score plus....?
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Hello Carisa... If u have the xpert high score plus software then first open the data file in the software...then go to treatment section and search peaks (u can do it by automatic mode or by selecting peaks manually) and click on accept. Then go to analysis section and go for search match....now before applying search go to restriction section...select the sub-file 'minerals'. if u know the probable mineralogy of the rock then in the restriction section select the possible elements in the periodic table. Now click on search tab. a set of possible minerals are appeared in the right tab of the screen. Now select the possible minerals and drop them in the upper pan and go for reitvield refinement for quantitative analysis.
Kindly note that this is the general process to get the quantitative values. For better results consult with some people who are frequently using this software (probably the chemistry or metallurgy student). they will guide u in a better way.
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XRD analysis
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first of all i am extremenly sorry for late reply..
i was trying to ask that is strain depend on crystal structure ?if yes then if we have two structures eg barium titanate having tetragonal structure and barium zirconate having cubic structure .then in which compound we can expect more strain ....
i am expecting that now my question is not so confusing..
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We've looked at an epitaxial film of GaN on a Si substrate using real time 2D Bragg XRD Microscopy (2D XRD rocking curve analysis). This specimen also had intermediate "buffer" layers of AlxGa1-xN and AlN. The XRD rocking curve Bragg profiles were examined at various topographic locations. The (0002)s reflection was utilized. The vicinity of the GaN (0002)s reflection was probed in reciprocal space using the ω-2ϴ scan mode to acquire the Bragg profiles.
We need some help! We're on the verge of a solution. Check out this data set and analyses for a GaN-AlxGa(1-x)N-AlN-Si sample wafer. I have the 3D XRD rocking curve data collected using a commonly available lab based XRD instrument below 2kW. I have the relative intensities for five distinct Bragg peaks around the GaN (0002)s reflection.
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SNR to COD relationship for the above data set at location "800" on topograph.
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ok so i know that it depends oon the radiation of the excitor. but i really want to know why does it happen and how does it happen. All the answers will be highly appreciated.
Thanks
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Depends what you mean by "different"
Some XRD machines can be more sensitive than others, so if an older version of XRD machine shows mostly amorphous powder with no clear peaks, new machines can give you a good resolution of peaks, or show some peaks that older versions did not show. However, the strong peaks should be there with just different intensity. Ignore the intensity because it is arbitrary unit. The 2theta angle is more important and it should be the same.
It may also happen that the whole spectra is a little shifted to the left or right, this really happens because of the average height of the surface (for powder) is not at the recommended height, so you need to be careful to flatten the powder surface at exactly the height it must be. It is not easy to make flat surface at the right height if your powder is coarse. Grinding your powder, especially with a high energy ball milling technique can change the composition (adding impurities etc.), as was said above.
However I think that grinding in a mortar by hand should not generally change the peaks unless your powder can absorb humidity during grinding time, and change the powder composition.
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Conformational properties of porphyrins have an importance in biological systems.
what are the factors that determine porphyrin conformation (planar or non planar)?
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thanks for your answer and for providing these references
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Hi all,
I am not a crystal structural biologist. I have few questions that could be rather technical. I am aware that there are some proteins that are difficult to study using x-ray crystalllography (e.g small heat shock proteins). What about these proteins that make them hard to study using x-ray crystallography? What are some other general features that makes a protein hard to study using x-ray crystallography? Also if there are some brief reasons at the level of fundamental principles, please feel free to let me know. 
Thanks
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I may add the following:  some proteins, especially membrane proteins, are exceedingly difficult to crystallize, but some researchers have solved this problem by genetically re-engineering the protein.  This would involve deleting regions that are known to be disordered, etc.  Thus when interpreting 3D crystal structures of re-engineered proteins, one should be very careful to consider the artificial changes that have been made to them.
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Hi, I used Apex-3 for structure determination and XShell for refinement for one crystal structure. The generated CIF file has one major Alert A; Large Value of Not (SHELXL) Weight Optimized S. I do not have much experience to solve these issues. Also, how can I omit reflections that have error/sigma values greater than 10 in the refinement.
In addition, how can I examine the LST file for refinements to check the Most Disagreeable Reflections list for possible reflections to omit.
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open your  .lst file there you will find hkl values of the bad reflections, so copy these hkl values in .ins file and with omit command ...
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Hi... I am working on a viral protein. When I purify it in the normal condition (Tris buffer, pH-7.5, NaCl & Glycerol, Temp- 4C), it is a monomer. But, as its crystal structure reveals, upon crystallization (pH-6.5, Temp- 20C) it converts into a crystallographic tetramer. What could be the possible reason behind this morphological transition of the protein ?
Your view would be a subject of appreciation!
Thanks.
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This could be a concentration dependent artifact. Consider that a crystal of a protein is an ultra high concentration of protein - even though you set up the condition at say 10mg/ml the amount of protein molecules in a crystal (depending on size of the crystal and protein) could be >500mg/ml (or >50mM). If the crystallographic tetramer is symmetrical it is possible that the quaternary structure is real, but concentration or pH dependent. You can submit your monomer to the PISA server to calculate the probability of multimerization also. 
You can easily experimentally assess this phenomena with size-exclusion chromatography at different concentrations and pH as well as dynamic light scattering and/or Small Angle Xray Scattering. Regarding SEC, make sure you choose a column that is capable of resolving a tetramer and monomer for your studies. 
Also, you didn't mention the crystallographic condition (salt and concentration, etc), but salting out is something to consider when dealing with proteins in solution. If the condition includes 1M Ammonium Sulfate, then the nucleation could start with salting out the protein (for instance). 
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My background is related to proteomics so a beginner's guide to crystallography or something would be good.
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Biomolecular Crystallography from Bernhard Rupp. Here is the link http://www.ruppweb.org/Garland/default.htm
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At present, I am having XRD analysis of powders in UXD format. Can anyone tell me the free software available online or link that can decode my UXD file..
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Dear Kannan, 
I can definitely recommend a universal file conversion tool for the XRD files: PowDLL available at: (free)
it's free and offer conversion between many different file types used in XRD.
Best regards,
Sebastian
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In order to calculate the crystallinity of a polycrystalline material (eg. clays), I would like to use XRD. It needs to deconvolute the XRD pattern coming from crystalline part and amorphous part of the material. How can I decompose or deconvolute the XRD graph using PANalytical X pert High score plus, Version 2.0 software.
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I'm not so sure about HSP V 2.0. But to do determine the amorphous phase if you know all the crystalline phases is by spiking method; add known wt% of crystalline material (not in the specimen candidates), do the quantitative analysis, change the refinement wt% of the crystalline material by its true wt%, in v3 u'll get the amorphous wt%. Or you can do POCNKS : "Quantification of phases with partial or no known crystal structure“ Nicola V.Y. Scarlett and Ian C. Madsen, Powder Diffraction (2006) Vol. 21(4), p. 278 – 284. doi.org/10.1154/1.2362855
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1. What should be the ideal resolution of a crystal structure, if one wants to compare the B-factors as defined by the structure and anisotropic atomic displacement parameters (ADP) obtained from refinement procedure like Translation-Libration-Screw (TLS).
2. Is it practically correct to refine a set of crystal structures from different research groups by TLS refinement to get a list of ADPs and compare them with the thermal or B-factors reported in PDB files?
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Both are known as temperature factors or B-factors, may also be represented by U,  where B = 8π2 U.
Thermal motion and positional uncertainties may be isotropic or anisotropic. Anisotropic atomic displacement parameters are represented by 6 parameters; 3 variances of x,y and z and the 3 covariances of the possible pairs of coordinates.
This parameter must be done at the end or u'll get unreasonable results.
What is the resolution of you synchrotron data?
"2. Is it practically correct to refine a set of crystal structures from different research groups by TLS refinement to get a list of ADPs and compare them with the thermal or B-factors reported in PDB files?" the crystal structure is a model for you to fit your data.
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All peaks are matching with the jcpds file. All seems to be in single phase, but when I am trying to do Rietveld refinement, the maximum intensity peak is not fitting. I even tried refining preferred orientation parameters, but it is of no use. I am not sure whether it is a different phase or it is a preferred orientation that is causing the problem. Data points are less; please exclude that.
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You could try a pawley/lebail refinement with the same lattice parameters and spacegroup to exclude problems with your peak profile. If you get a decent fit with pawley/lebail either your structure is not correct; you have preferred orientation or spotiness/graininess effects (try a different preparation method or grind your sample a bit more); or some intensity correction is not correctly applied e.g. LP factor. Probably the easiest way is to measure some kind of standard an see if your refinement routine works as expected. 
Regards
Dominique
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I did Rietveld refinement for my x-ray diffraction data using the GSAS+EXPGUI package. The fit seems to be good. Now i wish to extract the Integrated intensity ( both calculated and observed) of all reflections from GSAS software. I aware of the reflist option in GSAS, but it gives 4 different values (highlited in the attached figure). Can some one explain me, in what way they are different?.
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You can find this information in manual, page 219
FOSQ observed Fo2
FOTSQ Fo2 corrected for extinction and on scale of Fo2
FCSQ Fc2 with scale and extinction applied
FCTSQ Fc2 on absolute scale
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Hi every body
I have synthesized a new material in powder. Absolutely it is polycrystalline not single crystal. I am looking for a way to analyze this XRD pattern? I have read in papers about Refinement of the powder XRD but I don't know too much about it.
How can we analyze the XRD pattern of a new material without synthesizing its single crystal?
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Hi,
i hope the newly developed compound (polycrystalline) may depend on your parent compound. for example if you take bismuth ferrite, it belongs to rhombohedral structure(R3c). however, it is add "X" compound in either "Bi" nor "Fe" site, then we may get an new compound that may or maynot be in the same phase. but still it belongs to the parent family and hence i try to find suitable matching  file using JCPDS or freely availalbe databases, based on the percentage of adding compound, try to found their phases too. after the matching statergy, we will try to resolve the phase fraction intensities with the help of availalble Rietveld techniques (GSAS,FULLPROF,MAUD, etc.,).  
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Recently we synthesized some CdS particles. Prepared samples were characterized by X-ray diffraction. The ayanlysis result shows a hexagonal structure (ICSD 43599) in space-group of P 63 m c (186). Its cell parameters are a=4.1400 Å and c=6.7150 Å.
I use diamond3.2 opened the ICSD 43599.cif and created several planes on the crystal. I found that in the planes of (100), (101) and (103) there had no atoms presence. Yet in the X-ray diffraction results these three planes all showed diffraction peaks.
My question was: Must the corresponding crystal planes of the X-ray characteristic peaks have atoms present? If it is, why in the crystal models (ICSD 43599.cif) on the (100), (101) and (103) planes I created have no atoms presence; If it is not, why these three planes showed diffraction peaks?
Further more, the question is: did diffraction planes (which showed diffraction peaks) must have atoms presence? And the reasons.
Thanks!
Kun Li
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Thanks for the explanation of S. R. de Lazaro and Alexander B. Missyul’. Both of your answers are useful for me to further understand the growth mechanism of CdS particles  during preparation. Since we would want to know the preferentially grown planes and the atoms distributed on it, then we can judge the charges of each plane. Combining the pH condition of solution, we might able to deduce the effect of pH value on the preferentially grown planes, so as to the morphology of final CdS particles.
Thanks again for your explanation and concern. : )
Kun Li 
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hello
I used MAUD program to analyze my XRD patterns. Many times I noticed that MAUD gives different refinements for the same cif-files if I change the order of them in the phases window. Also, some times I repeat the same phase twicely in the phases window and I notice that each phase starts to has its own  persentage and fitting value and may has half of the peaks and the second one has the remaining half of peaks for the same phase. Also, when I make many changes in the structural coordinations of one phase, MAUD stops responding to the change after some tries and may give a strange refinement that will not appear again if I restart the program. Also, using my computer or other computers will give different results for the same procedure in the MAUD program.
1-do you have any experience in using MAUD program?And pleases explain my previous case
2- give me another more accurate program to analyze the XRD results?
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Also try GSAS-II, which is free.
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Hi,
I'm trying to refine the structure of double-mutated protein at 2.4 A resolution. For MR I used the structure (not fully refined, 2.75A Res) of the Wild Type. After first round of refinement I got Rwork/Rfree = 0.30/0.35. However, after the successive next rounds of refinement even if the Rwork/Rfreedecresases, the density map fit completely fails. Does anyone have an idea why it happens?
The X-ray data shows severe anisotropy. Do you think that refining  B-factors anisotropically may help?
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Cool! I am happy to hear it!
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Is this the only way to justify orientation of the crystals? If certain planes are more intense in XRD would that mean that others need to be less intense given that the amount is unchanged?
Thank you for your insights.
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Rizky! "the most popular equation model of preferred orientation is March-Dollase model", that is more than I know. I know a lot less than that I need to know. Thanks for the education :-)
I hope someone else in this erudite group can come up with the answer to your question so that I may learn as well. However, there is software similar to Bruker LEPTOS that allows folks to incorporate the latest theoretical models to simulate various linear diffractograms in order to compare with experimentally recorded diffractograms. It is critical to incorporate the "parameters" correctly to avoid errors and equivocation while using such simulation tools.
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I am looking for step by step procedure to find the crystallite size and microstrain by warren-averbach using xpowder and how can we interpret the plots. is this method able to estimate the dislocation density and is there empirical equation to estimate the dislocation density using xrd.
the attached picture is for the analysis using xpowder. in the instrumental profile, how can i find the instrumental broadening and compare it with measured pattern. 
looking for help to know much about the correct procedure from your wide experience. 
best regrads
P.S. Can we Use the experimental sample instead of the standard one to estimate the instrumental broadening after annealing.
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Hi Mohammed. It would be helpful if you include the question signs in your questions.
In order to extract the instrumental profile from your measurements you need to measure a free-of-strain sample first, with a crystalline size small enough to get a good statistic. There's a commercial sample, LaB6, you can get from NIST in the USA. It's very expensive but good to do the job. Another alternative would be preparing a powder from a single crystalline Si wafer, but it's not easy to do without applying some stress. If you can find a way to get rid of the strain in your sample, let's say, to a value below 10^-4, that could be useful as a reference for the instrumental profile.
Once you've measured your reference sample for the instrumental profile you fit the powder diffraction pattern in Xpowder and you store all the values of the reference pattern, which basically consist of the parameters of the Caglioti's formula. Then, the instrumental profile can be extracted from any other sample with a strain higher than the strain in the reference material.
If you change the set-up in the X-Ray diffractometer, the Caglioti's parameters have to be measured again.
You can't get the dislocation density from Xpowder directly. For that purpose I would suggest to take a look at an academic software developed by Mateo Leoni, in Italy. It's called PM2K. You can send an email to him to get a copy of the software.
If you want to develop your own code in Mathematica or Matlab to determine the dislocation density and crystallite size by Warren-Averbach method I can give some directions to get started, just send me an email to hf278@exeter.ac.uk
Best regards.
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I am having some difficulties for quatification analysis of Hap in a sample. In our Rietveld software there are 5 different cards for Hydroxyapatite, and they result in different values.
What should I do to choose the right one in order to get a trustable result?
thanks
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You should check the original source of those cards, a lot of conditions produce changes in apatite structures (pressure, °C, substitutions, doping, ...), but the database will not inform you about those conditions
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Hi everyone!
I'm a freshman in the crystallographic field.
Now I have a crystal that have been confirmed as protein, and it looks like a dot without clear edge.
I have tried to optimize the crystallographic condition,like the concentration of precipitant and the pH range of buffer.
but the resolutioin is only 5 Å using X-ray diffraction。
So could you please share your experience to improve the resolution of protein crystal?
Thanks, sincerely.
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You may simply want to attempt further (wide) screening to find additional crystal forms. I would also advise you to do additive screening (e.g. using the Silver Bullets additive screens). I have had a lot of success improving resolution via additives.
In situ proteolysis (addition of trace amounts of protease to your xtallisation experiment) has also been reported to be successful at finding new crystal forms with improved diffraction quality. You can read up on it here:
Another fast and efficient way of potentially improving your resolution is protein surface engineering in the form of lysine methylation (basically to reduce surface entropy). You can read up on this here:
The above methods won't require you to go back to cloning. However, stepping back to reflect on your construct is often best. You may want to introduce mutations that improve crystallisability through surface entropy reduction. Have a go at this server if you want:
Finally, use disorder prediction software to check if there are flexible regions on your protein which you can possibly remove.
Happy screening!
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Question for X-ray diffraction experts!
Let's assume a structure: layered mineral intercalated with organic long chain molecules. The X-ray diffraction pattern shows 3 peaks connected with 1st, 2nd and 3rd order reflections. Now, the structure is exposed to UV light which changes the conformation (geometry) of the intercalated molecules. After that the d spacing should change (1st order reflection), however we see a change of the 2nd and 3rd order reflection? The 1st order is not "moving". Do you have any suggestions?
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Thank you all for comments. I will get back to you when I will have more data on this complex.
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I have a cif file of one my compound, in the structural data file there is an atomic oxygen, which is definitely a water. But by the mistake of crystallographer during structure solving, addition of hydrogen on that atom was missed. Now we have lost the structure  factor files and we want to insert H-atoms on the said atom.
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First, are you sure that you don't have structure factors in your cif file?  That has been the common practice now for a couple of years.  However, even without the hkl values, you can use a GUI such as OLEX2 with SHELX to add H atoms at caculcated positions.  You can just open the .cif file in Olex2, select the atom and type HADD.
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I have GIXRD data for Ion irradiated Ni sample. I want to calculate domain size and microstrain using Warren–Averbach method. I donot get the option for WA analysis in the calculation tab using MARQX software after reading the input file. Can someone suggest what could be the reason?
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young people try to get quick answers for their problems with out putting much effort and they end up in social media with silly questions.
But the so called pseudo intellectual sales representative try to offer them a beautiful wife at the stake of ailing mother, rather than giving them what they require.
Dear RUMU try to spend some time with the software, you will figure out your self how to work with it or else there are plenty of other open source software's which are better than what you are using for the same analysis. The file format that the software required may not be the same as your data file, check for it.
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I would like to know details about Rietveld Refinement (Prof. Hugo Rietveld) in terms of the application. I have some questions on this technique.
FYI, I'm the user for PANalytical X'pert Pro with software X'pert Highscore Plus.
Normally I will interpret the diffractogram by looking the SemiQuantitative(%). However, for the sample with ratio composition, perhaps by only look at the SemiQuant result is not enough. Therefore, I engage with Rietveld Refinement (Basic) as this feature already included in the software. It seems like the result in terms of composition is make sense and it follow the composition of the sample(Example Graphene+ZnO. 1:1, 1:2, 1:4 and so on)
My question is,
1. How is the accuracy is Rietveld Refinement technique?Is it better than if I'm not using it?
2. How to confirm that Pseudo-Voigt Curves is fitting well under diffractogram curves?
3. How famous this technique to be included in the research?
4. Is there any similar technique or better compared to the Rietveld Refinement?
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Rietveld refinement has been introduced for structure refinement and only later it has been extended to quantitative phase analysis. If you enter Rietveld or better full-pattern refinement and XRD at google, bing, yahoo or whatever, you should get hundreds or even thousands of hits describing many different application examples. There are even several free software packages based on the least-square refinement (which is the basis of Rietvelds refinement and therefore no magic!) All mathematical assumptions like peak profiles, asymmetries, geometrical diffraction models etc. are limited since they reflect "never" real practical diffractograms. Therefore, the final decision whether a fit is reliable or not, you have to make. You can only read papers, judge, learn and decide what authors made wrong, how reliable their results are, or which idea is really suitable for your specific case. All software packages have some automatic mode which hopefully prevent to crash the refinement but the result is perhaps not very trustful and you have to play and learn and try to understand what is going on and which parameter affect what. Each software is a "stupid" least square refinement often optimized for a very specific problem. You have to find by yourself what do you need and what fits best. Only for this task you will need months or years. It is better, to ask more concrete questions. Commercial systems only want to give their customers a tool for a first analysis. And it mainly should impress how big is their competence. However, the better software is usually the free one since there are the guys who develop new approaches. XRD companies commonly "react" on the development and implement new and successful code later, when scientist checked their reliability. 
In order to learn how much a parameter will effect your pattern, the theoretical simulation will help more that starting with experimental patterns. You can simulate patterns and reload them as experimental signal and try to refine them. Then you learn more than speculating what some residual intensities may mean... You will perhaps find that you can describe the same patterns by different parameter settings which tells you that there is often not only one good solution which brings us back to my assumption that you as scientist need to decide how far you can go with your interpretation and when speculation begins... 
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Dear All
I am running pw.x calculations for Mo2C (orthorhombic) supercell of size 1x1x3 and 2x2x2. The calculations terminating with an error "Primary job terminated normally, but 1 process returned a non-zero exit code.. Per user-direction, the job has been aborted". The energy values goes up and down and the structure is not converging towards low energy value. The cell parameters are according to the .cif files (crystallography.net) and updated according to cell size. 
However the calculation with 1x1x2 Mo2C works fine without any error. By increasing the cell the above mention error arises. I tried with altering the nbnd, degauss, electron maximum steps, but the problem remains same.
openmpi-mpirun 
mpirun -np 32 ./pw.x -npool 8 < File.input > File.out 
Input file is as follows
&control
calculation = 'relax'
title = 'Mo2C'
verbosity = 'minimal'
wf_collect = .false
nstep = 2000
prefix = 'BP'
pseudo_dir ='/home/pr1edc00/pr1edc03/PSP/'
/
&SYSTEM
ibrav = 0
nat = 36
ntyp = 2
nbnd = 210
ecutwfc = 50
occupations = 'smearing'
degauss = 0.001
smearing = 'methfessel-paxton'/
&ELECTRONS
electron_maxstep = 300
conv_thr = 1D-5
startingpot = 'atomic'
startingwfc = 'atomic'
diagonalization = 'david'
/
&IONS
ion_dynamics = 'bfgs'
/
&CELL
cell_dynamics = 'bfgs'
cell_dofree = 'z'
/
Atomic species
#
so on
Can anyone assist me to solve this error.
Thank you in advance
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Dear Chethan,
giving a quick look at your input file and to your main problem ( the system doesn't go relaxing because of non-convergence of the energy), I have some suggestions that you can apply in order to fix (hopefully!) your problem:
1) Looking at the PBE Ultrasoft pseudopotential for the Molybdenum, the pseudopotential file suggest to use a "ecutwfc" not less than 48 Ry (where you use 50, which is potentially ok!), but also a "ecutrho" no less than 407. By default "ecutrho" is 4 times ecutwfc (200 Ry in your case, which probably affect negatively the convergence of the energy!): I suggest to increase both "ecutwfc" and "ecutrho" (not specified in your list) to 60 and 430 Ry. The carbon atoms should not be a problem.
2) try to reduce the value of the degauss from 0.001 to 0.01. It will make faster the running with a sufficient good precision.
3) the energy threshold for the convergence "conv_thr" I guess it's too high for having good realistic results. By default is set 1.0E-06. At least, follow this default setting for the convergence.
About the rest, for example the crystal structure, I don't know so much about this compound. I know that there are two phases, alpha and beta with respectively orthorhombic and hexagonal lattice. So, if you know the geometry of the system and the right atomic disposition, you can try to set an appropriate value for "ibrav" and insert the unit cell parameters.
I hope this can be helpful.
Best,
A.
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Dear All,
I have grown crystals of NLO material. I want to check the birefriengence property of my grown crystal. anybody please suggest me the place or institute where the birefriengence of crystal is available.
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The easiest way might be to use a polarizing optic, e.g. a petrographic microscope as these are usually polarizing microscopes. If your university has geologic faculty than they should own such a microscope. Assuming the material is translucent just prepare a thin section (~ 25 microns thick), place it on the sample stage and cross the polars. By rotating the stage the birefringence should sho up (4 times dakr, 4 times bright by 360° rotation) if there is any. From the interference colour you can at leat judge the amount of birfringence.
If you need the absolute value it turns out a bit more complicated, as you need a more special equipment. But any university with a petrologic (mineralogic) or crystallographic chair should own the equipment (more or less).
Hope it helps
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I read some protocols suggesting not lyophilizing the protein in sample preparation.  any practical tips? thanks a lot!
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Cryoprotectants, especially sugars like trehalose, are used to help stabilize proteins during lyophilization. Glycerol is also useful as a stabilizer, but it can't be used for lyophilization because it is a non-volatile liquid. It can be used as a stabilizer when freezing the protein for storage, but you will probably have to remove it before setting up your crystallization trials. The same goes for trehalose or other cryoprotectants.
If your protein is sticking to the concentrator, try using one with a different membrane chemistry. Another way to concentrate a protein sample is to put it in a dialysis bag and immerse the bag in a concentrated PEG solution, or bury it in a solid water-absorbent substance like carboxymethylcellulose. Still another method is to bind it to an ion-exchange resin, then elute it in a small volume of a high-salt buffer. Obviously, this leaves you with a salty sample. If the protein is His-tagged, you can do the same thing with nickel resin, eluting with a high concentration of imidazole.
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Hi! Currently I have two versions of the same protein, a native one and one in which I added a long flexible tail sequence. They both gave me crystals in the same condition, and by X-ray diffraction patterns they have very close symmetry and cell parameter.
I am wondering if any parameter from X-ray diffraction can show me the clear difference between these two crystals (prove that one of them has tail)? I know solvent % may show that the one with tail has less solvent in channels, but that's still estimated from the molecular weight I provided. Will any other experimental data differ for the two crystals?
Thanks a lot!
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Dissolve one crystal of each type in SDS-PAGE sample buffer, run them side-by-side on a gel, and see if one has a higher molecular weight. Or take diffraction data and compare the electron density maps.
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We have prepared bulk Gd0.7Sr0.3MnO3 materials by conventional solid state reaction technique. Their corresponding nanoparticles were prepared by using ultrasonic energy. The lattice parameters for the bulk polycrystalline sample and corresponding nanoparticles prepared by ultrasonication are almost unaltered, however, the atomic positions are significantly different between the materials prepared by two different techniques. By using FULLPROF studio we have generated the structural view of  Gd0.7Sr0.3MnO3 (a) bulk materials and (b) corresponding as shown in the attached figure. Is it realistic? Please let us know any expert opinion. Thank you very much in advance.
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Thank you very much everyone. We understood, it was not correct. Now we are getting the structure correctly. Many many thanks for your expert opinion.
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There are values of unit cell as well as transformation matrix to get fractional values of the coordinates. These values are related to only for the structures derived from X-Ray crystallographic method. I wanted to know how it is significant after the structure has already been solved. Are there any calculations/methods/algorithms related to the coordinates where this data is applied?
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No, the cell parameters are fixed for a given crystal. When Joseph says 'grow' he means expand the area being viewed, eg instead of looking at one brick, look at the wall.  For protein crystals, we can't yet predict how crystallisation conditions might affect the crystal morphology.
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Bragg's equation
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Hi Ankur,
You have to find out first d- values using Brag's law for respective 2 theta values in XRD pattern. Then you can take help of various XRD analysis software such as, JCPDS. In that software you have to chose your composition of your material then there will be several JCPDS files for that composition. After  that you have to match your d-values from the reported patterns. Once you find the matched pattern to your data, you will be able to index each 2-theta value in XRD pattern.
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