Computable Structures - Science topic

Dear Vilakkathala U Krishnapriya I used Chat GPT to answer of your question. Could you tets the relevance of this answer?

"To create a multiple XYZ file in ChemCraft, you can use the "File" menu and select "New" or "Open" to create or open a new file. Once you have a new file open, you can use the "File" menu again and select "Save As" to save the file as an XYZ file.

You can also use the "Import" option in the "File" menu to import a different file format, such as a PDB or MOL file, and then convert it to an XYZ file.

Another way of creating a multiple XYZ file would be to use the "Append" option from "File" menu and select the XYZ files which you want to merge.

It is important to note that in order to create a multiple XYZ file, all the XYZ files you want to merge must have the same number of atoms and the same atom ordering, otherwise, the merge may not work as expected.

In summary, to create a multiple XYZ file in ChemCraft, you can use the "File" menu and select "New" or "Open" to create or open a new file, then use the "Save As" option to save the file as an XYZ file, use "Import" option to import a different file format and convert it to an XYZ file or use "Append" option to merge multiple XYZ files that have the same number of atoms and the same atom ordering."

Hi Nataliya,

Consider that you have two color images c1 and c2, then you can split each image into R1G1B1 and R2G2B2. Having done this, the SSI can be applied upon each band from both images and finally take the average.

Hope this helps!

John,

You have asked an interesting question. For a senior member of structural biology community it shows the yearning for practical solutions as well as naivety of the real difficulties in even defining the problem. The protein folding problem is an ill-defined and most likely unsolvable problem in its classic sense of axiomatic reductionist sciences. If the old Anfinsen view was true about the minimum of global free energy there never would be life on Earth or anywhere else. The new paradigm that I partially formulated is that every protein (as a matter of fact every macromolecule of life) has its own specific recipe how to combine the structural with dynamical features to accomplish the desired function (PNAS 106(2009)10505). It means that there is a unique proportion of conditionally stable structure to conditionally unstable elements to perform given function. This ill defined condition is not solvable by classic axioms but it just might be partially solvable by fuzzy methods such as AI. Why AI is so good? Because the protein folding problem is a practical not a theoretical problem. Depending on conditions and their possible changes the protein suppose to perform a certain function. This is what physics call "self organized criticality". This is far from equivalency of having a certain structure nor a possible unique binding site nor anything that remotely can be called a solution. AI just simply captures better the set of heuristic rules than other methods particularly dynamical coupling with solvent. There are millions of examples to support this view. If anybody wants to engage I will be happy to, but not now. There is no place here to mention even a single one.

So the only hope is that we found an effective heuristic tool that gives us better approximation to reality. To be properly tested the method needs to be exposed to finding bordering cases when it breaks down. What conditions produce divergencies. What percentages of certain structures are folded and are not. For instance only around 30% of genomes of higher eukaryotes are properly folded. Around 30% is conditionally folded (on the target, in the particular compartment) since the misfolding diseases. And finally around 30% is almost never folded with residual presence of folding nuclei that precipitate the function. So all these classes of proteins must be tested against this new AI approach to see when the rules break down and how to enhance them.

Therefore, it is not a breakthrough that John is so excited about. But it is definitely progress. But, I would not see anytime in the future, abolishing or significant diminished importance of any particular field of science, in exactly the same way as radio did not get extinct by TV.

Bog

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.

Some of the high-quality peer-reviewed journals are:

https://www.journals.elsevier.com/automation-in-construction

2. Journal of Construction Engineering and Management

https://www.emerald.com/insight/publication/issn/0969-9988

https://www.journals.elsevier.com/building-and-environment

https://www.journals.elsevier.com/journal-of-building-engineering

I think CPS is different from Parallel system. Parallel system normally for simultaneous tasks, especially computation, i.e. parallel computing. Parallel computing is used for high performance computing.

CPS on the other hand is bringing together physical system into the cyber space with the help of various emerging and enabling technologies. This is especially for realizing smart systems and infrastructures, autonomous systems, etc. Parallel system may be just a drop in the ocean of CPS.

Ich würde tatsächlich "raumvariant" vorschlagen.

Dear 耸霄

The axial stiffness of rod elements are AE\L, where A is area, E is module of elasticity and L is length of element.

best regards

Panji

Hi Leon Raj J.

Thank you for your response and for sharing your works, greatly appreciated. 

Regards,

Ginghis

Dear Arshad,

Thanks for your immediate response and your valuable time & work. I want to know detailed steps of how you get these structure from the cif file. I am using gaussview3 in that i visualized breakup structures, so i little confused. If you furnish the steps u carried out to get structure elaborately, it will be helpful for me to carryout further and in future.

Thank you