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PostPosted: 2015.06.30 09:45 
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Hello everyone,

I have some beam time in later this year, and as a preparation for that I wanted to simulate some data. Using the pdb-entry 4N85, I calculated the theoretical scattering using crysol. The program calculated the scattering but also printed that it had skipped 24 rotamers. I also tried with another PDB-entry - 4PVL - and again crysol skipped some rotamers.

Is there a problem with the PDB models since crysol skips some of the side chains? according to the PDB validation report for 4N85, there are two rotamer outliers in chain B and only one in chain A. unfortunately, the report has skipped some of the residues in the model so there could still be some problems that are visually difficult to detect. In the case of 4PVL, one outlier in total was found.

Can someone elaborate why some side chains are skipped?

Cheers!
Martin

EDIT: attached screenshots from the crysol (4PVL) output, and of the PDB rotamers analysis


Attachments:
report.PNG
report.PNG [ 45.01 KiB | Viewed 1651 times ]
CrysolOutput.PNG
CrysolOutput.PNG [ 50.05 KiB | Viewed 1651 times ]
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PostPosted: 2015.07.01 20:18 
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This behavior is just to avoid taking into account one and the same side chain multiple times.
In essence, Crysol keeps the first rotamer and skips all the others


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PostPosted: 2015.07.02 10:22 
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Thanks for the reply SaxsMax,

I knew that NMR PDB files contains an ensemble of structures, but I was not aware that PDB files from crystal structures also contains multiple conformations for certain residues/side chains! It of course makes perfect sense that crysol only counts each residue once :)


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