Protein Data Bank, a publically available database of molecular structures of proteins
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votes
1answer
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Parse PDB using DSR-PDB Library
I'm trying to parse ATOM section of a PDB file. I'm using the dsr-pdb library for this purpose.
I've encountered a problem. This library interprets CD1 atom of ILE ...
9
votes
1answer
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Protein data bank syntax: Can two protein secondary structures “overlap”?
I have a technical question regarding the syntax in Protein Data Bank files. In the protein with PDB# 1AE9 (pdb file), there are two lines in the .pdb file:
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votes
3answers
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Compressing structural information in PDB files
There seems to be a lot of redundancy in PDB files. These files can of course be compressed with general-purpose compression programs like gzip, but I can't help but imagine that these tools are ...
5
votes
1answer
84 views
How do I prepare a PDB for submission to the Protein Data Bank?
I have a couple structures that are nearly ready to be deposited in the PDB. Out of curiosity, I ran them through the ADIT's precheck tool and they failed with one error after another, as I lacked ...
9
votes
2answers
191 views
How can I pare down a PDB file in Python to only include specific residues?
I'm trying to make a script that will take a MTZ file (reflections), convert it into a CCP4 map, then pare that map down to only encompass a desired area to cut down on the size of my PyMol session ...
