Protein Data Bank, a publically available database of molecular structures of proteins

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1answer
160 views

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: ...
9
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2answers
415 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 ...
6
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3answers
331 views

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
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3answers
227 views

Protein structures given in PDB and SNP's

There are millions of proteins given in PDB, the sequence for which we can download in FASTA format. There are also hundreds of SNP's given in NCBI dbSNP. My question is whether the proteins in PDB ...
5
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1answer
118 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 ...
4
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1answer
72 views

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 ...
3
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2answers
149 views

Proteins with alpha helices alone and beta sheets alone?

I would like to see some examples of proteins with PDB ID so that I can download and see them in VMD software. I need some proteins with alpha helix only and proteins with beta sheets alone.
2
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2answers
442 views

MOL2 to PDBQT conversion via OpenBabel and MGLTools removes hydrogen atoms

I am trying to convert a MOL2 file (includes partial charges and hydrogen atoms) into a PDBQT file for re-scoring in AutoDock Vina. However, both approaches that I tried don't keep the hydrogen atoms ...
2
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0answers
40 views

How to get a pdb file of a single atom?

I am trying to get a pdb file that contains a single atom, it doesn't matter if it's Hydrogen or another atom. How can I obtain this? Are there any pdb files with just a single atom available to ...
1
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2answers
94 views

PDB file for Osteopontin (SPP1)

I am looking for PDB file for Osteopontin (SPP1). The entry- 3CXD shows the structure of an Osteopontin antibody, not of the protein itself. Thanks
1
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1answer
32 views

PDB file SEQRES have different datas?

In PDB file, SEQRES represent the aminoacids but some pdb file present the "GLC" and some other. for example ...
1
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1answer
86 views

How to parse SCOP parseable files PDB residue identifiers?

I am trying to parse the SCOP parseable files, specifically dir.des.scop.txt ver 1.75. But, I have been facing problems with the PDB residue identifiers in the file. This is a tab limited file and the ...
1
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1answer
55 views

how to reconcile PDB structures' sequences via Uniprot references?

I’m trying to reconcile structures in PDB entries with their sequences as reported in their chemList.polymer.dbref entries. E.g.: considering structures for HIV ...
1
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1answer
77 views

How can I compare the STRIDE and DSSP output files of a particular pdb file?

I have the pdb file of H-ras protein 5P21.pdb. I am supposed to compare the output of DSSP and STRIDE files after feeding this pdb file to respective servers. My question is how to make a quick ...
1
vote
1answer
50 views

Where can I find pdb files for macromolecules like receptors?

I have tried going to the RCSB website and quite frankly it was useless since when I looked up receptors like say the metabotropic glutamate receptor 2 (mGluR2) I got no helpful results.
0
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2answers
81 views

Counting the number of hydrogen bonds of multiple PDB files

I've been trying to figure out a systematic way to count the number of hydrogen bonds for multiple PDB files. DSSP shows me the total number of hydrogen bonds when I make ...
0
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2answers
35 views

How to find a PDB structure of a protease with a peptide like inhibitor

I wonder how, for purposes of just illustrating some concepts like substrate alignment in the catalytic triad active site, I can quickly and efficiently find a protease structure (irrelevant of what ...
0
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0answers
3 views

Determine if two molecule structures are the same molecule (perhaps in different conformations)?

I have two .pdb files describing two (small ligand) molecular structures. I need to determine if these two pdbs describe the same molecule, perhaps in different spatial conformations. Is there a ...
0
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1answer
114 views

Color van der waals bonds in swiss PdbViewer

I'm trying to color certain amino acid's van der waals bonds as in the following picture: can anybody please describe the steps to accomplish that?