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9 votes

How can we find the distance between all residues in a PDB file?

If you need to process multiple files, you could use Biopython to parse a PDB structure. ...
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9 votes
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How to select high quality structures from the Protein Data Bank?

There is a very nice database, pdbcull (also known as the PISCES server in the literature). It filters the PDB for high resolution and reduced sequence identity. It also seems to be updated regularly. ...
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  • 206
8 votes
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How to extract RNA sequence and secondary structure restrains from a PDB file

I suggest you take a look at rna-pdb-tools we do way more than you need! :-) The tools can get you a sequence, secondary structure and much more using various ...
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6 votes

Best distance parameter for estimating physical interaction between residues in a PDB file

A popular (and I would say, respected and trusted) website is PDBsum https://www.ebi.ac.uk/pdbsum (which also has a Wikipedia article about it: https://en.wikipedia.org/wiki/PDBsum) They measure ...
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  • 507
6 votes
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BinaryCIF vs MMTF formats, which one to choose?

So binaryCIF is newer and is heavily inspired by MMTF. NGL, the most "loved" JS library (IMO) to show protein fetches proteins as MMTF, while Mol* uses bCIF —Mol* has the official repo of ...
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  • 3,469
6 votes
Accepted

BioPython internal_coords module returns different dihedral angles for the (seemingly) same protein structure

The problem got solved after posting on the official BioPython repo. Because of the processing (where some residues were removed in order to align the proteins), some consecutive residues were too far ...
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  • 385
5 votes

How to select high quality structures from the Protein Data Bank?

If you choose to perform your own culling of the PDB, resolution is probably the first thing you'll want to look at, which as Davidmh mentions is the main selection criteria for PISCES. High quality ...
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5 votes
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Can I traverse/enumerate PDB one at a time using a Python script without downloading all of them to my local disk?

The page https://www.wwpdb.org/ftp/pdb-ftp-sites gives the addresses of interest. PDB has an FTP site downloadable via rsync and the latter has a dry run mode. ...
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  • 3,469
4 votes
Accepted

PDB format: remark number for free text

From this document, it looks like REMARK 250 is the way to go.
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  • 602
4 votes

How can we find the distance between all residues in a PDB file?

Could you use CCP4's NCONT program? There's a GUI and a command line interface, whatever suits. You can specify which chains you want to target and interact with and set a cut off for distance. The ...
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  • 429
4 votes

How to extract RNA sequence and secondary structure restrains from a PDB file

Context The PDB file format is a fixed-column file format designed in 1970s for storing structural models of macromolecules. The format has been around for long time, has many uses, and although it ...
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  • 1,066
4 votes

How to get all PDB homologs from Uniprot (mapping + BLAST)?

For the correspondence between PDB and Uniprot entries you can use SIFTS -- a semi-automated mapping between PDB and UniProt maintained by PDBe. The pipeline that creates the mappings uses BLAST and ...
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  • 1,066
4 votes

How to read the "SEQRES" section from a PDB file, using R

I have not used Rpdb but I have used, and would recommend, bio3d. To read the PDB file 1A4G: ...
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  • 646
4 votes

Retrieval of genomic position by using biomaRt package

BiomaRt cannot do that I'm afraid. There is an Ensembl REST API endpoint that will get you the genomic location of protein coordinates. It needs an Ensembl peptide ID an input though, so you could use ...
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4 votes

If I modify a PDB file with a specific mutation, how to minimize energy?

Yes you can modify the reference PDB file and look for the changes and for this purpose you need visualizers. One among these is Chimera. You can easily carry out the energy minimization steps using ...
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4 votes
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Using R to import specific records from a PDB file

If your file is in PDB format as the one shown here in .pdb format then you can simply extract your desired fields using sed which is a programming language used to parse and transform text. As for ...
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4 votes
Accepted

PDB file downloading: pymol automation vs. manual

To expand on the comment by marcin: fetch downloads files in mmCIF format by default (https://pymolwiki.org/index.php/Fetch). Not all PDB entries have PDB format ...
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  • 901
4 votes

What is the aim of insertion codes in the pdb file format?

When I wondered it myself years ago and I found a good explanation in a mailing list archive. I think it was this one, by Frances C. Bernstein: The problem with numbering started when people wanted ...
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  • 1,066
4 votes

Extract residue sequence from pdb file (in biopython, but open to recommendations)

The discontinuity is normal: it is a missing stretch due to lack of density. In PyMOL you see them as dotted lines. I am sorry to say, the easiest/safest way to get the sequences is not using the PDB ...
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  • 3,469
4 votes
Accepted

Extract residue sequence from pdb file (in biopython, but open to recommendations)

There are other ways to do it (many and some might be easier), but if you want to do it with BioPython PDB module you can iterate the residues like this: ...
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  • 56
4 votes

How to draw a 3d structure using 3d coordinates from pdb file?

JSmol sounds like what you want - it'll let you display 3D structures from PDB files onto webpages using JavaScript. If you just want to view the structure rather than display them on webpages, there'...
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4 votes

How to draw a 3d structure using 3d coordinates from pdb file?

If you want to share a PDB file, you could try Michelanglo. It allows you to upload a PDB file (among other things) edit a description panel (which can feature special links that control the protein ...
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  • 3,469
4 votes
Accepted

How to extract subset of protein structure (PDB format) file based on a subsequence of that protein

In general, if you simply want to extract that part of the PDB file, you could loop over it (it's plain text) and check the fields you're interested in: ...
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4 votes
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Are the information stored in the PBD files in the protein data bank complete or incomplete?

A PDB file is the last step in a series of operations. For a crystal structure in very simple terms, it consists of the coordinates of the atoms placed to best fit the density map, which in turn (with ...
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  • 3,469
3 votes

Biopython: resseq doesn't match pdb file

Let's check it. I copied your file fragment into a.pdb. ...
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  • 1,066
3 votes
Accepted

How to map PDB chains to Uniprot IDs using API services

I found the answer and I thought it may be useful for others. we can use pypdb package for that purpose (it works in unix systems): ...
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  • 757
3 votes

How to find/build the evolutionary history of a protein from its sequence?

The general procedure is: Find the sequence for the same (or as similar as you can find (see mentions of blast in the comments above)) gene in other species. You can use uniprot or any other large ...
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  • 19.2k
3 votes
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Determining position of side chain hydrogen in glycine residues from coordinates of backbone atoms

Glycine has a single hydrogen atom as its side chain: All the six bond angles with the CA atom in the middle are about 109° (C-CA-N, C-CA-HA3, C-CA-HA2, N-CA-HA3, N-CA-HA2 and HA3-CA-HA2 using the ...
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  • 1,066
3 votes

Preparing PDB file for modeling with Swiss-Model

As explained in the website the data introduced must be: Format must be FASTA, Clustal, plain string, or a valid UniProtKB AC So you need to paste just the protein sequence. Without seeing the ...
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  • 4,602
3 votes
Accepted

How to select only RNA with Hetero atoms from pdb file with python?

Solution I found: (c/p of body) ...
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