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10 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. ...
Iakov Davydov's user avatar
9 votes
Accepted

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. ...
Davidmh's user avatar
  • 206
8 votes
Accepted

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 ...
Marcin Magnus's user avatar
7 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 ...
marcin's user avatar
  • 1,261
7 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 ...
Matteo Ferla's user avatar
  • 4,234
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 ...
Aalawlx's user avatar
  • 517
6 votes
Accepted

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 ...
Matteo Ferla's user avatar
  • 4,234
6 votes
Accepted

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. ...
Matteo Ferla's user avatar
  • 4,234
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 ...
CubeHead's user avatar
  • 415
6 votes
Accepted

What is the function of the heteroatoms

The text you cited mentions "input structure", so they work with structures, not just "protein sequences". Heteroatoms = atoms marked as HETATM ...
marcin's user avatar
  • 1,261
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 ...
Rosalind Was Robbed's user avatar
5 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 ...
Abdul Ahad's user avatar
5 votes
Accepted

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 ...
Matteo Ferla's user avatar
  • 4,234
5 votes
Accepted

Read PDB file, extract dihedral angles, modify dihedral angles, reconstruct Cartesian coordinates, and write PDB file

ok, here my input pdb, example_short.pdb : ...
pippo1980's user avatar
  • 1,043
5 votes

CONECT doesnt include all the connections the 1vfl macro molecule have in a pdb file

The CONECT entries specify the bonding of the ligands (HETATM), not your polymeric residues (...
Matteo Ferla's user avatar
  • 4,234
5 votes
Accepted

What is changed in this PDB file?

So the 'right' answer here would be for you to use a diff tool of some kind (WinDiff, or just the diff command in a Unix-like environment). That would show you the ...
gilleain's user avatar
  • 293
4 votes
Accepted

PDB format: remark number for free text

From this document, it looks like REMARK 250 is the way to go.
Dan's user avatar
  • 612
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 ...
TW93's user avatar
  • 449
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 ...
marcin's user avatar
  • 1,261
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 ...
marcin's user avatar
  • 1,261
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: ...
neilfws's user avatar
  • 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 ...
Emily_Ensembl's user avatar
4 votes
Accepted

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 ...
Ammar Sabir Cheema's user avatar
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 ...
jgreener's user avatar
  • 931
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: ...
Arap's user avatar
  • 56
4 votes

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

You can also use the SeqIO module from Biopython https://biopython.org/docs/1.75/api/Bio.SeqIO.PdbIO.html and do something like this: ...
cminima's user avatar
  • 51
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'...
Bioinfomrat's user avatar
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 ...
Matteo Ferla's user avatar
  • 4,234
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: ...
Jan Wilamowski's user avatar
4 votes
Accepted

How can I parse alternative atom information?

Generally alternate location are used in structures with partial occupancy. In https://www.wwpdb.org/documentation/file-format-content/format33/sect9.html you will see that the fourth numerical column ...
Matteo Ferla's user avatar
  • 4,234

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