# Tag Info

5

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. rsync --port=33444 -rlpt -v -z --dry-run --stats rsync.rcsb.org::ftp_data/structures/divided/pdb/ You get a bunch of folders names and the following: Number of files: 182479 Number of files ...

4

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: with open('2ly4.pdb') as pdb: for line in pdb: if line[:4] == 'ATOM': chain = line[21] res_idx = int(line[23:26]) if chain == 'A' and 1 <= res_idx <= 30: ...

4

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 view and representation) and share the link with whomever —without needing any installations on either side. Here is the page of shared protein: gallery (...

4

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's many programs that exist already like Swiss-PdbViewer and Pymol. There's even web-interfaces that let you upload a PDB file and they display it for you like ...

3

Here is an example how to do it using another Python library with another selection syntax. Requires pip install gemmi. import gemmi st = gemmi.read_structure('2ly4.pdb') subset = gemmi.parse_cid('/*/A/1-30').copy_structure_selection(st) subset.write_minimal_pdb('output.pdb')

3

If you go to the wwPDB ftp site https://ftp.wwpdb.org/ in your browser you can find the biological unit structures (and anything else available in the PDB). The caveat of course is that a biounit structure has to have been generated for your structure. By way of some examples, to get all biological units you could do (note the ftp instead of https in front ...

2

If you need to do it only once, for this one PDB file, it's easier to do it manually. When you open the file you can see it has 10 models from NMR. Do you want to extract a subset of one model or of all 10? In this file the residues are numbered according to the sequence. So you find the line where residue 31 begins in the first model: ATOM 500 N PRO A ...

2

I am not good as you are and needed to use a parser for the pdb file see https://mmcif.wwpdb.org/docs/software-resources.html: #!/usr/bin/env python3 # -*- coding: utf-8 -*- """ Created on Thu Nov 7 17:40:03 2020 @author: Pietro """ import matplotlib.pyplot as plt #matplotlib from pdbx.reader.PdbxReader import PdbxReader #...

2

As others said, there already exist javascript libraries to visualize a protein. The most complete and recent one would probably be Mol*, which is what is used on RCSB PDB website. Mol* actually works using NGL, a WebGL engine. But probably the oldest library used on RCSB PDB to visualize proteins would be JSMol. You can actually switch between these viewers ...

2

Per Atom You are correct. Rosetta scorefunction does not store any per atom data. The scoring operates at the per residue level. Whereas each atom has its coordinates and properties in full atom mode, in Pyrosetta it is clear that an atom is a just part of a residue and every operation is applied at the residue level. It's a team effort: the functional group ...

2

Consider mmJSON. Each of the three PDB sites had the same problem: using mmCIF files in web-based viewers is inefficient. To solve this problem three new file formats were introduced: MMTF at RCSB, BinaryCIF at PDBe, mmJSON at PDBj. MMTF has the smallest files – it's aggressively optimized for size. It is based on MessagePack, but on top of it uses a ...

2

You can use PyMol to change the PDB to mmtf or other format. First open the PDB file and then choose file->export molecule-> choose which format you want to save as

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Molecular structures are 3D. The records (lines) in the PDB files are in so-called fixed column format. The fields don't need to be separated with blank characters, but they must be in specified columns. For example, the X coordinate is in columns 31-38. Here is the specification of the ATOM record from PDB v3.3. COLUMNS DATA TYPE FIELD ...

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The data can be found here: https://bmrb.io/search/instant.php?term=2KB7 There is no link directly in the PBD as it is a one-to-many relationship. Clicking on the first value (a shifts dataset) you get somewhere in the middle a link to the actual dataset, which is a CIF like file with the following table: vvvvvvv 1 . 1 ...

2

Your $[i,j,k]$ coordinates in the PDB file are coordinates. You can readily compute Euclidean distances between any pair of coordinates as described in the wiki page: $d(p,q)=\sqrt{(p_1-q_1)^2 + (p_2-q_2)^2 + (p_3-q_3)^2}.$ This resource suggests one such approach (code reproduced below in case that site stops existing): import Bio.PDB import numpy def ...

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There is no consensus on how different programs do representations (example of NGL vs. PyMOL) or what they are called so there is not official way to store selections. Annotations can be REMARK lines, which have a specific format or simply lines after a hash at the bottom of the file get ignored by most viewers but that specific program may read. Here is a ...

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Since this is not a correct PDB file, it can be interpreted differently by different PDB reading libraries. The most reliable way to change it would be to read it as plain text and change the chain ID to B in the lines that have segment ID LA0. Note: Strings RA0 and LA0 start at column 73. Columns in the PDB format correspond to characters. This is not a ...

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I normally use PyMOL. In PyMOL you can generate a model of a sequence of DNA with the command fnab — a sister command to the better known fab, which makes a protein sequence of a given secondary structure. I've not encountered that site, but it says it uses experimental data, which is a better approach. Side note 1 OP is asking for DNA, but if anyone ...

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maybe you can use the "per-residue interaction scores" (wich is available via Schrödinger). On the other hand,to show if a Docking Pose is really "better" you could show specific interactions rather than the complete big molecule.. e.g. an important salt bridge is missing. (hydrogen bonds are not that important, due to the fact that they ...

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NB. This is a long comment as opposed to an answer which requires a colossal working chunk of code. Control Science is all about controls failing. A great control for docking is the barnase-barnstar complex (PDB:1BRS): both small, but form a strong interactions. If this is done, the RMSD against the original structure is very meaningful and useful. RMSF A ...

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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: from Bio import SeqIO for record in SeqIO.parse(target, "pdb-atom"): print(record.seq) where target is the path to your pdb file the parser has multiple input/output functions, and pdb-atom is the one that will ...

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