Search Results
| Search type | Search syntax |
|---|---|
| Tags | [tag] |
| Exact | "words here" |
| Author |
user:1234 user:me (yours) |
| Score |
score:3 (3+) score:0 (none) |
| Answers |
answers:3 (3+) answers:0 (none) isaccepted:yes hasaccepted:no inquestion:1234 |
| Views | views:250 |
| Code | code:"if (foo != bar)" |
| Sections |
title:apples body:"apples oranges" |
| URL | url:"*.example.com" |
| Saves | in:saves |
| Status |
closed:yes duplicate:no migrated:no wiki:no |
| Types |
is:question is:answer |
| Exclude |
-[tag] -apples |
| For more details on advanced search visit our help page | |
Results for pdb
Search options not deleted
6
votes
2
answers
283
views
Consistent atom names PDB
Lets say you have two times the same molecule in PDB format. … I left out most of the PDB to save space …
- 343
3
votes
3
answers
792
views
Bond angles in PDB
people I've been trying to adjust the bond angles in a protein data bank (PDB) file, but I'm a novice when it comes to computing so I would like to ask your assistance. … Here is the gif file I get out of this PDB file from Jmol.
This is what I got from optimisation. …
- 2,481
5
votes
2
answers
953
views
Generating electron density from protein coordinate (PDB)
In my case, I want the reverse - PDB to electron density mesh. I thought it was more trivial and a program should be available. But Google did not give me any luck. … Since there could be manipulation of the PDB upstream, some crystal structure information could be lost. …
- 161
0
votes
1
answer
497
views
Visualizing PDB file in VMD, how to upload molecules?
Problem: When I load PDB-file of my protein of interest in VMD, nothing happens. … Here is the PDB file that I want to open. …
- 928
5
votes
2
answers
194
views
How would you add saccharide residue information to PDB files?
I have multiple PDB files containing a single molecules of polysaccharides, with a single chain and a long list of all the atoms -they are not divided by residue. … The PDB files were created from ChemDraw files using OpenBabel and Corina applet form molecular-networks. The workflow was: .cdx <-> OpenBabel <-> smiles/sdf <-> Corina <-> pdb. …
- 51
7
votes
1
answer
8k
views
Converting a PDB file to XYZ file
I am trying to convert a pdb file of gold nanoparticle to the xyz file format to get the atomic coordinates. … .
*** Open Babel Error in ReadMolecule
ERROR: not a valid PDB file
My command is obabel shelxpro.pdb -O shelxpro.xyz
(shelxpro.pdb is at http://www.sciencemag.org/content/318/5849/430/suppl/DC1
inside …
- 83
2
votes
1
answer
2k
views
What does C-OXT stand for in PDB files?
I've been trying to create 3D structures of unionized tyrosine (and other amino acids, it's just tyrosine is the one I'm up to atm) using the structure of Zwitterions found within PDB files and to do this … The other oxygen in the carboxylate group is just called C-O in the PDB file. …
- 2,481
1
vote
1
answer
173
views
How to unify all the subunits in a PDB file?
A PDB may contain a TER token. For example, hemoglobin has 4 subunits separated by a TER identifier. … If we take hemoglobin's biological assembly pdb file we see:
ATOM 1067 NH1 ARG A 141 26.176 8.362 17.810 1.00 11.11 N
ATOM 1068 NH2 ARG A 141 24.650 9.068 16.200 1.00 …
- 924
1
vote
1
answer
164
views
Generating PDB file from electron density without force field minimization
Is there a step-by-step tutorial on how to generate a PDB file from an electron density file (*.ccp4)?
For my current project, I am trying to take some statistics of some PDB files. … As a result, I would like to use x-plorer to generate the raw PDB file myself (without minimization), but since I have never done this before, I was wondering if somebody could provide me some guidance …
- 455
1
vote
1
answer
1k
views
How to merge PDB-files to build trimer from monomers [closed]
Problem
Using WinCoot or SWISS PDB viewer, how would one merge monomeric structures that should be in dimer formation? … What I have done:
I have downloaded the PDB-file which shows the monomer with a bound drug (Infliximab Fab fragments), but it should be a trimetric structure as whole -although you only get the monomer …
- 928
6
votes
1
answer
1k
views
How to write an entire trajectory into a single PDB file?
I have a trajectory (few frames) that I want to stack together and build a single PDB. I thought either to use VMD or MDAnalysis library. … With MDAnalysis I saw this:
with MDAnalysis.Writer("all.pdb", multiframe=True) as pdb:
for ts in u.trajectory:
pdb.write(u)
However, I am not sure how to use it in a complete script. …
- 924
10
votes
1
answer
5k
views
How does one export a PDB structure to SVG?
All I want is some software that can export a PDB structure of a protein (displayed in ribbons style) or DNA double helix, or a combination of the two, to a high-quality SVG file. … I know that several pieces of software for 3D molecular modelling can create raster images of PDB files quite easily (e.g., Accelrys DS Visualizer, Jmol, PyMOL, etc.). …
- 2,481
0
votes
1
answer
437
views
Local resolution of a crystal structure in PDB File (protein data bank)
Usually, the resolution of the PDB is assigned the resolution of the highest resolved part of the protein/nucleic acid. However, it is actually a range of resolution (ie. 2-8 A). … I am wondering if it possible to extract the resolution of each atom from a PDB file? …
- 455
3
votes
0
answers
585
views
Getting warnings during SDF to PDB conversion using obabel?
I did batch conversion of SDF to PDB for the Maybridge Screening library (containing ~50000 ligands) using obabel batch conversion tool using the following code. …
- 120
3
votes
1
answer
1k
views
Adding hydrogens to multiple pdb files using Openbabel GUI software [duplicate]
I have about 9000 pdb files to which, I want to add hydrogens. It will be a very hectic task to open all of them 1 by 1 and then convert each of them. … Is there a way I could choose the destination where it would create another .pdb file and save the output in it? I guess I am missing something here while choosing the output file. …
