Stack Overflow
Stack Overflow

Questions tagged [pymol]

PyMOL is an open-source, cross-platform molecular visualization system. PyMOL is free to academic users, and has a community-run support wiki that includes documentation, sample scripts, plugins, and more.

PyMOL is a Python-based tool for visualizing molecules. It can manipulate molecules and produce publication-quality renderings and animations. The most current release, as of January 16, 2012 is PyMOL 1.5

Supported Platforms

PyMOL runs on many GNU/Linux distributions, Windows, and Mac OS X. See Supported Operating Systems for more detail.

Links

112 questions
7
votes
3 answers

Aligning 2 small molecules in PyMOL

I want to align to ligands in PyMOL like one would do it with protein structures, but I get an error message: ExecutiveAlign: mobile selection must derive from one object only I also copied the ligands into separate PDB files, renamed the HETATM…
user2015601
5
votes
2 answers

How do I add libraries to pymol?

I have pymol downloaded and in use on my mac. I open it from the applications folder. I can successfully run a python script in it. However, I cannot import any libraries within that script. The way I currently know to add importable libraries to a…
Ben
  • 121
  • 8
4
votes
1 answer

How to show distance between residues in Pymol

With the this PDB file and the following PyMOL code: cd /Users/foo/Desktop/ reinitialize load pdp_4gg6CD1_I.pdb as cartoon select chainI, chain I select chainC, chain C select chainD, chain D show sticks, chainI spectrum count, cyan_red,…
neversaint
  • 60,904
  • 137
  • 310
  • 477
4
votes
3 answers

change dihedral angles using the mouse in Pymol

Does anyone know the method to change the phi/psi/omega angles using the mouse in pymol? I know the command: Set_dihdral but want to play with the dihedral angles using the mouse. Thank you, Steve
Steve Grafton
  • 1,821
  • 4
  • 17
  • 18
3
votes
1 answer

Gromacs: .ene extension not recognized

I'm new to Gromacs (and protein-analysis coding in general, but have some experience with python-based code). I'm trying to convert a .ene file received from pyDock to a more readable format (it currently opens When I try to use different commands…
GoatsCantCode
  • 31
  • 2
3
votes
2 answers

R package Bio3D tutorial reproducing

I started working with R package called Bio3D (http://thegrantlab.org/bio3d/index.php) and encountered a problem during reproducing examples from "Protein Structure Networks with Bio3D"…
Konstantin
  • 35
  • 7
3
votes
4 answers

Getting all dihedral angles in Pymol

I want to get all the dihedral angles of a protein in Pymol (phi, psi, chi1, chi2, chi3, chi4) but I only manage to find a function that can shows me the phi and psi. For instance: PyMOL>phi_psi 1a11 SER-2: ( 67.5, 172.8 ) GLU-3: ( …
Daniel Bonetti
  • 2,306
  • 2
  • 24
  • 33
3
votes
2 answers

How do I output a .pdb file using python script?

I'm currently in the process of manipulating a .pdb (protein data bank) file in python. My end goal is to turn the python script back into a pdb file so that I can run simulations in either VMD or PyMol.Can someone please help?
Alicia Burns
  • 31
  • 1
  • 2
2
votes
1 answer

How do I decompress a DSN6 file into a readable format?

I am trying to isolate certain pieces of information within a dsn6 file. Specifically, I want to find the electron density around two atoms within a protein. I want to then run a python code to determine if there is positive electron density between…
Ben
  • 121
  • 8
2
votes
1 answer

PyMol: select residues for which I have found hydrogen bonds

Using PyMol, I can show hydrogen bonds using Action -> Find -> Polar Contacts. This produces the contacts, but I want to show them clearly by only showing residues which have these contacts and nothing else (currently, the view is very unclear due…
Zubo
  • 1,543
  • 2
  • 20
  • 26
2
votes
1 answer

Draw bonds PyMOL using R package Bio3d

Using the R package bio3d I would like to draw bonds between two atoms on a protein and parse the structure to PyMOL using the pymol(). library(bio3d) # Import PDB file pdb <- read.pdb( system.file("examples/1hel.pdb", package="bio3d") ) # Atom…
user 123342
  • 463
  • 1
  • 9
  • 21
2
votes
2 answers

IntVar().trace() not working

I'm just getting started coding in Python/Tkinter for a small Pymol plugin. Here I'm trying to have a toggle button and report its status when it is clicked. The button goes up and down, but toggleAVA never gets called. Any ideas why? from Tkinter…
ipetrik
  • 1,749
  • 18
  • 28
2
votes
1 answer

Why can't I start pymol?

I'm trying to run the biotech software pymol. It can't find the cmd.py module. However, it's in a directory, which is in the $PYTHONPATH. [mzhKU_work] @ modules $ python launch_pymol.py Traceback (most recent call last): File "launch_pymol.py",…
TMOTTM
  • 3,286
  • 6
  • 32
  • 63
2
votes
1 answer

Pymol not outputting image

I am trying to draw a protein structure from a pdb file using pymol. However, when I try to run the script below, a pymol window opens but it is just pitch black. Also, bizarrely, the pdb file is outputted to the shell. Here is my…
Charon
  • 2,344
  • 6
  • 25
  • 44
2
votes
1 answer

PyMOL: Get sequence of selection

I have made a selection of residues like this: fetch 1bsx select interface_1bsx, byres((1bs and chain A) within 5A of (1bsx and chain X)) How do I get the sequence of interface_1bsx?
Mehdi Nellen
  • 8,486
  • 4
  • 33
  • 48
1
2 3 4 5 6 7 8