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Questions tagged [pymol]

PyMOL is a cross-platform, free and open-source, molecular visualization software written in C, C++ and Python and developed by Schrödinger, LLC.

Use this tag for questions relating to PyMOL, its installation (in which case the software-installation tag may also be appropriate), customization and usage. Additional support resources may be found below in the Support section of this tag wiki.

Installation

PyMOL may be installed on Ubuntu by running sudo apt-get install pymol, keeping in mind that this version is often out of date (e.g., as of 16 May 2015 the latest version of PyMOL available on 15.04 is 1.7.2.1 and the latest version is 1.7.6). Alternatively the latest version of PyMOL may be compiled and installed from source code (instructions may usually be found in the INSTALL file within the source code directory, or here). If any issues are encountered in this process, feel free to ask a question here regarding its installation.

Usage

PyMOL may be used for a variety of different purposes, including making movies or images depicting the 3D structure of macromolecules or small molecules. It can also be used to calculate the electrostatic interactions between a macromolecule and its ligand(s) using the APBS plugin.

Support

  • PyMOL-users mailing list (you may go here to subscribe to it)
  • PyMOLWiki

Other links

9 questions
3
votes
2 answers

Pymol not starting after downloading using linux terminal command

Hello everyone Iam currently using Ubuntu 24.04.1 LTS I am downloading from linux terminal using "sudo apt-get install pymol" and successfully installing pymol. > sudo apt-get install pymol Reading package lists... Done Building dependency tree...…
Sambit Mandi
  • 31
1
vote
0 answers

APBS segment fault on pymol 1.8.x

I have been trying to run APBS on pymol but it always get terminated abruptly with the following error: In show error 1 Segmentation fault (core dumped) When select "set grid", the following popups GENERATING PQR FILE via PDB2PQR Erasing contents…
meAtStackOverflow
  • 21
1
vote
1 answer

Can not install pymol because I cannot install libfreetype6-dev

I am following this link http://www.pymolwiki.org/index.php/User:Tlinnet/Linux_Install to install pymol. I need libfreetype6-dev as a dependency, but it cannot be installed. fmp@eva03:~/Bins$ sudo apt-get install libfreetype6-dev [sudo] password…
murpholinox
  • 123
1
vote
1 answer

Where is PyMOL installed on 14.04?

I'd like to be able to install packages for PyMOL like eMovie and to do so I understand I need to know where it is installed (i.e., the file directory). I installed it using Ubuntu Software Centre.
Josh Pinto
  • 8,089
0
votes
1 answer

Python 2.7 crashes in pymol application

I am new to ubuntu, please forgive me for any logical comments. While attempting to load a pdb file in pymol, I will get a system crash report: ProblemType: Crash Architecture: amd64 CrashCounter: 1 CurrentDesktop: Unity DistroRelease: Ubuntu…
meAtStackOverflow
  • 21
0
votes
1 answer

pymol wont work with nvidia-driver 352.63 on ubuntu 14.04.3

I just installed Ubuntu 14.04.3 and did sudo apt-get install pymol. Pymol works well with the open driver (selected by default) in the additional drivers window. fmp@eva02:~$ pymol PyMOL(TM) Molecular Graphics System, Version 1.7.0.0. Copyright…
murpholinox
  • 123
0
votes
1 answer

Installing PyMOL from source code

I've tried running: prefix=/opt/pymol-svn modules=$prefix/modules python setup.py build install \ --home=$prefix \ --install-lib=$modules \ --install-scripts=$prefix with the following output (with several lines before it): cc1plus:…
Josh Pinto
  • 8,089
0
votes
0 answers

How to troubleshoot pymol downloaded from repository?

In my Ubuntu device 24.04 LTS I am downloading pymol from repository by using sudo apt-get install -y pymol. I am successfully installing pymol but whenever I am trying to open it, its shows nothing regardless whether I am using the application or…
Sambit Mandi
  • 1
0
votes
0 answers

Hi can someone provide me a solution for soft link removal?

sudo ln -s /home/user/Downloads/msms/msms.x86_64Linux2.2.6.1 /usr/local/bin/msms I created a wrong softlink in the afore mentioned script which I need to remove. Can someone please provide a suitable solution. I also cannot find the path of the…
Sambit Mandi
  • 1