[Chimera-users] Using UCSF Chimera inside python environment

Benjamin Basanta bbasanta at scripps.edu
Wed Dec 9 14:29:36 PST 2020

Hi Jeff,

I wrote a short explanation on how to put together a conda environment with pychemera in this git repo: https://github.com/GrotjahnLab/guided_tomo_align

You don't need all the files there, just pychimera.yml

I don't know enough about the cluster conformations function help you, sadly.

From: Chimera-users <chimera-users-bounces at cgl.ucsf.edu> on behalf of Jeff Saxon <jmsstarlight at gmail.com>
Sent: Wednesday, December 9, 2020 7:01 AM
To: chimera-users at cgl.ucsf.edu BB <chimera-users at cgl.ucsf.edu>
Subject: [Chimera-users] Using UCSF Chimera inside python environment

Dear Chimera Users,

I would like to use chimera to do some calculations on PDB filles
(mainly I am interesting to cluster conformations in multi-model PDB
using Ensemble cluster)

Could you explain to me how I could install chimera (I am using
python3 with conda) in order that I could use some of Chimera's
functions directly inside of my python scripts?

I have already tried install package pychimers but did not succeed

conda install -c insilichem pychimera

nsatisfiableError: The following specifications were found

to be incompatible with the existing python installation in your environment:


  - pychimera -> python[version='2.7.*|>=2.7,<2.8.0a0']

  - pychimera -> python[version='3.4.*|3.5.*']

Your python: python=3.8

May I use chimera with my python using alternative ways of installations?

Thank you in advance!
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