[Chimera-users] Using UCSF Chimera inside python environment

Jeff Saxon jmsstarlight at gmail.com
Thu Dec 10 01:19:02 PST 2020

Hello everyone,

Many thanks for your kind responses!
Anyway, I will try to integrate pychimera in my python environment to
test it for other purposes.
May someone suggest another python library suitable to do cluster
analysis of pdbs ?? In fact I am dealing with a trivial problem,
having a multi-model of PDB (ligand poses predicted by protein-ligand
docking), that I need to cluster based on the RMSD between these
models and then plot a bar plot representing the clusters and their

Many thanks in advance!

ср, 9 дек. 2020 г. в 23:29, Benjamin Basanta <bbasanta at scripps.edu>:
> 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.
> Best,
> Benja
> ________________________________
> 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:
> Specifications:
>   - 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!
> J.
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