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.
Unfortunately this is nigh impossible. First, the entire code base of Chimera is Python 2 and will not import into a Python 3 interpreter, so you can't use it directly. Second, the Ensemble Cluster code was written entirely with a graphical user interface in mind, and the computation code can't easily be called directly, even from a Python 2 script. I don't have any good suggestions for you here that don't involve a Herculean amount of effort. --Eric Eric Pettersen UCSF Computer Graphics Lab
On Dec 9, 2020, at 7:01 AM, Jeff Saxon <jmsstarlight@gmail.com> wrote:
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. _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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@cgl.ucsf.edu> on behalf of Jeff Saxon <jmsstarlight@gmail.com> Sent: Wednesday, December 9, 2020 7:01 AM To: chimera-users@cgl.ucsf.edu BB <chimera-users@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. _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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 populations.. Many thanks in advance! Cheers, J ср, 9 дек. 2020 г. в 23:29, Benjamin Basanta <bbasanta@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@cgl.ucsf.edu> on behalf of Jeff Saxon <jmsstarlight@gmail.com> Sent: Wednesday, December 9, 2020 7:01 AM To: chimera-users@cgl.ucsf.edu BB <chimera-users@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. _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (3)
-
Benjamin Basanta -
Eric Pettersen -
Jeff Saxon