chimerax python module - LigParGen tutorial
Dear ChimeraX users, I am trying to follow this tutorial to get the proper residues: http://zarbi.chem.yale.edu/ligpargen/gmx_tutorial.html I have found chimera (0.4.7) as pip module, but it's written in python2 and therefore no longer maintained. Is there a chimerax module I can import? Pychimera is also available and could install it with python2, but it also show compatibility problems with python3 Is DockPrep a separate module? I have found this thread on the chimera forum which doesn't really answer the question: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2014-July/010115.html Generally, how do I get unknown/custom residues (from LigParGen in this case) for Gromacs input files. Thank you for your support Marco ------------------- Marco Di Gennaro University of Liege
Dear Marco, The instructions in the LigParGen tutorial are about using the Chimera program, not ChimeraX. ChimeraX is a different program and does not (yet) have a Dock Prep tool. Both programs are available, so you could certainly just get Chimera and try it according to the instructions. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 7, 2021, at 12:30 AM, mdigennaro@uliege.be wrote:
Dear ChimeraX users,
I am trying to follow this tutorial to get the proper residues: http://zarbi.chem.yale.edu/ligpargen/gmx_tutorial.html
I have found chimera (0.4.7) as pip module, but it's written in python2 and therefore no longer maintained. Is there a chimerax module I can import? Pychimera is also available and could install it with python2, but it also show compatibility problems with python3 Is DockPrep a separate module?
I have found this thread on the chimera forum which doesn't really answer the question: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2014-July/010115.html
Generally, how do I get unknown/custom residues (from LigParGen in this case) for Gromacs input files.
Thank you for your support
Marco
Chimera is available from the "Download" link on the Chimera home page: www.cgl.ucsf.edu/chimera <http://www.cgl.ucsf.edu/chimera>. --Eric Eric Pettersen UCSF Computer Graphics Lab
On Apr 7, 2021, at 8:59 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Dear Marco, The instructions in the LigParGen tutorial are about using the Chimera program, not ChimeraX. ChimeraX is a different program and does not (yet) have a Dock Prep tool. Both programs are available, so you could certainly just get Chimera and try it according to the instructions. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 7, 2021, at 12:30 AM, mdigennaro@uliege.be wrote:
Dear ChimeraX users,
I am trying to follow this tutorial to get the proper residues: http://zarbi.chem.yale.edu/ligpargen/gmx_tutorial.html
I have found chimera (0.4.7) as pip module, but it's written in python2 and therefore no longer maintained. Is there a chimerax module I can import? Pychimera is also available and could install it with python2, but it also show compatibility problems with python3 Is DockPrep a separate module?
I have found this thread on the chimera forum which doesn't really answer the question: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2014-July/010115.html
Generally, how do I get unknown/custom residues (from LigParGen in this case) for Gromacs input files.
Thank you for your support
Marco
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participants (3)
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Elaine Meng -
Eric Pettersen -
mdigennaro＠uliege.be