[chimerax-users] chimerax python module - LigParGen tutorial

[Eric Pettersen]

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 at 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 at 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 I have found chimera (0.4.7) as pip module, but it's written in python2 and therefore no longer maintained.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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