[chimerax-users] Questions about ChimeraX

[Elaine Meng]

Hi Joshua,
ChimeraX is a new and different program, not a version of Chimera.  So all the features have to be developed separately... it does have several completely new features and advantages compared to Chimera, but also it does not have all of the commonly used tools of Chimera (yet).  ChimeraX is being actively developed and new features are being added constantly, however.

ChimeraX does allow fetching structures for SMILES strings, but maybe the backslash in your example is causing a problem. I will make a bug report for that.

ChimeraX does not have a general minimization tool for nonstandard residues like ligands, but there are "tug" and "minimize" mouse modes for openMM dynamics when the structure has hydrogens and only standard residues, see:
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html#mousemode>
<http://rbvi.ucsf.edu/chimerax/docs/user/tools/mousemodes.html>
<http://rbvi.ucsf.edu/chimerax/docs/user/tools/mousemodes.html#openmm>

There is no docking tool in ChimeraX, only ViewDockX for looking at results from docking done separately.  
<http://rbvi.ucsf.edu/chimerax/docs/user/tools/viewdockx.html>

However, it is important to understand that Chimera does not do docking either; although it has an "Autodock Vina" tool, that only uses an outside web service that does a very short docking that is not suitable for most research purposes, as mentioned in the boxed warning in its help page:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html>

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 4, 2020, at 6:11 PM, Yuhua Fang <fangy34 at myumanitoba.ca> wrote:
> 
> Hi 
>  
> Recently I transferred to ChimeraX from the old version. I found:
> 	• Some SMILE strings copied directly from ChemDraw cannot be recognized by ChimeraX, such as O=C1NC2=C(/C1=C3NC4=CC=CC=C4C/3=C\O)C=CC(Br)=C2
> 	• Correct me if I am wrong but ChimeraX seems not able to do molecule docking/ligand minimization like the old version, right?
> Thank you
>  
> Joshua