[chimerax-users] ChimeraX does not write DMS

[Elaine Meng]

Regarding Chimera surface-calculation failures:

Yes, you can try workaround #2 on any system including Windows, but it is only something to try -- it might not work.  (#2 is to make small changes in VDW radii or in molecular surface calculation parameters like vertex density or  probe radius).
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html>

It is true that the Chimera surface calculation failures are more common on Windows than on other types of computer.  There is no absolute rule of what will work or not work, unfortunately.  You can only try and see if changing any of those parameters helps.

Elaine

> On Nov 6, 2020, at 5:30 AM, Diego Fernando Leon Vargas <difleonva at unal.edu.co> wrote:
> 
> Dear Elaine,
> 
> Thank you so much for your support.
> 
> I want to ask you something more, If I use Chimera in Windows I could be able to try the Workaround #2? I believe that this approach requests  other systems.
> 
> 
> 
> 
> El jue., 5 nov. 2020 a las 12:42, Elaine Meng (<meng at cgl.ucsf.edu>) escribió:
> Greetings,
> I changed the subject line to something descriptive.
> 
> Sorry, ChimeraX does not write DMS files.  
> 
> Unfortunately, as you saw, Chimera molecular surface calculations fail on some structures.  If you can't get the calculation to work in Chimera (e.g. with workaround #2 in this page):
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html>
> 
> ...then my only other suggestion is to get the separate open-source program "dms"... this is an older program in C:
> <http://www.cgl.ucsf.edu/Overview/software.html#dms>
> 
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> 
> > On Nov 5, 2020, at 8:58 AM, Diego Fernando Leon Vargas <difleonva at unal.edu.co> wrote:
> > 
> > Greetings,
> > 
> > Hope that you're doing well.
> > 
> > Currently, I'm using dock6 to develop some experiments  as you understand this software needs Chimera as visualizator, however, I was tried to create a surface for a specific protein and this software generated an issue because my protein exceed the size, so I read the possible solutions and one of them is using ChimeraX, nevertheless, I downloaded ChimeraX and I was able to create the surface, however, I didn't find an option to save this surface and I didn't find and option to create a DMS file. Then I have already read your user guide to ChimeraX but I didn't find information about how to create the DMS file, or how to save the surface information in any format that Chimera would be able to open, because I found a lot of differences between "Structure editing" option in Chimera and ChimeraX, then I'm requesting your help to create the DMS file using ChimeraX or indicanting me a way to save the surface information to use it later using Chimera.
> > 
> > Thank you so much for your help.
> > 
> > Kind regards,
> > 
> > B.Sc Diego Fernando León Vargas, Ph.D (c)
> 
> 
> 
> -- 
> Cordialmente,
> 
> Q.F Diego Fernando León Vargas
> Estudiante - Doctorado en ciencias farmacéuticas
> Grupo de estudios en síntesis y aplicaciones de compuestos heterocíclicos - (GESACH)
> Facultad de Ciencias 
> Universidad Nacional de Colombia
> Sede Bogotá 
> 
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