[Chimera-users] Coulombic ESP on multiple models

Elaine Meng meng at cgl.ucsf.edu
Sat May 14 11:01:31 PDT 2016


Sorry folks, I have no idea why sometimes my messages send twice!

Danny, I don’t know what you mean by keeping surfaces/sequences open.  There is no need to keep windows open other than the main Chimera window and the dialog for the tool (for example, Coulombic coloring)  that you are actually using.  The structures and their surfaces in the main Chimera window won’t be closed or deleted unless you closed or deleted them yourself.

Elaine

On May 14, 2016, at 10:52 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Danny,
> It should not make any difference whether you are using the graphical interfaces (dialog windows) or commands.  I only put commands in my example because it is much less typing to describe.  
> 
> As I mentioned before, just make sure that in the Coulombic coloring dialog, you have chosen all of the surfaces…. the most obvious reason it might only color one surface is if you only chose (highlighted) one surface in the list.
> Best,
> Elaine
> 
> On May 13, 2016, at 1:13 PM, zona cat <azrucu at yahoo.com> wrote:
> 
>> Hi Elaine,
>> 
>> Thank you for the quick response.  I was doing my work via windows, not the command line.  Is there something I need to do to keep all of the surfaces/sequences open??
>> -Danny
>> 
>> 
>> On Friday, May 13, 2016 3:57 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>> 
>> 
>> Hi Dan,
>> I wasn’t able to reproduce this problem.  I just tested in Chimera 1.10.2 on 3 related proteins, with commands:
>> 
>> open 2mnr
>> open 1muc
>> open 4enl
>> delete :.b
>> mm #0 #1
>> mm #0 #2
>> tile
>> surf
>> 
>> … then invoking Coulombic Surface Coloring, just clicking Apply because all three surfaces were already chosen in the dialog. Image of the result attached (after applying publication preset 1).   
>> 
>> I can’t think of any reason your system would behave differently, and all I can say is to make sure all the surfaces are chosen in the dialog.  However, if that still doesn’t work you can always try submitting a bug report (menu: Help… Report a Bug) and attach the session so we could try to reproduce it.
>> 
>> Best,
>> Elaine
>> -----
>> Elaine C. Meng, Ph.D.                       
>> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>> 
>> <3surfs.png>
>> On May 13, 2016, at 11:10 AM, zona cat <azrucu at yahoo.com> wrote:
>> 
>>> Good afternoon,
>>> 
>>> My name is Daniel Heller, and I am working with Helen Berman at Rutgers University on a PDB project.  We are trying to analyze multiple DNA binding proteins simultaneously (via matchmaker) and looking to visualize the surface electrostatic potential of each structure as a tiled picture. We are deleting the nucleotide chains for all proteins when complexed with DNA.  However, I am only able to get the surface electrostatic coloring for one structure (the reference structure), subsequent structures will not apply the columbic coloring after i hit apply, they just maintain the monotone default surface structure .  Could you please help me with this issue.
>>> 
>>> Thank you very much,
>>> Dan
> 
> 
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