[Chimera-users] Surface-display option
s.puthiyaveetil at wsu.edu
Fri Dec 4 17:52:21 PST 2015
Many thanks for your suggestions. I tried your command lines and it worked. I hid the dimers I didn't want. I still had to do the split function for some reason.
By the way, Chimera is a great program! I used it recently for http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3828554/.
Also, John Allen from whom I learned about Chimera.
From: Elaine Meng [mailto:meng at cgl.ucsf.edu]
Sent: Friday, December 04, 2015 8:57 AM
To: Puthiyaveetil, Sujith
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] Surface-display option
This page lists possible workarounds to surface calculation failures:
Sounds like you already tried #1 and #2 in that page, but the "molmap" method (#3) should always work, as it uses a completely different calculation.
As to the other methods and whether they are needed, it depends on how you made the assembly. If I use the following commands, I get a tetramer from 1Q90 and each monomer is already a separate model, so there is no reason to split. I can show the surfaces without any problems on my machine, but perhaps it is a numerical failure on yours:
If I open the model panel, I can see that the original model is #0 and the additional copies are models #1.1, 1.2, 1.3. I don't know which two are the dimer you want, but if the above works for you, you can just hide or close the models you don't want.
I hope this helps,
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 3, 2015, at 6:14 PM, Puthiyaveetil, Sujith <s.puthiyaveetil at wsu.edu> wrote:
> Hi Chimera developer,
> I encounter a problem with surface calculation/display when using the biological assembly (dimer) of 1Q90. The monomer on its own, as in pdb file 1Q90, displays the surface with no problem. I have tried the "split" command without success on the biological assembly. Also tried changing parameters to no effect. Would you please help.
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