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. Regards, Sujith Sujith Puthiyaveetil Postdoctoral research associate Institute of Biological Chemistry Washington State University Pullman, WA 99164. Phone: +1 509-715-7435
Dear Sujith, This page lists possible workarounds to surface calculation failures: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html> 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: open 1q90 sym #0 focus rainbow models surface 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 ----- 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@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. Regards, Sujith
Dear Elaine, 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. http://www.sciencedirect.com/science/article/pii/S1360138504000275 Regards, Sujith -----Original Message----- From: Elaine Meng [mailto:meng@cgl.ucsf.edu] Sent: Friday, December 04, 2015 8:57 AM To: Puthiyaveetil, Sujith Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Surface-display option Dear Sujith, This page lists possible workarounds to surface calculation failures: <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chimer... > 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: open 1q90 sym #0 focus rainbow models surface 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 ----- 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@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. Regards, Sujith
Dear Sujith, Thanks for the kind words, and I’m glad you were able to get what you wanted. Nice to see Chimera used in structural biology of plants! Best, Elaine
On Dec 4, 2015, at 5:52 PM, Puthiyaveetil, Sujith <s.puthiyaveetil@wsu.edu> wrote:
Dear Elaine,
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.
http://www.sciencedirect.com/science/article/pii/S1360138504000275
Regards,
Sujith
participants (2)
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Elaine Meng -
Puthiyaveetil, Sujith