I am struggling to show an electrostatic surface on the solvent accessible surface for several related proteins. It works fine in Pymol with APBS but with Chimera I continue to get "surface calculation failed, mscalc returned code 5". I have read posts going back at least 5 years about this problem and I have tried all of the various work-arounds (vdwdef, split, probe radius and vertex density). Has this problem been solved? I am using version 1.8.1 on a PC. Is there a way to identify which part of the protein is causing the problem? Criss Hartzell Professor Department of Cell Biology Emory University School of Medicine Atlanta, GA 30322 ________________________________ This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).
Hello Criss Hartzell, Sorry about the difficulties. The basic problem still exists, but there is at least one solution, a completely different method of surface generation. It sounds like you already tried #1 and 2 in the following, but I recommend using the "molmap" command as detailed in workaround #3: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html> Basically molmap is used to simulate a density map from the atoms. An isosurface is shown for that simulated map and can be colored by ESP with the Electrostatic Surface Coloring tool or the "coulombic" command with the "atoms" option (it cannot be done with the Coulombic GUI). See the link above for details and suggested parameter settings. 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 1, 2014, at 6:53 PM, "Hartzell Jr., Criss" <criss.hartzell@emory.edu> wrote:
I am struggling to show an electrostatic surface on the solvent accessible surface for several related proteins. It works fine in Pymol with APBS but with Chimera I continue to get "surface calculation failed, mscalc returned code 5". I have read posts going back at least 5 years about this problem and I have tried all of the various work-arounds (vdwdef, split, probe radius and vertex density). Has this problem been solved? I am using version 1.8.1 on a PC. Is there a way to identify which part of the protein is causing the problem?
Criss Hartzell Professor Department of Cell Biology Emory University School of Medicine Atlanta, GA 30322
I found that subdividing the structure with Surfcat did the trick, although molmap will likely be useful for other situations. Thanks for pointing me in the right direction. Criss Criss Hartzell Professor Department of Cell Biology Emory University School of Medicine Atlanta, GA 30322 404-242-5719 (cell) For Fedex, UPS, other courier: Criss Hartzell 615 Michael St. 535 Whitehead Building Emory University Atlanta, GA 30322 ________________________________________ From: Elaine Meng [meng@cgl.ucsf.edu] Sent: Tuesday, December 02, 2014 12:12 PM To: Hartzell Jr., Criss Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] show surface fails Hello Criss Hartzell, Sorry about the difficulties. The basic problem still exists, but there is at least one solution, a completely different method of surface generation. It sounds like you already tried #1 and 2 in the following, but I recommend using the "molmap" command as detailed in workaround #3: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html> Basically molmap is used to simulate a density map from the atoms. An isosurface is shown for that simulated map and can be colored by ESP with the Electrostatic Surface Coloring tool or the "coulombic" command with the "atoms" option (it cannot be done with the Coulombic GUI). See the link above for details and suggested parameter settings. 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 1, 2014, at 6:53 PM, "Hartzell Jr., Criss" <criss.hartzell@emory.edu> wrote:
I am struggling to show an electrostatic surface on the solvent accessible surface for several related proteins. It works fine in Pymol with APBS but with Chimera I continue to get "surface calculation failed, mscalc returned code 5". I have read posts going back at least 5 years about this problem and I have tried all of the various work-arounds (vdwdef, split, probe radius and vertex density). Has this problem been solved? I am using version 1.8.1 on a PC. Is there a way to identify which part of the protein is causing the problem?
Criss Hartzell Professor Department of Cell Biology Emory University School of Medicine Atlanta, GA 30322
________________________________ This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).
Hi Criss, The Chimera molecular surface calculation fails on most large molecules (over 10,000 atoms) and is about 10x more likely to fail on 64-bit Windows than on other Linux or Mac. The 32-bit Windows Chimera also fails less often than the 64-bit Windows, although more than Linux and Mac — so you might try 32-bit Chimera. There are two newer versions of Chimera (1.9 and 1.10) but the surface calculation code has not changed so those will not improve the surface calculation success rate. Tom
On Dec 1, 2014, at 6:53 PM, Hartzell Jr., Criss wrote:
I am struggling to show an electrostatic surface on the solvent accessible surface for several related proteins. It works fine in Pymol with APBS but with Chimera I continue to get "surface calculation failed, mscalc returned code 5". I have read posts going back at least 5 years about this problem and I have tried all of the various work-arounds (vdwdef, split, probe radius and vertex density). Has this problem been solved? I am using version 1.8.1 on a PC. Is there a way to identify which part of the protein is causing the problem?
Criss Hartzell Professor Department of Cell Biology Emory University School of Medicine Atlanta, GA 30322
This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited.
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participants (3)
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Elaine Meng -
Hartzell Jr., Criss -
Tom Goddard