Chimera Issue: Surface Calculation Failed - MSCalc returned code 5
Hello, I'm having some trouble generating surface models of large antibodies for an urgent project. I keep getting the mscalc return code 5 error message. I read through the forums and it seems that using the split command is the way to go, but I would not like to split this antibody. I'm trying to get a full rendition of the surface model of the antibody so that it is possible to 3D print the antibody. Can you please let me know if that would be possible? The pdb files of the 4 antibodies are attached. Thank you very much, Meg
Hello Meg, Please see the “workarounds for surface failures” page — I suggest #3 in that page, using the command “molmap”: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html> … or using ChimeraX instead of Chimera to show the molecular surface, as it uses a more robust calculation method: <http://www.rbvi.ucsf.edu/chimerax/> <http://www.rbvi.ucsf.edu/chimerax/download.html> …ChimeraX “surface” command documentation: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 24, 2019, at 2:21 PM, Megan Yung <my449@georgetown.edu> wrote:
Hello,
I'm having some trouble generating surface models of large antibodies for an urgent project. I keep getting the mscalc return code 5 error message. I read through the forums and it seems that using the split command is the way to go, but I would not like to split this antibody. I'm trying to get a full rendition of the surface model of the antibody so that it is possible to 3D print the antibody. Can you please let me know if that would be possible? The pdb files of the 4 antibodies are attached.
Thank you very much,
Meg <amgen pdb files.zip>_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Thank you so much, Elaine! I was able to generate a surface model with molmap, but was wondering how that was different from using the surface command? Thank you, Meg On Thu, Jan 24, 2019 at 6:52 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hello Meg, Please see the “workarounds for surface failures” page — I suggest #3 in that page, using the command “molmap”: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html>
… or using ChimeraX instead of Chimera to show the molecular surface, as it uses a more robust calculation method: <http://www.rbvi.ucsf.edu/chimerax/> <http://www.rbvi.ucsf.edu/chimerax/download.html>
…ChimeraX “surface” command documentation: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 24, 2019, at 2:21 PM, Megan Yung <my449@georgetown.edu> wrote:
Hello,
I'm having some trouble generating surface models of large antibodies for an urgent project. I keep getting the mscalc return code 5 error message. I read through the forums and it seems that using the split command is the way to go, but I would not like to split this antibody. I'm trying to get a full rendition of the surface model of the antibody so that it is possible to 3D print the antibody. Can you please let me know if that would be possible? The pdb files of the 4 antibodies are attached.
Thank you very much,
Meg <amgen pdb files.zip>_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Meg, Basically surface is a calculation that uses the classical definition of a molecular surface based on probe sphere and atomic VDW radii, whereas molmap generates an approximate density map from the atom centers and allows you to show a contour surface of that density map. Further details in their manual pages: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/surface.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html> Elaine
On Jan 24, 2019, at 4:49 PM, Megan Yung <my449@georgetown.edu> wrote:
Thank you so much, Elaine! I was able to generate a surface model with molmap, but was wondering how that was different from using the surface command?
Thank you,
Meg
On Thu, Jan 24, 2019 at 6:52 PM Elaine Meng <meng@cgl.ucsf.edu> wrote: Hello Meg, Please see the “workarounds for surface failures” page — I suggest #3 in that page, using the command “molmap”: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html>
… or using ChimeraX instead of Chimera to show the molecular surface, as it uses a more robust calculation method: <http://www.rbvi.ucsf.edu/chimerax/> <http://www.rbvi.ucsf.edu/chimerax/download.html>
…ChimeraX “surface” command documentation: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 24, 2019, at 2:21 PM, Megan Yung <my449@georgetown.edu> wrote:
Hello,
I'm having some trouble generating surface models of large antibodies for an urgent project. I keep getting the mscalc return code 5 error message. I read through the forums and it seems that using the split command is the way to go, but I would not like to split this antibody. I'm trying to get a full rendition of the surface model of the antibody so that it is possible to 3D print the antibody. Can you please let me know if that would be possible? The pdb files of the 4 antibodies are attached.
Thank you very much,
Meg <amgen pdb files.zip>_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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Elaine Meng -
Megan Yung