VMD-L Mailing List

From: Christian Seitz (cseitz_at_ucsd.edu)
Date: Mon Mar 08 2021 - 01:50:03 CST

Hello,

I am trying to visualize the electrostatics distribution on a very large
protein complex. I have created the pqr, opened it in vmd, and tried to set
the drawing method to surf. The terminal then shows the surf commands being
executed, but after ~5 seconds it freezes, each time in the same place:

find_circle(): Negative circle radius: atoms (32737 32725) radius -3.191360
find_circle(): Negative circle radius: atoms (32737 32725) radius -3.191360
.......find_circle(): Negative circle radius: atoms (33522 32605) radius
-0.001328
find_circle(): Negative circle radius: atoms (33598 32530) radius -0.906329
find_circle(): Negative circle radius: atoms (33598 32530) radius -0.906329
.find_circle(): Negative circle radius: atoms (33654 32449) radius -0.002413
find_circle(): Negative circle radius: atoms (33683 31563) radius -0.008748
.find_circle(): Negative circle radius: atoms (33710 31575) radius -0.004737
....

canceling the surf command shows that it created the surf representation
for maybe a fourth of the protein complex before freezing. There is no
error message given. Do you know how I can fix this? Perhaps there are
memory limits on what Surf can accomplish? The QuickSurf drawing method
colors the whole protein complex, but does not look as good as Surf would
look. Thank you!

Best,
Christian 

-- 
*Christian Seitz*
PhD Candidate, Biochemistry & Biophysics | UC-San Diego
NSF GRFP Fellow, Amgen Scholar
McCammon lab <https://urldefense.com/v3/__https://mccammon.ucsd.edu/__;!!DZ3fjg!r8ugw-RGE4Rv-J60Vj_TFcztIPY2uVROqfkbTjEIxNPbalPvabOLz9cUSuunZ1v98g$ > and Amaro lab
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cseitz_at_ucsd.edu <cseitz_at_elon.edu>
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