VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Mar 08 2021 - 01:58:43 CST

Hi,
  The best options here are to use either NanoShaper or MSMS instead
of Surf, for solvent surface representations. If you just want an
approximate Gaussian surface, then QuickSurf is much faster than the
other methods and can also be colored by electrostatic potential, etc,
if you have an associated DX file to load with it, e.g. from APBS.

Best,
  John Stone

On Sun, Mar 07, 2021 at 11:50:03PM -0800, Christian Seitz wrote:
> 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 |Â UC-San Diego
> NSF GRFP Fellow, Amgen Scholar
> [1]McCammon lab and [2]Amaro lab
> [3]cseitz_at_ucsd.edu
> [4]www.linkedin.com/in/christianseitz21
>
> References
>
> Visible links
> 1. https://urldefense.com/v3/__https://mccammon.ucsd.edu/__;!!DZ3fjg!r8ugw-RGE4Rv-J60Vj_TFcztIPY2uVROqfkbTjEIxNPbalPvabOLz9cUSuunZ1v98g$
> 2. https://urldefense.com/v3/__https://amarolab.ucsd.edu/__;!!DZ3fjg!r8ugw-RGE4Rv-J60Vj_TFcztIPY2uVROqfkbTjEIxNPbalPvabOLz9cUSus14fNYRw$
> 3. mailto:cseitz_at_elon.edu
> 4. https://urldefense.com/v3/__http://www.linkedin.com/in/christianseitz21__;!!DZ3fjg!r8ugw-RGE4Rv-J60Vj_TFcztIPY2uVROqfkbTjEIxNPbalPvabOLz9cUSusXoope7g$ 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/