[Chimera-users] betacavity web and chimera

Elaine Meng meng at cgl.ucsf.edu
Sun Jan 3 09:47:35 PST 2021

On Jan 2, 2021, at 10:42 PM, Jacqueline Vitali <jackie.vitali at gmail.com> wrote:
> Hi Elaine,
> is there a way to incorporate in chimera the option to read cavities from betacavity web (Nucleic Acids Res 2015 vol 43 W413-W418) ?  Right now you do it for CASTP.
> Please let me know. 
> THank you.
> Jackie Vitali
> Cleveland State University

Hi Jackie,
Unfortunately we don't have resources to provide visualization capability for the many useful web servers that exist.  A related server with Chimera visualization capability is MOLEonline:  <https://mole.upol.cz/>

I hadn't heard of betacavity before.  In general it would be useful to say or give examples of what outputs they do provide, to give some idea of whether it might be possible... I had to run it myself to figure that out.  

Looks like they just give Jmol visualization in the web browser and a script for Pymol.   Maybe you could ask the authors of betacavity if they would also provide a Chimera script too, but it's probably unlikely.

I also see they give lists of atoms on the right side of the results page, but not in PDB format.  You could try manually showing surface for those atoms in Chimera (with a Chimera command) but it would be (1) tedious, and (2) just the molecular surface of those atoms, so there may be jagged edges and bits sticking out, not a nice enclosed blob as in their Jmol visualization.  Our Castp visualization has this same issue.

E.g. for 2gbp I get in the betacavity results:

VOID   3
VOID-VOLUME                   8.468 A^3
VOID-BNDRY-AREA              41.050 A^2
ATOM    131  CE1 PHE A  16    0.064 A^2
ATOM    689  CA  ASN A  91    0.978 A^2
ATOM    691  O   ASN A  91    3.921 A^2
ATOM    695  ND2 ASN A  91    1.857 A^2
ATOM    705  N   GLU A  93    0.796 A^2
ATOM    709  CB  GLU A  93    1.116 A^2
ATOM    713  OE2 GLU A  93    1.118 A^2
ATOM    829  CE2 TYR A 107    0.001 A^2
ATOM    831  OH  TYR A 107    5.812 A^2
ATOM    840  CA  GLY A 109    0.897 A^2
ATOM    843  N   THR A 110    0.696 A^2
ATOM    846  O   THR A 110    1.145 A^2
ATOM    848  OG1 THR A 110    2.830 A^2
ATOM    849  CG2 THR A 110    2.985 A^2
ATOM    863  OG  SER A 112    2.918 A^2
ATOM   1174  CE1 HIS A 152    0.504 A^2
ATOM   1180  CB  PRO A 153    2.424 A^2
ATOM   1182  CD  PRO A 153    0.061 A^2
ATOM   1183  N   ASP A 154    0.007 A^2
ATOM   1188  CG  ASP A 154    1.146 A^2
ATOM   1189  OD1 ASP A 154    3.493 A^2
ATOM   1190  OD2 ASP A 154    1.781 A^2
ATOM   1944  OD1 ASN A 256    0.193 A^2
ATOM   1945  ND2 ASN A 256    0.811 A^2
ATOM   1982  OE1 GLN A 261    2.372 A^2
ATOM   2240  OH  TYR A 295    0.069 A^2
ATOM   2356  O1  BGC A 310    1.045 A^2

...and then in Chimera I could 

open 2gbp
surf :16 at ce1:91 at o,nd2:93 at n,cb,oe2:107 at c32,oh:109 at ca:110 at n,o,og1,cg2:112 at og:152 at ce1:153 at cb,cd:154 at n,cg,od1,od2:256 at od1,nd2:261 at oe1:195 at oh:310 at o1

...where the surf command is all one line although the mail program may break it up.  (Or you could have multiple surf commands for subsets of those atoms.)

I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

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