[Chimera-users] betacavity web and chimera

[Jacqueline Vitali]

Hi Elaine,

Thank you very much.  The command works well for my purposes.

Sorry for not including an example.  I need only internal voids (packing
defects).  I use betacavity web because all the cavities are internal
without the jagged lines on the surface that castp gives.

The jsmol is fine when I use coil for illustrating the protein but one
cannot superimpose cavities and structures there.

Thank you very much again.

Jackie

On Sun, Jan 3, 2021 at 12:47 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:

>
> 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
> VOID-DEFINING-ATOMS     27
> 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
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>
>
>
>
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