[Chimera-users] betacavity web and chimera
jackie.vitali at gmail.com
Sun Jan 3 14:54:15 PST 2021
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.
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>
> > 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 C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
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