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@cgl.ucsf.edu> wrote:
On Jan 2, 2021, at 10:42 PM, Jacqueline Vitali <jackie.vitali@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@ce1:91@o,nd2:93@n,cb,oe2:107@c32,oh:109@ca:110@n,o,og1,cg2:112@og :152@ce1:153@cb,cd:154@n,cg,od1,od2:256@od1,nd2:261@oe1:195@oh:310@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