Question about the tool Find Cavities
Hi, the tool Find Cavities returns as information about each detected cavity the number of points describing the what has been found. It is possible to obtain the coordinate of that points so to calculate the "center" of a found cavity of interest? Thanks. Saverio
Hi Saverio, The points are added as fake atoms, so you can get any/all of their coordinates in the same ways used for normal atoms, such as with: (a) "getcrd" command <https://rbvi.ucsf.edu/chimerax/docs/user/commands/getcrd.html> (b) saving to file, e.g. a PDB file <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#pdb> ... or you can compute their centroid directly with the "define centroid" command <https://rbvi.ucsf.edu/chimerax/docs/user/commands/define.html#centroid> For any of these commands/actions you could use the model number of the cavity, which you can see in the cavity list dialog or in the Models panel, or you could select specific points with the mouse (although I can imagine that might be difficult). Example: open 2gbp kvfinder define centroid #1.2.3 color yellow radius 1.0 .... which would report centroid coordinates in the Log I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 15, 2025, at 7:46 AM, saverio via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi, the tool Find Cavities returns as information about each detected cavity the number of points describing the what has been found. It is possible to obtain the coordinate of that points so to calculate the "center" of a found cavity of interest? Thanks. Saverio
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Hi Elaine, thanks for your solutions to my question. Saverio Il 15.01.2025 18:53 Elaine Meng ha scritto:
Hi Saverio, The points are added as fake atoms, so you can get any/all of their coordinates in the same ways used for normal atoms, such as with:
(a) "getcrd" command
(b) saving to file, e.g. a PDB file
... or you can compute their centroid directly with the "define centroid" command
For any of these commands/actions you could use the model number of the cavity, which you can see in the cavity list dialog or in the Models panel, or you could select specific points with the mouse (although I can imagine that might be difficult).
Example: open 2gbp
kvfinder
define centroid #1.2.3 color yellow radius 1.0
.... which would report centroid coordinates in the Log
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics
Department of Pharmaceutical Chemistry
University of California, San Francisco
On Jan 15, 2025, at 7:46 AM, saverio via ChimeraX-users wrote: Hi, the tool Find Cavities returns as information about each detected cavity the number of points describing the what has been found. It is possible to obtain the coordinate of that points so to calculate the "center" of a found cavity of interest? Thanks. Saverio _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu [2] To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu [3] Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ [4]
Hi Elaine, a follow-up question on this topic. When we click on a volume, there is an automatic re-centering on the volume with a narrowing of the view field and depth of view, which can be seen in the side view panel. Could you share the command lines that narrow the 2 side bars around the center of the view field? Thank you Vincent Le 15/01/2025 à 18:53, Elaine Meng via ChimeraX-users a écrit :
Hi Saverio, The points are added as fake atoms, so you can get any/all of their coordinates in the same ways used for normal atoms, such as with:
(a) "getcrd" command <https://rbvi.ucsf.edu/chimerax/docs/user/commands/getcrd.html>
(b) saving to file, e.g. a PDB file <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#pdb>
... or you can compute their centroid directly with the "define centroid" command <https://rbvi.ucsf.edu/chimerax/docs/user/commands/define.html#centroid>
For any of these commands/actions you could use the model number of the cavity, which you can see in the cavity list dialog or in the Models panel, or you could select specific points with the mouse (although I can imagine that might be difficult).
Example: open 2gbp kvfinder define centroid #1.2.3 color yellow radius 1.0
.... which would report centroid coordinates in the Log
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 15, 2025, at 7:46 AM, saverio via ChimeraX-users<chimerax-users@cgl.ucsf.edu> wrote:
Hi, the tool Find Cavities returns as information about each detected cavity the number of points describing the what has been found. It is possible to obtain the coordinate of that points so to calculate the "center" of a found cavity of interest? Thanks. Saverio
_______________________________________________ ChimeraX-users mailing list --chimerax-users@cgl.ucsf.edu To unsubscribe send an email tochimerax-users-leave@cgl.ucsf.edu Archives:https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
_______________________________________________ ChimeraX-users mailing list --chimerax-users@cgl.ucsf.edu To unsubscribe send an email tochimerax-users-leave@cgl.ucsf.edu Archives:https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
-- Vincent Chaptal, PhD Director of GdR APPICOM Drug Resistance and Membrane Proteins Lab MMSB -UMR5086 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.appicom.cnrs.fr http://mmsb.cnrs.fr/en/
Hi Vincent, I guess you mean when you choose a row in the cavities list and you have the option turned on "Focus view on cavity"? You can click anywhere in the row (not necessarily the Volume column) to choose that row. In the Side View, the two bars are the clipping planes. In that case, just look in the Log. The commands used are listed there. It will depend which options you have turned on. The commands that focus the view are (1) "view" specifying atoms within 3.5 Angstroms of that cavity model (the set of dots) (2) "zoom" with factor 0.75 I believe both of those move the clipping planes, although only zoom says something about it in the Log. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 15, 2025, at 11:43 PM, Vincent CHAPTAL <vincent.chaptal@cnrs.fr> wrote:
Hi Elaine,
a follow-up question on this topic. When we click on a volume, there is an automatic re-centering on the volume with a narrowing of the view field and depth of view, which can be seen in the side view panel. Could you share the command lines that narrow the 2 side bars around the center of the view field?
Thank you Vincent
Le 15/01/2025 à 18:53, Elaine Meng via ChimeraX-users a écrit :
Hi Saverio, The points are added as fake atoms, so you can get any/all of their coordinates in the same ways used for normal atoms, such as with:
(a) "getcrd" command <https://rbvi.ucsf.edu/chimerax/docs/user/commands/getcrd.html>
(b) saving to file, e.g. a PDB file <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#pdb>
... or you can compute their centroid directly with the "define centroid" command <https://rbvi.ucsf.edu/chimerax/docs/user/commands/define.html#centroid>
For any of these commands/actions you could use the model number of the cavity, which you can see in the cavity list dialog or in the Models panel, or you could select specific points with the mouse (although I can imagine that might be difficult).
Example: open 2gbp kvfinder define centroid #1.2.3 color yellow radius 1.0
.... which would report centroid coordinates in the Log
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 15, 2025, at 7:46 AM, saverio via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi, the tool Find Cavities returns as information about each detected cavity the number of points describing the what has been found. It is possible to obtain the coordinate of that points so to calculate the "center" of a found cavity of interest? Thanks. Saverio
participants (3)
-
Elaine Meng -
svle＠tiscali.it -
Vincent CHAPTAL