Finding interacting residues between receptor and ligand
Hi Elaine, I used the HPEPDOCK server (http:// huanglab.phys.hust.edu.cn/hpepdock /) to dock a ligand onto a receptor and downloaded the conformation (pose) of the ligand with lowest energy. Next I opened the receptor and ligand structure in UCSF chimera. The ligand fitted perfectly in the binding site. Now is it possible to know which residues of the ligand are interacting with the receptor and what is the type of non-covalent interaction between them? Thanks in advance, Prathvi
Hi Prathvi, If you are using the ViewDock tool, see this tutorial. <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/vdtut.html> If you aren't using ViewDock, instead you can take a look at the "Structure Analysis and Comparison Tutorial" for examples of using some relevant tools: Distance measurements, H-Bonds, Contacts, etc. <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html> You might consider switching to using our newer program ChimeraX instead of Chimera. It has features that Chimera does not, and in my opinion, it is easier to use. We are not developing Chimera any more. See the ChimeraX tutorial: Protein-Ligand Binding Sites <https://www.rbvi.ucsf.edu/chimerax/docs/user/tutorials/binding-sites.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 29, 2023, at 11:48 PM, Prathvi Singh via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi Elaine,
I used the HPEPDOCK server (http:// huanglab.phys.hust.edu.cn/hpepdock /) to dock a ligand onto a receptor and downloaded the conformation (pose) of the ligand with lowest energy.
Next I opened the receptor and ligand structure in UCSF chimera. The ligand fitted perfectly in the binding site.
Now is it possible to know which residues of the ligand are interacting with the receptor and what is the type of non-covalent interaction between them?
Thanks in advance, Prathvi
Dear Chimera, I want to extract a submap around some parts of an atomic model that is aligned to the main map. For this I am using the volume region command, but I am running into a problem converting the atomic coordinates to voxel coordinates when the pixel size of the map is different from 1 and the map origin is not at 0,0,0. What would be the right formula to go from one set the coordinates to the other and be able to get a submap in the right place? i.e. If a sub-volume were to be extracted at coordinates x1,y1,z1 and x2,y2,z2 of the atomic model what would be the volume coordinates to use in the command volume #mainmap region VX1, VY1, VZ1, VX2, VY2, VZ2 assuming the map voxel size is Mapvsize and the map orig Orig is at cx,cy,cz. To go from one set of coordinates to the other I have tried: MapCoord = (ModelCoord - Orig) / Mapvsize and MapCoord = (ModelCoord /Mapvsize) - Orig None seems to extract the volume at the right place. The first one seems closer (??) Thanks Hernando
Hi Hernando, This isn't my area of expertise, but did you really need a rectangular region of the map? I was thinking that if you are basing this on some atom or set of atoms, it may be easier to use "vop zone" to get all parts of the map within some distance cutoff of those atom(s). <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#zone> Or if a cubic region centered on a specific atom or marker would be OK, see "vop boxes" <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#boxes> If you must use the rectangular "region" my guess is that it should be your first equation, but it may not come out exactly because the map is gridded rather than continuous. Also note that the Volume Viewer dialog does not report the coordinates of the origin. Instead it reports the grid indices of the XYZ origin (0,0,0 coordinate). So you have to do more math to figure out the actual coordinates of the grid origin. If you are considering switching to ChimeraX, note that ChimeraX also has the same "vop" capabilities as mentioned above for Chimera, except as the ChimeraX commands "volume zone" and "volume boxes": <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#vop> ... and ChimeraX will actually tell you the coordinates of the grid origin as well as the map indices of the XYZ origin (0,0,0), if you use ChimeraX command "volume settings" 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 2, 2024, at 1:47 PM, Hernando J Sosa via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Dear Chimera,
I want to extract a submap around some parts of an atomic model that is aligned to the main map. For this I am using the volume region command, but I am running into a problem converting the atomic coordinates to voxel coordinates when the pixel size of the map is different from 1 and the map origin is not at 0,0,0.
What would be the right formula to go from one set the coordinates to the other and be able to get a submap in the right place?
i.e. If a sub-volume were to be extracted at coordinates x1,y1,z1 and x2,y2,z2 of the atomic model
what would be the volume coordinates to use in the command
volume #mainmap region VX1, VY1, VZ1, VX2, VY2, VZ2 assuming the map voxel size is Mapvsize and the map orig Orig is at cx,cy,cz.
To go from one set of coordinates to the other I have tried:
MapCoord = (ModelCoord - Orig) / Mapvsize
and
MapCoord = (ModelCoord /Mapvsize) - Orig
None seems to extract the volume at the right place. The first one seems closer (??)
Thanks
Hernando
More information about how to transform coordinates or find volume boxes around atoms in ChimeraX can be found on the ChimeraX mailing list https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/... Tom
On Jan 2, 2024, at 2:08 PM, Elaine Meng via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi Hernando, This isn't my area of expertise, but did you really need a rectangular region of the map?
I was thinking that if you are basing this on some atom or set of atoms, it may be easier to use "vop zone" to get all parts of the map within some distance cutoff of those atom(s). <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#zone>
Or if a cubic region centered on a specific atom or marker would be OK, see "vop boxes" <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#boxes>
If you must use the rectangular "region" my guess is that it should be your first equation, but it may not come out exactly because the map is gridded rather than continuous. Also note that the Volume Viewer dialog does not report the coordinates of the origin. Instead it reports the grid indices of the XYZ origin (0,0,0 coordinate). So you have to do more math to figure out the actual coordinates of the grid origin.
If you are considering switching to ChimeraX, note that ChimeraX also has the same "vop" capabilities as mentioned above for Chimera, except as the ChimeraX commands "volume zone" and "volume boxes": <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#vop>
... and ChimeraX will actually tell you the coordinates of the grid origin as well as the map indices of the XYZ origin (0,0,0), if you use ChimeraX command "volume settings"
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 2, 2024, at 1:47 PM, Hernando J Sosa via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Dear Chimera,
I want to extract a submap around some parts of an atomic model that is aligned to the main map. For this I am using the volume region command, but I am running into a problem converting the atomic coordinates to voxel coordinates when the pixel size of the map is different from 1 and the map origin is not at 0,0,0.
What would be the right formula to go from one set the coordinates to the other and be able to get a submap in the right place?
i.e. If a sub-volume were to be extracted at coordinates x1,y1,z1 and x2,y2,z2 of the atomic model
what would be the volume coordinates to use in the command
volume #mainmap region VX1, VY1, VZ1, VX2, VY2, VZ2 assuming the map voxel size is Mapvsize and the map orig Orig is at cx,cy,cz.
To go from one set of coordinates to the other I have tried:
MapCoord = (ModelCoord - Orig) / Mapvsize
and
MapCoord = (ModelCoord /Mapvsize) - Orig
None seems to extract the volume at the right place. The first one seems closer (??)
Thanks
Hernando
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participants (4)
-
Elaine Meng -
Hernando J Sosa -
Prathvi Singh -
Tom Goddard