Dear All, We started to use Chimera since few time. I have, maybe, a very easy question. How we can visualise interactions pairs between the ligand and the receptor for which we computed blind docking. For the sake of clarity I attach a figure showing what we wish to get. Thank you. Francesco Pappalardo
Hi! You woule have to manually create pseudobonds and labels for that. There are automated tools like PLIP (Protein Ligand Interaction Profiler) for which we (InsiliChem) provide Chimera integrations in our Tangram Suite. Feel free to check it here (http://tangram-suite.readthedocs.io/en/latest/) and ask any further questions! Cheers, Jaime. El vie., 29 jun. 2018 20:31, Francesco Pappalardo < francesco.pappalardo@unict.it> escribió:
Dear All,
We started to use Chimera since few time. I have, maybe, a very easy question.
How we can visualise interactions pairs between the ligand and the receptor for which we computed blind docking.
For the sake of clarity I attach a figure showing what we wish to get.
Thank you.
Francesco Pappalardo
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Hi Francesco, It is just several very commonly used steps, but actually NOT easy to answer since there are so many different ways you could do it! There are also many artistic decisions like colors, outlines, etc. to make the figures look good. Since we have many tutorials to help people learn this stuff, it is just beyond the scope of this mailing list to explain it all here. Looking at the images, you want to show ribbons but hide most atoms except near to the ligand, and to show H-bonds with lines. I can give a brief outline of one possibility (below), but if you become more familiar with Chimera, it would help you decide which way is easiest for you. Each step could be done with the menus or with commands. See “getting started”: <http://www.rbvi.ucsf.edu/Outreach/Tutorials/GettingStarted.html> If you are using the ViewDock tool to look through the results, see this tutorial: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/vdtut.html> See this tutorial for looking at contacts and H-bonds between protein and ligand: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html> See hints for making nice figures, and several image tutorials: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/print.html#tips> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/frametut.html> In e-mail it is shorter to describe commands, but it may actually be easier for you to use the graphical interfaces. The following commands would be one approach (I’m pretending your ligand residue is named UNK and you want to show residues within 5 angstroms… could use model number and/or residue number instead of name, different distance, etc.): ~display ribbon display :unk z<5 preset apply pub 1 select :unk findhbond selRestrict cross reveal true color purple linewidth 3 ~select color sky blue :unk & C Commands like “findhbond” have several options, and they all have help pages: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/framecommand.html> … or use the FindHBond graphical interface, as described in the protein-ligand analysis tutorial linked above. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 29, 2018, at 3:48 AM, Francesco Pappalardo <francesco.pappalardo@unict.it> wrote:
Dear All, We started to use Chimera since few time. I have, maybe, a very easy question. How we can visualise interactions pairs between the ligand and the receptor for which we computed blind docking. For the sake of clarity I attach a figure showing what we wish to get. Thank you. Francesco Pappalardo
Dear Elaine, Thank you for your message. It helped a lot! Best, Francesco
On 29 Jun 2018, at 20:59, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Francesco, It is just several very commonly used steps, but actually NOT easy to answer since there are so many different ways you could do it! There are also many artistic decisions like colors, outlines, etc. to make the figures look good. Since we have many tutorials to help people learn this stuff, it is just beyond the scope of this mailing list to explain it all here.
Looking at the images, you want to show ribbons but hide most atoms except near to the ligand, and to show H-bonds with lines.
I can give a brief outline of one possibility (below), but if you become more familiar with Chimera, it would help you decide which way is easiest for you. Each step could be done with the menus or with commands.
See “getting started”: <http://www.rbvi.ucsf.edu/Outreach/Tutorials/GettingStarted.html>
If you are using the ViewDock tool to look through the results, see this tutorial: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/vdtut.html>
See this tutorial for looking at contacts and H-bonds between protein and ligand: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html>
See hints for making nice figures, and several image tutorials: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/print.html#tips> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/frametut.html>
In e-mail it is shorter to describe commands, but it may actually be easier for you to use the graphical interfaces. The following commands would be one approach (I’m pretending your ligand residue is named UNK and you want to show residues within 5 angstroms… could use model number and/or residue number instead of name, different distance, etc.):
~display ribbon display :unk z<5 preset apply pub 1 select :unk findhbond selRestrict cross reveal true color purple linewidth 3 ~select color sky blue :unk & C
Commands like “findhbond” have several options, and they all have help pages: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/framecommand.html> … or use the FindHBond graphical interface, as described in the protein-ligand analysis tutorial linked above.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 29, 2018, at 3:48 AM, Francesco Pappalardo <francesco.pappalardo@unict.it> wrote:
Dear All, We started to use Chimera since few time. I have, maybe, a very easy question. How we can visualise interactions pairs between the ligand and the receptor for which we computed blind docking. For the sake of clarity I attach a figure showing what we wish to get. Thank you. Francesco Pappalardo
participants (3)
-
Elaine Meng -
Francesco Pappalardo -
Jaime Rodríguez-Guerra