Re: [Chimera-users] Modification of COX Demo
Dear Elaine, Thank you very much for the quick reply I am really happy about the news. How should I refer ucsf chimera in my dissertation? Thanks, Noel
Dear Noel, You're welcome! How to cite Chimera can be viewed here: <http://www.cgl.ucsf.edu/chimera/docs/credits.html> (or the same shown using the Chimera menu: Help... Citation Info) Best wishes, Elaine On Feb 5, 2013, at 9:56 AM, Noel Pace wrote:
Dear Elaine, Thank you very much for the quick reply I am really happy about the news. How should I refer ucsf chimera in my dissertation? Thanks, Noel
Hi Elaine I am currently progressing in my DEMO however I require a command line to display Name of residue only and not name+specifier, i tried looking at lots of references and guides but cannot find it. currently using *"command: rlabel"* * * thanks, Noel
Hi Noel, You can use the "labelopt" command to customize residue labels. If the label is already shown, you would have to show it again to see the changes. Example: labelopt resinfo %(name)s rlabel :85.A Manual pages here, or you can use the help command, e.g. "help rlabel" .... the rlabel page mentions labelopt and links to its page: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rlabel.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/labelopt.html> Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Feb 6, 2013, at 4:16 PM, Noel Pace wrote:
Hi Elaine I am currently progressing in my DEMO however I require a command line to display Name of residue only and not name+specifier, i tried looking at lots of references and guides but cannot find it.
currently using "command: rlabel"
thanks, Noel
Dear Elaine, Thank you for your constant help...I am getting more proficient with the program language however I have encountered a difficulty and cannot resolve it using the manual. I require the command to run the UTILITY: *Structure diagram*, then make it load SMILES code: C1[C@H]2[C@@H]([C@@H](S1)CCCCC(=O)O)NC(=O)N2 How can I make this possible please? Thanks again, Noel
Hi Noel, Sorry, there is no command to show structure diagrams. If the demo must do this, the only possibility (that I know of) is to do it in a python script. In the demo, you can use the "open" command to open and execute the *.py file (the script, which would be one of your demo data files). For example, in the "Hormone-Receptor Complex Demo" that comes with Chimera, there is an "undo" command in panel 6 that opens a python script. The script simply closes the sequence alignment window. I don't know python, so someone else would need to help with the script itself. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Feb 12, 2013, at 5:02 PM, Noel Pace wrote:
Dear Elaine,
Thank you for your constant help...I am getting more proficient with the program language however I have encountered a difficulty and cannot resolve it using the manual.
I require the command to run the UTILITY: Structure diagram, then make it load SMILES code: C1[C@H]2[C@@H]([C@@H](S1)CCCCC(=O)O)NC(=O)N2
How can I make this possible please?
Thanks again, Noel
The Python would be: from chimera import dialogs from StructureDiagram.gui import StructureDiagramDialog dlg = dialogs.display(StructureDiagramDialog.name) dlg.updateImageFromSmiles("C1[C@H]2[C@@H]([C@@H](S1)CCCCC(=O)O)NC(=O)N2") Put the above in a file with a ".py" suffix and just follow the instructions Elaine gave. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Feb 13, 2013, at 10:14 AM, Elaine Meng wrote:
Hi Noel, Sorry, there is no command to show structure diagrams. If the demo must do this, the only possibility (that I know of) is to do it in a python script. In the demo, you can use the "open" command to open and execute the *.py file (the script, which would be one of your demo data files).
For example, in the "Hormone-Receptor Complex Demo" that comes with Chimera, there is an "undo" command in panel 6 that opens a python script. The script simply closes the sequence alignment window.
I don't know python, so someone else would need to help with the script itself.
Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 12, 2013, at 5:02 PM, Noel Pace wrote:
Dear Elaine,
Thank you for your constant help...I am getting more proficient with the program language however I have encountered a difficulty and cannot resolve it using the manual.
I require the command to run the UTILITY: Structure diagram, then make it load SMILES code: C1[C@H]2[C@@H]([C@@H](S1)CCCCC(=O)O)NC(=O)N2
How can I make this possible please?
Thanks again, Noel
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
THANKSS!!!! :) I am not proficient with programming language itself but i'm trying my best to.. thanks for all the help deeply appreciated. On 14 February 2013 23:20, Eric Pettersen <pett@cgl.ucsf.edu> wrote:
The Python would be:
from chimera import dialogs from StructureDiagram.gui import StructureDiagramDialog dlg = dialogs.display(StructureDiagramDialog.name) dlg.updateImageFromSmiles("C1[C@H]2[C@@H]([C@@H](S1)CCCCC(=O)O)NC(=O)N2")
Put the above in a file with a ".py" suffix and just follow the instructions Elaine gave.
--Eric
Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
On Feb 13, 2013, at 10:14 AM, Elaine Meng wrote:
Hi Noel, Sorry, there is no command to show structure diagrams. If the demo must do this, the only possibility (that I know of) is to do it in a python script. In the demo, you can use the "open" command to open and execute the *.py file (the script, which would be one of your demo data files).
For example, in the "Hormone-Receptor Complex Demo" that comes with Chimera, there is an "undo" command in panel 6 that opens a python script. The script simply closes the sequence alignment window.
I don't know python, so someone else would need to help with the script itself.
Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 12, 2013, at 5:02 PM, Noel Pace wrote:
Dear Elaine,
Thank you for your constant help...I am getting more proficient with the program language however I have encountered a difficulty and cannot resolve it using the manual.
I require the command to run the UTILITY: Structure diagram, then make it load SMILES code: C1[C@H]2[C@@H]([C@@H](S1)CCCCC(=O)O)NC(=O)N2
How can I make this possible please?
Thanks again,
Noel
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi again Elaine, I have a second question apart from the Utility enquiry. I would like to first superimpose different SDF files (e.g. 1.sdf, 2.sdf, 3.sdf) of the same molecule [*Biotin:* a small molecule and not a protein] and then show conformational changes from one SDF to the other. However the program is not letting me do this as the molecules do not contain nucleic or amino acids. How can I do this with commands? Thanks again, Noel
Hi Noel, It sounds like you were trying to use MatchMaker, which (as you said) is only for superimposing biopolymer chains. Instead you would need to use the "match" command, which lets you specify exactly which atoms to use in the fit. See discussion of the different ways to superimpose structures in Chimera: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/superposition.html> ...and specifically the "match" command: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Feb 12, 2013, at 6:22 PM, Noel Pace wrote:
Hi again Elaine,
I have a second question apart from the Utility enquiry.
I would like to first superimpose different SDF files (e.g. 1.sdf, 2.sdf, 3.sdf) of the same molecule [Biotin: a small molecule and not a protein] and then show conformational changes from one SDF to the other. However the program is not letting me do this as the molecules do not contain nucleic or amino acids.
How can I do this with commands?
Thanks again, Noel
participants (3)
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Elaine Meng -
Eric Pettersen -
Noel Pace