Hi everyone, I wanted to know if custom "chimera command line" commands / macros can be created by a user? Is there any documentation available on that? Thanks, Thomas ---------------------------------- Thomas Hrabe (Ph.D.) Sanford-Burnham Medical Research Institute 10901 Torrey Pines Road 92037, La Jolla, CA, USA
Hi Thomas, Yes and yes. There are at least a couple ways... (a) the "alias" command: you can alias some short string to a longer string, which could be an atom specification, or an entire command with or without arguments, or even multiple commands joined together with semicolons. Aliases are saved in the preferences file, and all can be used in the command line. In addition, start-of-line aliases indicated with "hat" symbol ^ and that do not require arguments (see documentation) are put into a top-level Aliases menu. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/alias.html> (b) custom presets (Chimera 1.7 and newer): you can create Chimera command files and/or Python files to be treated as macros, and then specify their location to Chimera (menu Presets... Add Custom Presets). Although we are calling them presets, in principle you could put any commands in there. This mechanism doesn't allow for argument substitution but it would be reasonable to include generic atom specifications (e.g. "protein" "sel" etc.). Your custom presets can be accessed from the Presets menu and with the "preset" command. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/preferences.html#Presets> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/preset.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 Apr 8, 2013, at 6:14 PM, Thomas Hrabe wrote:
Hi everyone, I wanted to know if custom "chimera command line" commands / macros can be created by a user? Is there any documentation available on that? Thanks, Thomas
Hi Thomas, As a short addendum to Elaine's answer, if the things you want to do can't be performed as a series of currently-available commands then you would need to resort to implementing a command yourself in Python. This is described in the "Adding Command-Line Commands" example in the programmer's guide: http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Examples/index.html --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Apr 9, 2013, at 8:50 AM, Elaine Meng wrote:
Hi Thomas, Yes and yes. There are at least a couple ways...
(a) the "alias" command: you can alias some short string to a longer string, which could be an atom specification, or an entire command with or without arguments, or even multiple commands joined together with semicolons. Aliases are saved in the preferences file, and all can be used in the command line. In addition, start-of-line aliases indicated with "hat" symbol ^ and that do not require arguments (see documentation) are put into a top-level Aliases menu. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/alias.html>
(b) custom presets (Chimera 1.7 and newer): you can create Chimera command files and/or Python files to be treated as macros, and then specify their location to Chimera (menu Presets... Add Custom Presets). Although we are calling them presets, in principle you could put any commands in there. This mechanism doesn't allow for argument substitution but it would be reasonable to include generic atom specifications (e.g. "protein" "sel" etc.). Your custom presets can be accessed from the Presets menu and with the "preset" command. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/preferences.html#Presets> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/preset.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 Apr 8, 2013, at 6:14 PM, Thomas Hrabe wrote:
Hi everyone, I wanted to know if custom "chimera command line" commands / macros can be created by a user? Is there any documentation available on that? Thanks, Thomas
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Thanks, I guess the links will suffice for what I am looking for. Cheers, Thomas On Apr 9, 2013, at 11:13 AM, Eric Pettersen <pett@cgl.ucsf.edu<mailto:pett@cgl.ucsf.edu>> wrote: Hi Thomas, As a short addendum to Elaine's answer, if the things you want to do can't be performed as a series of currently-available commands then you would need to resort to implementing a command yourself in Python. This is described in the "Adding Command-Line Commands" example in the programmer's guide: http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Examples/index.html --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu<http://www.cgl.ucsf.edu/> On Apr 9, 2013, at 8:50 AM, Elaine Meng wrote: Hi Thomas, Yes and yes. There are at least a couple ways... (a) the "alias" command: you can alias some short string to a longer string, which could be an atom specification, or an entire command with or without arguments, or even multiple commands joined together with semicolons. Aliases are saved in the preferences file, and all can be used in the command line. In addition, start-of-line aliases indicated with "hat" symbol ^ and that do not require arguments (see documentation) are put into a top-level Aliases menu. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/alias.html> (b) custom presets (Chimera 1.7 and newer): you can create Chimera command files and/or Python files to be treated as macros, and then specify their location to Chimera (menu Presets... Add Custom Presets). Although we are calling them presets, in principle you could put any commands in there. This mechanism doesn't allow for argument substitution but it would be reasonable to include generic atom specifications (e.g. "protein" "sel" etc.). Your custom presets can be accessed from the Presets menu and with the "preset" command. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/preferences.html#Presets> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/preset.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 Apr 8, 2013, at 6:14 PM, Thomas Hrabe wrote: Hi everyone, I wanted to know if custom "chimera command line" commands / macros can be created by a user? Is there any documentation available on that? Thanks, Thomas _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu<mailto:Chimera-users@cgl.ucsf.edu> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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Elaine Meng -
Eric Pettersen -
Thomas Hrabe