Open model from pdb with designated model id?
Hi all, I would like to write an alias to load a pdb and the associated 2fo-fc and fo-fc maps with a single command (and adjust the contours and appearance of the maps and model). To do this, I need to be able to open the models with specific output ids, so I can issue commands to alter their appearance later in the alias. Looking at the documentation (http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/open.html <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/open.html>), it seems like this should be possible, but when I give an output model id it seems that chimera is ignoring it and still choosing the lowest available id. I have tried the following commands, “open 1bl8 100”, “open 1bl8 #100”, “open 1bl8 model-id:100” but they all either fail or load 1bl8 with model id 1. Am I missing something about the syntax here? Or is there another flag for the output model id? Cheers, Oliver.
Hi Oliver, The filename should be last, e.g.: open 100 1bl8 In the older commands that simply have arguments without keywords (e.g. just the model number instead of something like “model N”), the order of arguments is important… it would be difficult to tell which argment is which otherwise. Sorry, it could probably be explained more clearly now that we have many newer commands with a more keyword-dependent syntax. 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 Jul 31, 2015, at 1:43 PM, Oliver Clarke <olibclarke@gmail.com> wrote:
Hi all, I would like to write an alias to load a pdb and the associated 2fo-fc and fo-fc maps with a single command (and adjust the contours and appearance of the maps and model).
To do this, I need to be able to open the models with specific output ids, so I can issue commands to alter their appearance later in the alias.
Looking at the documentation (http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/open.html), it seems like this should be possible, but when I give an output model id it seems that chimera is ignoring it and still choosing the lowest available id.
I have tried the following commands, “open 1bl8 100”, “open 1bl8 #100”, “open 1bl8 model-id:100” but they all either fail or load 1bl8 with model id 1.
Am I missing something about the syntax here? Or is there another flag for the output model id?
Cheers, Oliver. _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Ah, got it, thanks Elaine! Using that I can write the following alias, which will load the pdb and associated maps from the EDS and make them look pretty: alias ^load_pdb_and_maps open 1000 $1; open 1001 edsID:$1; open 1002 edsdiffID:$1; cootmode #; map_sig #1001 1; diffmap_sig #1002 3; map_sphere 30; ca_and_sidechains_smooth #1000 (cootmode, map_sig, diffmap_sig etc are aliases which modify how the maps and models look). Cheers, Oliver.
On Jul 31, 2015, at 4:59 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Oliver, The filename should be last, e.g.:
open 100 1bl8
In the older commands that simply have arguments without keywords (e.g. just the model number instead of something like “model N”), the order of arguments is important… it would be difficult to tell which argment is which otherwise.
Sorry, it could probably be explained more clearly now that we have many newer commands with a more keyword-dependent syntax. 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 Jul 31, 2015, at 1:43 PM, Oliver Clarke <olibclarke@gmail.com> wrote:
Hi all, I would like to write an alias to load a pdb and the associated 2fo-fc and fo-fc maps with a single command (and adjust the contours and appearance of the maps and model).
To do this, I need to be able to open the models with specific output ids, so I can issue commands to alter their appearance later in the alias.
Looking at the documentation (http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/open.html), it seems like this should be possible, but when I give an output model id it seems that chimera is ignoring it and still choosing the lowest available id.
I have tried the following commands, “open 1bl8 100”, “open 1bl8 #100”, “open 1bl8 model-id:100” but they all either fail or load 1bl8 with model id 1.
Am I missing something about the syntax here? Or is there another flag for the output model id?
Cheers, Oliver. _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (2)
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Elaine Meng -
Oliver Clarke