Dear James.
Switch to use the python command syntax and string printing in input
arguments.
*reinitialize*
*cd C:\Users\tlinnet\Desktop*
*
*
*prot="1dwq"*
*
*
*#fetch 1dw1*
*cmd.fetch(prot,async=0)*
*
*
*select visible*
*#load 1dw1.map.ccp4*
*cmd.fetch(prot,async=0,type="2fofc")*
*
*
*#isomesh map, 1dw1.map, 3.0, sele, carve=1.6*
*cmd.isomesh("%s_map"%prot, "%s_2fofc"%prot, 3.0, "sele", carve=1.6)*
*
*
*#color br2, map*
*cmd.color("br2", "%s_map"%prot)*
*#cmd.color("yellow", "%s_map"%prot)*
*
*
*#set mesh_width, 0.5*
*print cmd.get_setting_text('mesh_width')*
*cmd.set("mesh_width", 0.5)*
*print cmd.get_setting_text('mesh_width')*
*
*
*#bg_color black*
*cmd.bg_color("white")*
*
*
*#set ray_trace_fog, 0*
*print cmd.get_setting_text('ray_trace_fog')*
*cmd.set("ray_trace_fog", 0)*
*print cmd.get_setting_text('ray_trace_fog')*
*
*
*#set depth_cue, 0*
*print cmd.get_setting_text('depth_cue')*
*cmd.set("depth_cue", 0)*
*print cmd.get_setting_text('depth_cue')*
*
*
*#set ray_shadows, off*
*print cmd.get_setting_text('ray_shadows')*
*cmd.set("ray_shadows", "off")*
*print cmd.get_setting_text('ray_shadows')*
*
*
*#ray 1280,1024*
*#cmd.ray(1280,1024)*
*
*
*#png 1dw1.png*
*#cmd.png("1dw1.png")*
Troels Emtekær Linnet
Ved kløvermarken 9, 1.th
2300 København S
Mobil: +45 60210234
2012/10/1 James Starlight <jmsstarli...@gmail.com>
> Dear PyMol users!
>
> I wounder to know how to define variables in pml scripts.
>
> E.g in below command sets for processing of ccp4 maps the PDB ID
> (1dw1) of the processed pdb file is mentioned several times. How I
> could define variable for that pdb id only once in the start of that
> simple script to allow me edit pdb id only once at that defined
> variable each time when I change pdb file ?
>
> fetch 1dw1
>
> select visible
> load 1dw1.map.ccp4
>
>
> isomesh map, 1dw1.map, 3.0, sele, carve=1.6
>
> color br2, map
> set mesh_width, 0.5
> bg_color black
> set ray_trace_fog, 0
> set depth_cue, 0
> set ray_shadows, off
> ray 1280,1024
> png 1dw1.png
>
>
> Thanks for help
>
> James
>
>
> ------------------------------------------------------------------------------
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------------------------------------------------------------------------------
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http://info.appdynamics.com/FreeJavaPerformanceDownload.html
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