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")


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2012/10/1 James Starlight <jmsstarlight@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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