[PyMOL] symexp in scripts

[Cynthia F. <cn...@it...>]

Warren,

I am able to create symmetry-related molecules by typing the symexp 
command into the PyMol window interactively, but including the 
identical command in my script (see below) does not work.  This is 
frustrating, as I need to create H-bonds to the symmetry molecules, 
and now must type all of these commands in by hand (or as a later 
script, I suppose).

Am I doing something wrong?  Or is this a bug you're aware of?

Another question related to symexp:  Is there a pattern to how PyMol 
names the object created by symexp?  The object created by:

symexp S=mainA,(resi 202),5

is S05000000.  Can I predict this? (currently the only way I guessed 
this name is by typing the command into the PyMol window and reading 
the output)  Can I rename this object name to something more useful 
to me?

Thanks for all your work. This is a great program.  I'm excited to 
hear that a more thorough manual is on the way--I'm looking forward 
to learning more about what we can do with PyMol!

-Cynthia (David Agard's lab, UCSF :) )

Script I'm using:

#  LOAD PDB AND MAP
#load /Users/cynthia/Desktop/sgi_files/wtalp_19c_2fofc_sm.xplor, 2fofc
#load /Users/cynlap/Desktop/sgi_files/from_iMac/wtalp_19c_pymol.ent, main
load /Users/cynthia/Desktop/sgi_files/wtalp_19c_pymolA.ent, mainA
load /Users/cynthia/Desktop/sgi_files/wtalp_19c_pymolB.ent, mainB

# ALTER SETTINGS FOR PUBLICATION QUALITY
set mesh_radius = 0.008
set antialias = 1
set stick_radius = 0.1
bg_color white
set depth_cue=1
set ray_trace_fog=1
set spec_power = 200 #to increase glossyness, see faq
set spec_refl=1.5 #to increase glossyness, see faq
set dash_radius=0.05

hide all

#  CREATE GROUPS
create interest, (resi 36,143,202)
show sticks, interest
create oxyhole, (resi 140:144)
show sticks, oxyhole

symexp S=mainA,(resi 202),5     #create symmetry-related molecules
show sticks, S05000000

create water, (resn HOH)
show nb_spheres, water
#hide (not (resi 202 expand 8))	  #only atoms w/in 8A of 202
#hide (!(byres ((mainA///202) around 8))) #not working: symexp not recognized

#  DISTANCE LINES (H-BONDS)
distance one=(143/OG),(mainA///202/O1)
distance two=(mainB///143/OG),(resi 36 and name NE2)
distance three=(resi 202 and name O1),(resi 141 and name N)
distance four=(mainA///202/O4),(resi 140 and name NE)
distance five=(mainB///202/O3),(resi 140 and name NE)
distance six=(mainB///202/O4),(S05000000///89/NH1)

color grey, one
color grey, two
color grey, three
color grey, four
color grey, five
color grey, six

set dash_radius=0.03   #see maillist search dash for more edit options

#  DRAW MAP
#isomesh msh_2fofc, 2fofc, 2, interest, carve=1
#color cyan, msh_2fofc

#  SET UP FOR DISPLAY
set_view (\
     -0.085494332,   -0.754236877,    0.651016355,\
      0.352779120,    0.588155329,    0.727744758,\
     -0.931792915,    0.291883081,    0.215793610,\
      0.000000000,    0.000000000,  -39.378192902,\
     13.142999649,   30.863000870,   14.019000053,\
     35.878196716,   43.628189087,    0.000000000 )

symexp S=mainA,(resi 202),5     #symexp not recognized here, either
show sticks, S05000000

-- 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cynthia N. Fuhrmann
Department of Biochemistry & Biophysics			cn...@it...
University of California, San Francisco			(415) 502-2930
513 Parnassus Ave., Box 0448 				(415) 476-1902 (fax)
San Francisco, CA  94143-0448 		       http://www.msg.ucsf.edu/agard
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~