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 cnf...@itsa.ucsf.edu
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
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
