[PyMOL] discrepancy between python and commandline script

[Pawel]

Hello,

I'm trying to understand what seems like an inconsistency between PyMOL 
commandline and python scripts. I have the following commandline script:


   delete all
   load ../4lzt_quasi.pdb, full
   cmd.create("anew", "full", 1, 1)
   cmd.alter_state(1,"anew" , "x,y,z = x+nm[(ID-1)*3],
   y+nm[(ID-1)*3+1], z+nm[(ID-1)*3+2]")
   iterate_state 1, full & id 1, print x, y,z
   iterate_state 1, anew & id 1, print x, y,z

Which I then run:

   PyMOL>@pymoltest1.txt
   ...
   PyMOL>iterate_state 1, full & id 1, print x, y,z
   2.6908474 4.5853815 13.698093
 IterateState: iterated over 1 atom coordinate states.
   PyMOL>iterate_state 1, anew & id 1, print x, y,z
   2.41267466545 5.63420581818 12.6615524292
 IterateState: iterated over 1 atom coordinate states.

Now I have this python script:

   cmd.delete( all)
   cmd.load( "../4lzt_quasi.pdb", "full")
   cmd.create("anew", "full", 1, 1)
   cmd.alter_state(1,"anew" , "x,y,z = x+nm[(ID-1)*3],
   y+nm[(ID-1)*3+1], z+nm[(ID-1)*3+2]")
   xyz1=[]
   cmd.iterate_state(1, 'full & id 1', 'xyz1.append([x,y,z])')
   xyz2=[]
   cmd.iterate_state(1, 'anew & id 1', 'xyz2.append([x,y,z])')
   print xyz1
   print xyz2

Which I run:

   PyMOL>run pymoltest1.py
   [[2.69084741211, 4.58538146973, 13.69809265137]]
   [[2.5646746158599854, 4.600205898284912, 13.6191040039]]

Why am I getting different coordinates for the second atom? The second 
set of coordinates from the first script are actually the coordinates of 
the 5th atom in my structure (CA of a LYS). I'm guessing that the 
alter_state command is somehow doing something different in one and the 
other case but it's hard to understand why.


Thanks for the help,
Pawel
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[PyMOL] Caver 3.01 with Pymol 1.6.0.0 on Windows 7

[Jed Goldstone]

I just upgraded to Pymol 1.6.0.0 on Windows 7, and Caver 3.01, which 
worked nicely on Pymol 1.5, has stopped working. I've appended the error 
message below. Has anyone else had problems with the Caver 3 plugin? Can 
anyone decipher the Tk callback? I know what the 'no such file' error is 
- there is no output generated.

Thanks,
Jed

java -Xmx500m -cp "C:/Program Files (x86)/Caver3/lib" -jar "C:/Program 
Files (x86)/Caver3/caver.jar" -home "C:/Program Files (x86)/Caver3" -pdb 
"C:/Users/Jed/modeling/caver/caver_output/6/inputs" -conf 
"C:/Users/Jed/modeling/caver/caver_output/6/inputs/config_2013-11-07-11-58.txt" 
-out "C:/Users/Jed/modeling/caver/caver_output/6"

Error: 1
 Exception in Tk callback
   Function: > 
(type: )
   Args: ()
Traceback (innermost last):
   File "C:\Program 
Files\PyMOL\PyMOL/modules\Pmw\Pmw_1_2\lib\PmwBase.py", line 1747, in 
__call__
 return apply(self.func, args)
   File "C:\Program 
Files\PyMOL\PyMOL/modules\pmg_tk\startup\Caver3_0_1.py", line 634, in 
details
 fc = self.loadFileContent("%s/warnings.txt" % (self.out_dir))
   File "C:\Program 
Files\PyMOL\PyMOL/modules\pmg_tk\startup\Caver3_0_1.py", line 638, in 
loadFileContent
 handler = open(file)
: [Errno 2] No such file or directory: 
'C:/Users/Jed/modeling/caver/caver_output/2/warnings.txt'

-- 

Jed Goldstone, PhD
Research Specialist
Woods Hole Oceanographic Institution
Redfield 3-52 MS#32
Woods Hole, MA 02543
http://www.whoi.edu/hpb/Site.do?id=481
Phone: 508-289-4823


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