Hello pymol users,
I apologize if this posting is not appropriate for the pymol user list.
If there is a better place to direct these questions please let me know.
I have installed the vasco plugin into pymol on my mac by:
"python setup_vasco_x.py install" in the Vasco modules directory. I have
also installed the plugin into pymol.
"python VASCo.py -testrun
1. However instead of making a test_out directory it makes an input.ppix
to use on the next run.
2. When I add my pdb and run I get an error message. Here is the log file:
(Is this a problem with PDB format?)
Write ./CIN4sfA.pdb_atoms.csv file (for HydroCalc)
Write ./CIN4sfA.pdb_c2fmtx.csv file (for PatchCalc)
________________________________________________________________________________
Run MSMS...
-no_header
-probe_radius 1.4
-density 1
-all_components
Delete Inner MSMS Surface files...
MSMS Warnings: 0
ERROR: msms calculation error
MSMS surface calculating error, try to skip file and continue run.
CODE ;TIME SEC ;DATE ;RUN_ID;STATUS
;REASON;PROPERTIES ;CHAINS ;UNITS ;ATOMS
;SURFPNT ; PATCHPNT
CIN4sfA ;0.000 ;Wed Feb 23 20:57:24 2011 ;0 ;ERROR
;MSMS:ERROR: msms calculation error; ;1
;1 ;3152 ; ;
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Finish: time:16 sec
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Thank you for your help.
-Yarrow
--
Yarrow Madrona
Graduate Student
Molecular Biology and Biochemistry Dept.
University of California, Irvine
Natural Sciences I, Rm 2403
Irvine, CA 92697
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