Hi, Yarrow, It says MSMS calculation error.
*Possible reason* MSMS is a brilliant program for computing protein solvent excluded surfaces. It is a 3rd-party program (see http://mgltools.scripps.edu/downloads ) and its binary is included in VASCo. The version shipped with VASCo by default is for Linux (msms255i86Linux.5 and msms261x86_64Linux). Since you are using a mac (I suppose it is not running Linux), the binary MSMS will not execute successfully. *Possible solution* Solution 1. Try using VASCo on Linux (e.g. remove your mac OS X and install Linux on your mac :) Solution 2. replace the linux version of MSMS by the mac OsX version (again, see http://mgltools.scripps.edu/downloads). Then, you either have to look for where MSMS is invoked in the python source code of VASCo and replace all the names of the MSMS program, or, cheat VASCo by renaming the mac version of MSMS to the linux version MSMS (this is a easier way, but I do not have a mac at hand and can not tell you whether this trick will work). hope that helps, hongbo On 02/24/2011 05:18 PM, Yarrow Madrona wrote: > > 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 > > > > > -- Hongbo ZHU Postdoctoral Researcher Structural Bioinformatics Technische Universität Dresden Biotechnology Center Tatzberg 47/49 01307 Dresden, Germany Tel.: +49 (0) 351 463-40083 Fax: +49 (0) 351 463-40087 E-Mail: hongbo....@biotec.tu-dresden Webpage: www.biotec.tu-dresden.de ------------------------------------------------------------------------------ Free Software Download: Index, Search & Analyze Logs and other IT data in Real-Time with Splunk. Collect, index and harness all the fast moving IT data generated by your applications, servers and devices whether physical, virtual or in the cloud. Deliver compliance at lower cost and gain new business insights. http://p.sf.net/sfu/splunk-dev2dev _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
