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Re: [PyMOL] APBS
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From: Todd M. L. <tod...@gm...> - 2007-05-29 19:45:00
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I also continually had this problem unless I got pqr coordinates =20 (with hydrogens) below is the instructions I wrote for myself and group so that I =20 would be able to do it again next time (getting old and the memory =20 isn't what it used to be) pqr corrdinates - Can do it on the web at http://pdb2pqr.sourceforge.net/ http://agave.wustl.edu/pdb2pqr/server.html I just used the defaults Under plugins go to APBS tools Choose use another PQR. (maybe if you select Use PDB2PQR it might do =20= this automatically without first going on line to do it?) default configuration Each time I=92ve always had to set the APBS binary location. The other =20= sections leave blank default Temporary File Locations To start APBS 1st select Set Grid, then do Run APBS =96 I don=92t know =20= why the buttons are placed in that order. Also, it seems you must =20 click on Run APBS twice before it launches. Run Top in unix window =20 to make sure it runs For Hfq, ~400 residues, APBS took about a minute. Go to Visualization and click on Update For most reasonable looking Molecular Surfaces I turn off Solvent =20 Accessible Surface and turn on Color by potential on sol. acc. surf. =20= Select Show. If you change the range you must also click on Update When I tried to do this with another loaded structure, it actually =20 looked like it mapped the first EPS onto the surface of the second =20 structure. Make sure to remove waters (and probably everyother non-protein =20 residue). EP on the left was done with waters in structure. Notice =20 red surface where ever water molecules appeare non-linear Bolzman Linear Bolzman On May 24, 2007, at 1:16 PM, Michael Lerner wrote: > Hi, > > Can you try installing the most recent version of my plugin from > http://www-personal.umich.edu/~mlerner/Pymol/index.html (you can use > the normal Install Plugin menu option .. there's no need to do things > by hand anymore)? It fixes some problems and gives better error > messages on others. > > Thanks, > > -Michael > > --=20 > Biophysics Graduate Student > Carlson Lab, University of Michigan > http://www.umich.edu/~mlerner > > > On 5/24/07, Oganesyan, Vaheh <Oga...@me...> wrote: >> >> >> >> >> I'll appreciate some help with APBS plugin. >> >> >> >> In both Win or Lin the same error appears: >> >> >> >> ObjectMapLoadDXFile-Error: Unable to open file! >> >> >> >> After googling with this error message I've checked all of the >> possibilities: >> >> Map file is loaded OK, folders with apbs.exe and psize.py files do =20= >> not >> contain blanks, >> >> the *.pqr file is created using pdb2pqr server with and without chain >> identifier. >> >> >> >> At this point I do not know what else to try. Before (about 1 year =20= >> ago) I've >> used it with no problems. >> >> Could someone point me to the problem? >> >> Windows version is 0_99rc6 installed using binaries. >> >> Thanks in advance. >> >> >> >> Vaheh Oganesyan >> >> >> ---------------------------------------------------------------------=20= >> ---- >> This SF.net email is sponsored by DB2 Express >> Download DB2 Express C - the FREE version of DB2 express and take >> control of your XML. No limits. Just data. Click to get it now. >> http://sourceforge.net/powerbar/db2/ >> _______________________________________________ >> PyMOL-users mailing list >> PyM...@li... >> https://lists.sourceforge.net/lists/listinfo/pymol-users >> >> > > ----------------------------------------------------------------------=20= > --- > This SF.net email is sponsored by DB2 Express > Download DB2 Express C - the FREE version of DB2 express and take > control of your XML. No limits. Just data. Click to get it now. > http://sourceforge.net/powerbar/db2/ > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users |