apbs - pymol

[ji...@ualberta.ca]

Anyone have this working with the educational version of Pymol? I assume so... but not sure where to go with this.. 

Using:

Win7 x64 OS

I have pymol edu - v1.3r1 

APBS 1.41

I have submitted a number of proteins to the pdb2pdk server - have all the outputs. 

Generated a single surface in pymol (using C:\APBS folder - and removed a space from the *.pqr output from server).   

When it did work - the surface created did not resemble the jmol version supplied by the server.

I am trying to compare a number of pdb files with mutations... not sure I trust the generated data in Pymol due to all the errors/defaults not found etc.

definitely not a fan of inputting the defaults everytime.. since the program says it 'cant find the file' even though it is looking at the default directory.. 

Per the doc pages: 

Saving default locations

Via environment variables

Set the environment variables APBS_BINARY_DIR, APBS_WEB_DIR, APBS_PSIZE_DIR, APBS_PDB2PQR_DIR, and/or TEMP, and things should work properly as long as you're using the most recent version of the plugin."

"APBS_BINARY_DIR, APBS_WEB_DIR, APBS_PSIZE_DIR, APBS_PDB2PQR_DIR, and/or TEMP

i tried setting these in the pymolrc file - no dice.

eg: 

set APBS_BINARY_DIR, c:\APBS\apbs.exe 

set APBS_PSIZE_DIR, c:\APBS\psize.py

set APBS_PDB2PQR_DIR, C:\APBS\pdb2pq\pdb2pqr.exe

set TEMP, c:\APBS\temp

added square brackets as a try... pymol does not know what these variables are (ie: get APBS_BINARY_DIR  returns "Error: unknown setting"

Any ideas? are there alternate methods that I can use?? (tried a delphi pkg - didn't work either). 

The temp "pymol-generated.dx" file is being deleted every time also - and then it says "cannot find  pymol-generated.dx does it exist?"  of course it does. grrr. isnt this supposed to be a temp file? just make a new one ffs.

Anyway - getting frustrated. 

Thanks for any and all advice,

Jason 

[David Hall]

These are not pymol variables and they are not set in pyloric

See http://itechtalk.com/thread3595.html for how to set environment variables on windows 7.

-David

On Dec 17, 2014, at 3:50 AM, ji...@ualberta.ca wrote:

Via environment variables

Set the environment variables APBS_BINARY_DIR, APBS_WEB_DIR, APBS_PSIZE_DIR, APBS_PDB2PQR_DIR, and/or TEMP, and things should work properly as long as you're using the most recent version of the plugin."

"APBS_BINARY_DIR, APBS_WEB_DIR, APBS_PSIZE_DIR, APBS_PDB2PQR_DIR, and/or TEMP

i tried setting these in the pymolrc file - no dice.

eg: 

set APBS_BINARY_DIR, c:\APBS\apbs.exe 

set APBS_PSIZE_DIR, c:\APBS\psize.py

set APBS_PDB2PQR_DIR, C:\APBS\pdb2pq\pdb2pqr.exe

set TEMP, c:\APBS\temp

added square brackets as a try... pymol does not know what these variables are (ie: get APBS_BINARY_DIR  returns "Error: unknown setting"

Any ideas? are there alternate methods that I can use?? (tried a delphi pkg - didn't work either). 

The temp "pymol-generated.dx" file is being deleted every time also - and then it says "cannot find  pymol-generated.dx does it exist?"  of course it does. grrr. isnt this supposed to be a temp file? just make a new one ffs.

Anyway - getting frustrated. 

Thanks for any and all advice,

Jason 

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[ji...@ualberta.ca]

Thanks David - I was able to define the variables based on the link here. 

Sorry for the lack of a response earlier. 

I was also able to fix a lot of issues by moving the files to c:\APBS\temp_folder

At least I was able to complete the calculations that way.

thanks again for your help.

Jason