Public bug reported:
The current pymol 1.8.4.0+dfsg-1build1 packaging fails to set the
APBS_PSIZE_LOCATION and APBS_PDB2PQR_LOCATION variables in
modules/pmg_tk/startup/apbs_tools.py which breaks the ability to perform
electrostatic surface calculations in the APBS Tools 2.1 plugin. The fix
is to apply the trivial patch...
diff -uNr a/modules/pmg_tk/startup/apbs_tools.py
b/modules/pmg_tk/startup/apbs_tools.py
--- a/modules/pmg_tk/startup/apbs_tools.py 2018-04-01 11:54:24.156233715
-0400
+++ b/modules/pmg_tk/startup/apbs_tools.py 2018-04-01 12:00:35.510665069
-0400
@@ -167,8 +167,8 @@
#
APBS_BINARY_LOCATION = None # corresponding environment variable:
APBS_BINARY_DIR
APBS_WEB_LOCATION = None # corresponding environment variable: APBS_WEB_DIR
-APBS_PSIZE_LOCATION = None # corresponding environment variable: APBS_PSIZE_DIR
-APBS_PDB2PQR_LOCATION = None # corresponding environment variable:
APBS_PDB2PQR_DIR
+APBS_PSIZE_LOCATION = '/usr/share/pdb2pqr/src/' # corresponding environment
variable: APBS_PSIZE_DIR
+APBS_PDB2PQR_LOCATION = '/usr/share/pdb2pqr/' # corresponding environment
variable: APBS_PDB2PQR_DIR
TEMPORARY_FILE_DIR = tempfile.gettempdir() # corresponding environment
variable: TEMP
apbs_plea = ("IMPORTANT REQUEST: If you have not already done so, please
register\n"
Note that with pymol, apbs and pdb2pqr installed the APBS Tools 2.1
plugin functionality can be tested with the steps
1) Enter the following in the Pymol command line window
Download: examples/apbsplugin_1.pml
This code has been put under version control in the project Pymol-script-repo
reinitialize
fetch 3IG7, async=0
#load 3ig7.pdb, 3IG7
create cdk2, 3IG7 and polymer
create EFP, 3IG7 and organic and not resn ACE
delete 3IG7
hide everything, all
#h_add cdk2
#h_add EFP
show_as cartoon, cdk2
show_as sticks, EFP
util.cbay EFP
select flexible, byres cdk2 within 3.5 of EFP
show sticks, flexible
util.cbag flexible
disable flexible
zoom cdk2
2) Open the "APBS Tool2.1..." plugin.
3) Click in "Selection to use", and write "cdk2".
4) Click "Set grid"
5) To the left in "Molecular Surface", click "Show".
Currently the location of the required psize.py and pdb2pqr.py scripts
can't be found.
** Affects: pymol (Ubuntu)
Importance: Undecided
Status: New
** Tags: patch
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https://bugs.launchpad.net/bugs/1760449
Title:
pymol can't find ubuntu pdb2pqr files
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