pymol can't find ubuntu pdb2pqr files

Bug #1760449 reported by Jack Howarth
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pymol (Ubuntu)
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Bug Description

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.

Tags: patch
Revision history for this message
Jack Howarth (jwhowarth) wrote :

Patch to set APBS_PSIZE_LOCATION and APBS_PDB2PQR_LOCATION to the locations used in the ubuntu pdb2pqr package for psize.py and pdb2pqr.py scripts required by the APBS Tools 2.1 plugin.

Revision history for this message
Jack Howarth (jwhowarth) wrote :

To clarify, the steps to reproduce the functionality of the patched pymol, the correct steps are described for Example 1 at https://pymolwiki.org/index.php/Apbsplugin

Revision history for this message
Ubuntu Foundations Team Bug Bot (crichton) wrote :

The attachment "apbs_path_fix.diff" seems to be a patch. If it isn't, please remove the "patch" flag from the attachment, remove the "patch" tag, and if you are a member of the ~ubuntu-reviewers, unsubscribe the team.

[This is an automated message performed by a Launchpad user owned by ~brian-murray, for any issues please contact him.]

tags: added: patch
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