pymol can't find ubuntu pdb2pqr files
Affects | Status | Importance | Assigned to | Milestone | |
---|---|---|---|---|---|
pymol (Ubuntu) |
New
|
Undecided
|
Unassigned |
Bug Description
The current pymol 1.8.4.0+
diff -uNr a/modules/
--- a/modules/
+++ b/modules/
@@ -167,8 +167,8 @@
#
APBS_BINARY_
APBS_WEB_LOCATION = None # corresponding environment variable: APBS_WEB_DIR
-APBS_PSIZE_
-APBS_PDB2PQR_
+APBS_PSIZE_
+APBS_PDB2PQR_
TEMPORARY_FILE_DIR = tempfile.
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/
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.
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.