It's not too hard to configure PDB2PQR and APBS in
Ubuntu or any other Linux distro:
For PDB2PQR:
Extract binaries from tarball, e.g. "tar xvzf pdb2pqr-1.4.0.tar.gz"
copy or move extracted directory to desired location, e.g. "mv
pdb2pqr-1.4.0 /usr/local/xtal"
Enter pdb2pqr directory, e.g. "cd /usr/local/xtal/pdb2pqr-1.4.0"
run configure command, e.g. "./configure" to create pdb2pqr.py
create alias in your run environment (can go in .tcshrc), "alias
pdb2pqr 'python /usr/local/xtal/pdb2pqr-1.4.0/pdb2pqr.py"
A plugin for APBS use is already installed in pymol, but if you want
the latest version, extract the tarball and copy the directory to the
desired location, e.g. /usr/local/xtal. Create a softlink in your
/usr/local/xtal directory, e.g. "ln -s apbs-1.1.0/bin/apbs". If
/usr/local/xtal is in your path, you can run apbs from the command
line. To have pymol use this apbs binary, change the path to binary in
the apbs plugin configuration dialog box. Alternatively, you could just
copy the apbs binary into the freemol/bin/ directory of pymol as
apbs.exe (I think).
Cheers, Roger Rowlett
On 4/15/2010 1:53 PM, Maia Cherney wrote:
Hi David,
I downloaded apbs and pdb2pqr, but I don't know how to install them on
my ubuntu 9.04. Is it possible to make an easy to install release?
For now, could you please send me the instruction.
Maia
David Hall wrote:
In my incentive build, freemol is present with the following readme:
This is a binary distribution of the FreeMOL Open-Source Compilation.
The FreeMOL project home page can be found at:
http://bioinformatics.org/freemol
Complete source code for building FreeMOL and its various components
can be browsed via:
http://www.bioinformatics.org/websvn/listing.php?repname=freemol
and fetched via:
svn co svn://bioinformatics.org/svnroot/freemol/trunk
Licensing information can be found in LICENSE.txt
If you have any questions about FreeMOL, please contact:
Warren L. DeLano, Ph.D.
DeLano Scientific LLC
war...@delsci.com
Thank You!
I don't have any instructions how to incorporate this into building from pymol trunk necessarily though. In the incentive builds, the freemol folder is not inside ext or modules or anything, but instead is a top level directory like those. You will have to build the sources of the things that come with it (apbs, mengine, mpeg_encode, pdb2pqr).
I think pymol autodetects the presence of freemol based on this grep output on the pymol source.
modules/pymol/__init__.py: # auto-detect bundled FREEMOL (if present)
modules/pymol/__init__.py: if not os.environ.has_key("FREEMOL"):
modules/pymol/__init__.py: test_path = os.path.join(os.environ['PYMOL_PATH'],"freemol")
modules/pymol/__init__.py: os.environ['FREEMOL'] = test_path
modules/pymol/__init__.py: # include FREEMOL's libpy in sys.path (if present)
modules/pymol/__init__.py: if os.environ.has_key("FREEMOL"):
modules/pymol/__init__.py: freemol_libpy = os.path.join(os.environ['FREEMOL'],"libpy")
modules/pymol/__init__.py: if os.path.isdir(freemol_libpy):
modules/pymol/__init__.py: if freemol_libpy not in sys.path:
modules/pymol/__init__.py: sys.path.append(freemol_libpy)
Hopefully this all helps.
-David
----- Original Message ----
From: Maia Cherney <ch...@ualberta.ca>
To: Jason Vertrees <jason.vertr...@schrodinger.com>
Cc: pymol-users@lists.sourceforge.net
Sent: Wed, January 20, 2010 9:37:46 PM
Subject: Re: [PyMOL] new ideas
Thanks,
But I could not find the download site for FreeMol.
Could somebody send me a link to FreeMol?
Maia
Jason Vertrees wrote:
Maia,
You can already move structures independently. If you install
PyMOL+FreeMOL you can have access to the MMFF-enabled PyMOL that will
allow you to do small molecule cleanup and editing.
Try putting your mouse into "Editing Mode" and moving atoms around.
It's not hard. Check this out:
http://pymolwiki.org/index.php/Molecular_Sculpting for some help.
Regards,
-- Jason
On Wed, Jan 20, 2010 at 11:52 AM, Maia Cherney wrote:
Hi Jason
I need such features. I open two different pdbs and I want to manually move
one structure relative to another. I want to dock one structure into another
or superpose 2 structures manually. Is it possible?
Or I want to move a fragment of the molecule relative to the rest of the
molecule.
Is it possible?
Maia
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