[PyMOL] Pymol and APBS

2010-07-20 Thread RaDaniel Christian 성준
Edited the subject. Thanks!

On Tue, Jul 20, 2010 at 6:15 PM, RaDaniel Christian 성준
renderea...@gmail.com wrote:
 I want to bring to your attention the wiki entry I posted in pymolwiki
 regarding the default loading paths for apbs:
 After installing with fink, none of the default paths work.

 http://pymolwiki.org/index.php/Talk:APBS#Making_the_default_paths_to_work.3F

 If someone knows what is going on, please drop a line!
 Many thanks in advance,
 Daniel Ra

 -- Forwarded message --
 From: RaDaniel Christian 성준 renderea...@gmail.com
 Date: Mon, Jun 7, 2010 at 7:07 PM
 Subject: Help setting apbs tools2 on Mac
 To: supp...@delsci.com


 Can I get help with setting configuration files on pymol (cvs fink
 version1.2r3pre)?

 I modified the apbsplugin.py to have the following default locations
 (taken from 
 http://www.poissonboltzmann.org/apbs/examples/visualization/apbs-electrostatics-in-pymol#TOC-Visualization-through-the-new-APBS-
  OR  
 http://pymolapbsplugin.svn.sourceforge.net/viewvc/pymolapbsplugin/trunk/src/apbsplugin.py)
 :

 APBS_BINARY_LOCATION = '/sw64/bin/apbs-mpi-openmpi'
 APBS_PSIZE_LOCATION = '/sw64/share/apbs-mpi-openmpi/tools/manip/psize.py'
 APBS_PDB2PQR_LOCATION = '/sw64/bin/pdb2pqr'
 TEMPORARY_FILE_DIR = '/apbstemp'
 but after installing by running xpymol as root, I still get this error:

 Search dirs ['/sw64/lib/pymol-py26/ext/bin',
 '/sw64/lib/pymol-py26/freemol/bin',
 '/sw64/lib/pymol-py26/freemol/share/apbs',
 '/sw64/lib/pymol-py26/freemol/share/pdb2pqr',
 '/sw64/bin/apbs-mpi-openmpi',
 '/sw64/share/apbs-mpi-openmpi/tools/manip/psize.py',
 '/sw64/bin/pdb2pqr', '/sw/share/pdb2pqr',
 '/usr/local/phenix-dev-403/build/mac-intel-osx/bin', '/sw64/bin',
 '/sw64/sbin', '/usr/bin', '/bin', '/usr/sbin', '/sbin',
 '/usr/local/bin', '/usr/X11/bin', '/usr/libexec', '/Developer/Tools',
 '/usr/X11R6/bin', '/sw64/share/xtal/ccp4-6.1.3/etc',
 '/sw64/share/xtal/ccp4-6.1.3/bin',
 '/sw64/share/xtal/ccp4-6.1.3/ccp4i/bin',
 '/sw64/share/xtal/ccp4-6.1.3/share/dbccp4i/bin',
 '/sw64/share/xtal/ccp4-6.1.3/share/XIAROOT/xia2/Applications',
 '/usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test',
 '/usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test/Compiled/mac_386',
 '/usr/local/xia2-0.3.1.6/xia2-0.3.1.6/Applications', '/usr/local/bin',
 '/opt/local/bin', '/sw/bin']
 get_default_location will search the following:
 ['/sw64/lib/pymol-py26/ext/bin', '/sw64/lib/pymol-py26/freemol/bin',
 '/sw64/lib/pymol-py26/freemol/share/apbs',
 '/sw64/lib/pymol-py26/freemol/share/pdb2pqr',
 '/sw64/bin/apbs-mpi-openmpi',
 '/sw64/share/apbs-mpi-openmpi/tools/manip/psize.py',
 '/sw64/bin/pdb2pqr', '/sw/share/pdb2pqr',
 '/usr/local/phenix-dev-403/build/mac-intel-osx/bin', '/sw64/bin',
 '/sw64/sbin', '/usr/bin', '/bin', '/usr/sbin', '/sbin',
 '/usr/local/bin', '/usr/X11/bin', '/usr/libexec', '/Developer/Tools',
 '/usr/X11R6/bin', '/sw64/share/xtal/ccp4-6.1.3/etc',
 '/sw64/share/xtal/ccp4-6.1.3/bin',
 '/sw64/share/xtal/ccp4-6.1.3/ccp4i/bin',
 '/sw64/share/xtal/ccp4-6.1.3/share/dbccp4i/bin',
 '/sw64/share/xtal/ccp4-6.1.3/share/XIAROOT/xia2/Applications',
 '/usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test',
 '/usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test/Compiled/mac_386',
 '/usr/local/xia2-0.3.1.6/xia2-0.3.1.6/Applications', '/usr/local/bin',
 '/opt/local/bin', '/sw/bin']
 trying /sw64/lib/pymol-py26/ext/bin/psize.py
 trying /sw64/lib/pymol-py26/ext/bin/psize
 trying /sw64/lib/pymol-py26/freemol/bin/psize.py
 trying /sw64/lib/pymol-py26/freemol/bin/psize
 trying /sw64/lib/pymol-py26/freemol/share/apbs/psize.py
 trying /sw64/lib/pymol-py26/freemol/share/apbs/psize
 trying /sw64/lib/pymol-py26/freemol/share/pdb2pqr/psize.py
 trying /sw64/lib/pymol-py26/freemol/share/pdb2pqr/psize
 trying /sw64/bin/apbs-mpi-openmpi/psize.py
 trying /sw64/bin/apbs-mpi-openmpi/psize
 trying /sw64/share/apbs-mpi-openmpi/tools/manip/psize.py/psize.py
 trying /sw64/share/apbs-mpi-openmpi/tools/manip/psize.py/psize
 trying /sw64/bin/pdb2pqr/psize.py
 trying /sw64/bin/pdb2pqr/psize
 trying /sw/share/pdb2pqr/psize.py
 trying /sw/share/pdb2pqr/psize
 trying /usr/local/phenix-dev-403/build/mac-intel-osx/bin/psize.py
 trying /usr/local/phenix-dev-403/build/mac-intel-osx/bin/psize
 trying /sw64/bin/psize.py
 trying /sw64/bin/psize
 trying /sw64/sbin/psize.py
 trying /sw64/sbin/psize
 trying /usr/bin/psize.py
 trying /usr/bin/psize
 trying /bin/psize.py
 trying /bin/psize
 trying /usr/sbin/psize.py
 trying /usr/sbin/psize
 trying /sbin/psize.py
 trying /sbin/psize
 trying /usr/local/bin/psize.py
 trying /usr/local/bin/psize
 trying /usr/X11/bin/psize.py
 trying /usr/X11/bin/psize
 trying /usr/libexec/psize.py
 trying /usr/libexec/psize
 trying /Developer/Tools/psize.py
 trying /Developer/Tools/psize
 trying /usr/X11R6/bin/psize.py
 trying /usr/X11R6/bin/psize
 trying /sw64/share/xtal/ccp4-6.1.3/etc/psize.py
 trying /sw64/share/xtal/ccp4-6.1.3/etc/psize
 trying /sw64/share/xtal/ccp4-6.1.3/bin/psize.py
 trying /sw64/share/xtal/ccp4-6.1.3/bin/psize
 trying /sw64

[PyMOL] Pymol and APBS

2010-04-15 Thread J. Fleming
Hi all,

  I've been trying to get APBS Tools and/or APBSTools2 running for a
few weeks now on multiple linux systems (RedHat and Fedora).  I've
Installed MALOC and APBS Tools.  I can start up Pymol through Phenix,
load a .pqr generated from a PDB2PQR server, start APBS Tools, set the
grid, but when I click on Run APBS I get: ObjectMapLoadDXFile-Error:
Unable to open file!

  If I use the pymol generated PQR option with my .pqr even though
it is a PDB2PQR server generated file APBS runs and states X atoms
did not have properties assigned and to either remove or fix the
atoms.  How can I fix them?  The problem residues are just regular
amino acids; no split confrimations etc.  I've also tried editing out
the PDBs chain name before converting to the PDB to PQR but that
didn't work.

Another things I've tried is using APBSTools 2 but it errors as soon
as I click set grid with: Error: 2 ... Attribute Error: elec_radius.

I really need to get this to work but I have no clue what to try next.

Thanks in advance for any thoughts.
-Jon

--
Download Intel#174; Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev
___
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Re: [PyMOL] Pymol and APBS

2010-04-15 Thread Shiven Shandilya
Hi Jon,

Perhaps you could look at VASCo  http://genome.tugraz.at/VASCo/

I have found it to work extremely well on Windows and Linux platforms.
You not only get electrostatics but also hydrophobic surface coloring, and
all without the APBS and Python hassles and headaches.

Sorry to be knocking down APBS+PyMOL integration like this, but IMHO VASCo
does a stellar job as far as integrating outside programs with PyMOL goes.

Good luck!

Best,
Shiven


On Thu, Apr 15, 2010 at 12:01 AM, J. Fleming moloch...@gmail.com wrote:

 Hi all,

  I've been trying to get APBS Tools and/or APBSTools2 running for a
 few weeks now on multiple linux systems (RedHat and Fedora).  I've
 Installed MALOC and APBS Tools.  I can start up Pymol through Phenix,
 load a .pqr generated from a PDB2PQR server, start APBS Tools, set the
 grid, but when I click on Run APBS I get: ObjectMapLoadDXFile-Error:
 Unable to open file!

  If I use the pymol generated PQR option with my .pqr even though
 it is a PDB2PQR server generated file APBS runs and states X atoms
 did not have properties assigned and to either remove or fix the
 atoms.  How can I fix them?  The problem residues are just regular
 amino acids; no split confrimations etc.  I've also tried editing out
 the PDBs chain name before converting to the PDB to PQR but that
 didn't work.

 Another things I've tried is using APBSTools 2 but it errors as soon
 as I click set grid with: Error: 2 ... Attribute Error: elec_radius.

 I really need to get this to work but I have no clue what to try next.

 Thanks in advance for any thoughts.
 -Jon


 --
 Download Intel#174; Parallel Studio Eval
 Try the new software tools for yourself. Speed compiling, find bugs
 proactively, and fine-tune applications for parallel performance.
 See why Intel Parallel Studio got high marks during beta.
 http://p.sf.net/sfu/intel-sw-dev
 ___
 PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
 Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
 Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

--
Download Intel#174; Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

Re: [PyMOL] Pymol and APBS

2010-04-15 Thread Michael Lerner
Hi,

Which version of PyMOL, APBS and PDB2PQR are you using?

If you send me a PQR file off-list, I can take a closer look at what's going
on.

Thanks,

-Michael

On Thu, Apr 15, 2010 at 12:01 AM, J. Fleming moloch...@gmail.com wrote:

 Hi all,

  I've been trying to get APBS Tools and/or APBSTools2 running for a
 few weeks now on multiple linux systems (RedHat and Fedora).  I've
 Installed MALOC and APBS Tools.  I can start up Pymol through Phenix,
 load a .pqr generated from a PDB2PQR server, start APBS Tools, set the
 grid, but when I click on Run APBS I get: ObjectMapLoadDXFile-Error:
 Unable to open file!

  If I use the pymol generated PQR option with my .pqr even though
 it is a PDB2PQR server generated file APBS runs and states X atoms
 did not have properties assigned and to either remove or fix the
 atoms.  How can I fix them?  The problem residues are just regular
 amino acids; no split confrimations etc.  I've also tried editing out
 the PDBs chain name before converting to the PDB to PQR but that
 didn't work.

 Another things I've tried is using APBSTools 2 but it errors as soon
 as I click set grid with: Error: 2 ... Attribute Error: elec_radius.

 I really need to get this to work but I have no clue what to try next.

 Thanks in advance for any thoughts.
 -Jon


 --
 Download Intel#174; Parallel Studio Eval
 Try the new software tools for yourself. Speed compiling, find bugs
 proactively, and fine-tune applications for parallel performance.
 See why Intel Parallel Studio got high marks during beta.
 http://p.sf.net/sfu/intel-sw-dev
 ___
 PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
 Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
 Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net




-- 
Michael Lerner, Ph.D.
IRTA Postdoctoral Fellow
Laboratory of Computational Biology NIH/NHLBI
5635 Fishers Lane, Room T909, MSC 9314
Rockville, MD 20852 (UPS/FedEx/Reality)
Bethesda MD 20892-9314 (USPS)
--
Download Intel#174; Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

Re: [PyMOL] Pymol and APBS

2010-04-15 Thread Michael Lerner
On Thu, Apr 15, 2010 at 10:30 AM, Shiven Shandilya 
shiven.shandi...@gmail.com wrote:

 Sorry to be knocking down APBS+PyMOL integration like this, but IMHO VASCo
 does a stellar job as far as integrating outside programs with PyMOL goes.


I initially wrote the PyMOL/APBS plugin for my own use and I now
maintain/develop it as a community resource in my limited free time. Despite
this, several hundred users (at least) have found it quite helpful in their
research, and I've included many newer features based on their feedback. The
plugin is certainly not perfect, and I don't mind people knocking it down,
but I appreciate it when that knocking down comes with constructive
feedback.

Additionally, unlike VASCo, the PyMOL/APBS/PDB2PQR toolchain is provided as
completely free and open source suite of programs. For many reasons, I
believe that free and open source software is vital to to good science. I
would strongly urge users to consider such issues before settling on a suite
of software products, especially when you're already working with programs
like PyMOL and APBS.

Cheers,

-Michael



 Good luck!

 Best,
 Shiven



 On Thu, Apr 15, 2010 at 12:01 AM, J. Fleming moloch...@gmail.com wrote:

 Hi all,

  I've been trying to get APBS Tools and/or APBSTools2 running for a
 few weeks now on multiple linux systems (RedHat and Fedora).  I've
 Installed MALOC and APBS Tools.  I can start up Pymol through Phenix,
 load a .pqr generated from a PDB2PQR server, start APBS Tools, set the
 grid, but when I click on Run APBS I get: ObjectMapLoadDXFile-Error:
 Unable to open file!

  If I use the pymol generated PQR option with my .pqr even though
 it is a PDB2PQR server generated file APBS runs and states X atoms
 did not have properties assigned and to either remove or fix the
 atoms.  How can I fix them?  The problem residues are just regular
 amino acids; no split confrimations etc.  I've also tried editing out
 the PDBs chain name before converting to the PDB to PQR but that
 didn't work.

 Another things I've tried is using APBSTools 2 but it errors as soon
 as I click set grid with: Error: 2 ... Attribute Error: elec_radius.

 I really need to get this to work but I have no clue what to try next.

 Thanks in advance for any thoughts.
 -Jon


 --
 Download Intel#174; Parallel Studio Eval
 Try the new software tools for yourself. Speed compiling, find bugs
 proactively, and fine-tune applications for parallel performance.
 See why Intel Parallel Studio got high marks during beta.
 http://p.sf.net/sfu/intel-sw-dev
 ___
 PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
 Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
 Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net




 --
 Download Intel#174; Parallel Studio Eval
 Try the new software tools for yourself. Speed compiling, find bugs
 proactively, and fine-tune applications for parallel performance.
 See why Intel Parallel Studio got high marks during beta.
 http://p.sf.net/sfu/intel-sw-dev
 ___
 PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
 Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
 Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net




-- 
Michael Lerner, Ph.D.
IRTA Postdoctoral Fellow
Laboratory of Computational Biology NIH/NHLBI
5635 Fishers Lane, Room T909, MSC 9314
Rockville, MD 20852 (UPS/FedEx/Reality)
Bethesda MD 20892-9314 (USPS)
--
Download Intel#174; Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

Re: [PyMOL] Pymol and APBS

2010-04-15 Thread Shiven Shandilya
Dear Michael,

First, let me thank you for your time and effort in providing the community
with your contributions. I do sincerely appreciate your hard work and your
willingness to share it with us all. Without the contributions of users such
as yourself, PyMOL's stature and utility would be far less than what it is
now.

I have used the APBS plugin in the past, successfully and without problems.
And yes, it has been helpful in solving the problem(s) at hand.

As for the knocking down, it was more of a comparison with VASCo than a
direct criticism of your work. I am no expert at programming PyMOL/python
plugins but I have used quite a few over the years. All I speak is from my
own user experience when I say that some plugins work better than others.
VASCo, in my experience, happens to belong to the better category.


Now why the better plugins work the way do may depend on many factors but
some that I feel important are listed below (nothing specifically
for/against the APBS plugin).

I only speculate when I write the following, but in hopes that it may be
considered constructive feedback:

(1). Whenever possible, farm out the heavy lifting to external executables
(apbs, python scripts, black magic shamans etc.)...

(2). Clearly ask for all the defaults a user must specify at first run
(executable location, temporary directory, other knick-knacks your plugin
requires) Do not allow execution to begin unless you are reasonably sure
you have everything needed to properly finish the job.

(3). And, for heaven's sake, save those user-specified defaults for the rest
of posterity in a location (pymolrc, yourpluginrc) that your plugin can
always find... never, ever make a user specify such mundane things over and
over again... nothing kills the user experience quicker than that.

(4). Overwrite result files only if you have to... create a new directory
for every new run (and clearly display the location)...
Remember, (storage) space is cheap and (a user's) time is expensive, respect
that.

(5). If possible, give the users a clear indication of the status of the
back-end job doing the heavy lifting...

(6). Once you are done running the back-end job(s), prompt the user
immediately and (if agreed) automatically load the results.

(7). If your back-end job fails, parse the error in your plugin and inform
the user where in the entire process the error occurred, why it may have
occurred and what the user should do to prevent this error from occurring
again. If it is an error your plugin does not understand let the user know,
clearly and loudly.  If an error log file, hopefully text, was written,
specify its location (full path) in your error prompts. Prefrably, display
that error file in the system %editor% so that the user does not have to go
hunting for it.

...and I'll leave it at that...  ;-)

I welcome your feedback and views of other community members on this.

Thank you!

With best regards,
Shiven

P.S.  Apologies again if my criticism hit a personal note. Like everyone
else writing to the list and answering questions, my aim was to help a
fellow user get that job done.


---


On Thu, Apr 15, 2010 at 12:00 PM, Michael Lerner mgler...@gmail.com wrote:



 On Thu, Apr 15, 2010 at 10:30 AM, Shiven Shandilya 
 shiven.shandi...@gmail.com wrote:

 Sorry to be knocking down APBS+PyMOL integration like this, but IMHO VASCo
 does a stellar job as far as integrating outside programs with PyMOL goes.


 I initially wrote the PyMOL/APBS plugin for my own use and I now
 maintain/develop it as a community resource in my limited free time. Despite
 this, several hundred users (at least) have found it quite helpful in their
 research, and I've included many newer features based on their feedback. The
 plugin is certainly not perfect, and I don't mind people knocking it down,
 but I appreciate it when that knocking down comes with constructive
 feedback.

 Additionally, unlike VASCo, the PyMOL/APBS/PDB2PQR toolchain is provided as
 completely free and open source suite of programs. For many reasons, I
 believe that free and open source software is vital to to good science. I
 would strongly urge users to consider such issues before settling on a suite
 of software products, especially when you're already working with programs
 like PyMOL and APBS.

 Cheers,

 -Michael



 Good luck!

 Best,
 Shiven



 On Thu, Apr 15, 2010 at 12:01 AM, J. Fleming moloch...@gmail.com wrote:

 Hi all,

  I've been trying to get APBS Tools and/or APBSTools2 running for a
 few weeks now on multiple linux systems (RedHat and Fedora).  I've
 Installed MALOC and APBS Tools.  I can start up Pymol through Phenix,
 load a .pqr generated from a PDB2PQR server, start APBS Tools, set the
 grid, but when I click on Run APBS I get: ObjectMapLoadDXFile-Error:
 Unable to open file!

  If I use the pymol generated PQR option with my .pqr even though
 it is a PDB2PQR server generated file APBS runs and states X atoms
 did not have properties