pymol-users Mailing List for PyMOL Molecular Graphics System

Hi all.

I am wondering if it is possible to fake mouse events in pymol. I would
like to be able to simulate a click/drag in a specific position of the
viewport. Thanks!

-- Camilo Jiménez

Hi,

I am using a cmd.iterate command to get the residue ids for selected
residues. I works fine for a single structure. But when I run the program
with a loop for more than one file, cmd.iterate command appends the ids to
previous ids... How can I get rid of this

-----
Bharat

by the way have someone had problems with the pdb2pqr usage with APBS in pymol?


I've tried to install pdb2pqr from source as well as via packages
then I've add usr/bin/pdb2pqr to the APBs plugin window

and when I've started APBS I obtained error like

Error: 5
<type 'exceptions.UnboundLocalError'> Exception in Tk callback
  Function: <function <lambda> at 0x333fcf8> (type: <type 'function'>)
  Args: ()
Traceback (innermost last):
  File "/usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwBase.py",
line 1747, in __call__
    return apply(self.func, args)
  File "/usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwDialog.py",
line 153, in <lambda>
    command=lambda self=self, name=name: self._doCommand(name))
  File "/usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwDialog.py",
line 132, in _doCommand
    return command(name)
  File "/usr/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py",
line 1036, in execute
    good = self.generatePqrFile()
  File "/usr/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py",
line 1007, in generatePqrFile
    good = self._generatePdb2pqrPqrFile()
  File "/usr/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py",
line 1615, in _generatePdb2pqrPqrFile
    if retval != 0:
<type 'exceptions.UnboundLocalError'>: local variable 'retval'
referenced before assignment

If I launch pdb2pqr from the terminal I've obtained

own@starlight ~/Desktop $ pdb2pqr
Usage: pdb2pqr.py [options] PDB_PATH PQR_OUTPUT_PATH

pdb2pqr.py: error: Incorrect number (0) of arguments!
argv: ['/usr/share/pdb2pqr/pdb2pqr.py'], args: []

should I provide some addition paths to the bash?
James

2013/3/27 James Starlight <jms...@gm...>:
> As I understood the APBs plugin which already exist in PyMol is the
> very efficient device for electrostatic potential calculations.
>
> 2 questions have been arisen:
>
>
> 1- How I could change cut-off distances for the electrostatic? E.g I'd
> like to consider only interactions within 5 A between any charged
> groups.
>
>
> 2- What advantages has the usage of pdb2pqr plugin? Also in the
> pdb2pqr tools options I've found some options for force fields. As I
> know Poisson-Boltzmann equation on which APBS is based doesnt need any
> force fields (charge calculation from ab initio principles). Why force
> fields used here ?
>
> 3- IS there other plugins for the electrostatic surface calculation
> with (1) possibility to change cut-offs and (2) charge assignment from
> the force fields or ab initio calculations ?
>
>
> Thanks for help,
> James
>
> 2013/3/27 Mike Marchywka <mar...@ho...>:
>>
>>
>>
>> I have a similar requirement, taking density and potential dstriutbutions from
>> jdftx which are written as plain binarry doubles. I use a script and
>> some code to create an xplor file which seems to work but I have
>> to adjust the position and scale to let it
>> overlay the ion positions that I read from an xyz file.
>>
>> AFAICT xplor is about the only easy format that pymol takes
>> but I was debating about trying to find others. i think
>> I dug through my older version of pymol, went to the
>> effort of changing it all to c++/extern c and then dropped it.
>> The xplor approch seems to work well enough for now.
>>
>>
>> Is there an easier way?
>> Thanks.
>>
>>
>> ----------------------------------------
>>> Date: Wed, 27 Mar 2013 13:41:24 +0400
>>> From: jms...@gm...
>>> To: pym...@li...
>>> Subject: [PyMOL] Electrostatic potential surface
>>>
>>> Dear PyMol users!
>>>
>>>
>>> I wounder to know about built-in PyMol option for electrostatic
>>> potential visualisation.
>>>
>>> For example I have pdb coordinates of my protein as well as its
>>> electrostatic potential distribution (calculated by another software).
>>> Using MolMol with both of that files I can visualize the electrostatic
>>> potential surface by means of "PaintSurface" option. Can I do the same
>>> with the PyMOl?
>>>
>>>
>>>
>>> Thanks for help,
>>>
>>>
>>> James
>>>
>>> ------------------------------------------------------------------------------
>>> Own the Future-Intel® Level Up Game Demo Contest 2013
>>> Rise to greatness in Intel's independent game demo contest.
>>> Compete for recognition, cash, and the chance to get your game
>>> on Steam. $5K grand prize plus 10 genre and skill prizes.
>>> Submit your demo by 6/6/13. http://p.sf.net/sfu/intel_levelupd2d
>>> _______________________________________________
>>> PyMOL-users mailing list (PyM...@li...)
>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>>> Archives: http://www.mail-archive.com/pym...@li...
>>

Hi Sabuj,

Do you have it working under linux?
>

Yes, I have demonstrated the same functionality on Ubuntu (12.10). Ubuntu
is the only Linux distro currently supported by Leap.

Cheers,

-- Jason

-- 
Jason Vertrees, PhD
Director of Core Modeling Products
Schrödinger, Inc.

(e) Jas...@sc...
(o) +1 (603) 374-7120

> Specifically, we'll have a demo version of PyMOL v1.6, PyMOL on the iPad,
> and even a sneak peek of Leap Motion (https://www.leapmotion.com/)
> controller integration with PyMOL.

Do you have it working under linux?

Greetings,

If you will be at the April ACS meeting in New Orleans, please feel free to
stop by the Schrödinger booth (#400). I will be there much of the time
answering questions, demoing new features, and generally discussing science
and visualization.

Specifically, we'll have a demo version of PyMOL v1.6, PyMOL on the iPad,
and even a sneak peek of Leap Motion (https://www.leapmotion.com/)
controller integration with PyMOL.

Cheers,

-- Jason

-- 
Jason Vertrees, PhD
Director of Core Modeling Products
Schrödinger, Inc.

(e) Jas...@sc...
(o) +1 (603) 374-7120

As I understood the APBs plugin which already exist in PyMol is the
very efficient device for electrostatic potential calculations.

2 questions have been arisen:


1- How I could change cut-off distances for the electrostatic? E.g I'd
like to consider only interactions within 5 A between any charged
groups.


2- What advantages has the usage of pdb2pqr plugin? Also in the
pdb2pqr tools options I've found some options for force fields. As I
know Poisson-Boltzmann equation on which APBS is based doesnt need any
force fields (charge calculation from ab initio principles). Why force
fields used here ?

3- IS there other plugins for the electrostatic surface calculation
with (1) possibility to change cut-offs and (2) charge assignment from
the force fields or ab initio calculations ?


Thanks for help,
James

2013/3/27 Mike Marchywka <mar...@ho...>:
>
>
>
> I have a similar requirement, taking density and potential dstriutbutions from
> jdftx which are written as plain binarry doubles. I use a script and
> some code to create an xplor file which seems to work but I have
> to adjust the position and scale to let it
> overlay the ion positions that I read from an xyz file.
>
> AFAICT xplor is about the only easy format that pymol takes
> but I was debating about trying to find others. i think
> I dug through my older version of pymol, went to the
> effort of changing it all to c++/extern c and then dropped it.
> The xplor approch seems to work well enough for now.
>
>
> Is there an easier way?
> Thanks.
>
>
> ----------------------------------------
>> Date: Wed, 27 Mar 2013 13:41:24 +0400
>> From: jms...@gm...
>> To: pym...@li...
>> Subject: [PyMOL] Electrostatic potential surface
>>
>> Dear PyMol users!
>>
>>
>> I wounder to know about built-in PyMol option for electrostatic
>> potential visualisation.
>>
>> For example I have pdb coordinates of my protein as well as its
>> electrostatic potential distribution (calculated by another software).
>> Using MolMol with both of that files I can visualize the electrostatic
>> potential surface by means of "PaintSurface" option. Can I do the same
>> with the PyMOl?
>>
>>
>>
>> Thanks for help,
>>
>>
>> James
>>
>> ------------------------------------------------------------------------------
>> Own the Future-Intel® Level Up Game Demo Contest 2013
>> Rise to greatness in Intel's independent game demo contest.
>> Compete for recognition, cash, and the chance to get your game
>> on Steam. $5K grand prize plus 10 genre and skill prizes.
>> Submit your demo by 6/6/13. http://p.sf.net/sfu/intel_levelupd2d
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
>

I have a similar requirement, taking density and potential dstriutbutions from 
jdftx which are written as plain binarry doubles. I use a script and
some code to create an xplor file which seems to work but I have
to adjust the position and scale to let it
overlay the ion positions that I read from an xyz file.

AFAICT xplor is about the only easy format that pymol takes
but I was debating about trying to find others. i think 
I dug through my older version of pymol, went to the
effort of changing it all to c++/extern c and then dropped it. 
The xplor approch seems to work well enough for now.


Is there an easier way?
Thanks.


----------------------------------------
> Date: Wed, 27 Mar 2013 13:41:24 +0400
> From: jms...@gm...
> To: pym...@li...
> Subject: [PyMOL] Electrostatic potential surface
>
> Dear PyMol users!
>
>
> I wounder to know about built-in PyMol option for electrostatic
> potential visualisation.
>
> For example I have pdb coordinates of my protein as well as its
> electrostatic potential distribution (calculated by another software).
> Using MolMol with both of that files I can visualize the electrostatic
> potential surface by means of "PaintSurface" option. Can I do the same
> with the PyMOl?
>
>
>
> Thanks for help,
>
>
> James
>
> ------------------------------------------------------------------------------
> Own the Future-Intel® Level Up Game Demo Contest 2013
> Rise to greatness in Intel's independent game demo contest.
> Compete for recognition, cash, and the chance to get your game
> on Steam. $5K grand prize plus 10 genre and skill prizes.
> Submit your demo by 6/6/13. http://p.sf.net/sfu/intel_levelupd2d
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
 		 	   		  

Dear PyMol users!


I wounder to know about built-in PyMol option for electrostatic
potential visualisation.

For example I have pdb coordinates of my protein as well as its
electrostatic potential distribution (calculated by another software).
Using MolMol with both of that files I can visualize the electrostatic
potential surface by means of "PaintSurface" option. Can I do the same
with the PyMOl?



Thanks for help,


James

Hi Matt,

use the "sort" command after adding atoms:

PyMOL> h_add 1ycr
PyMOL> sort

See also:
http://pymolwiki.org/index.php/Sort

Cheers,
  Thomas

Matthew Baumgartner wrote, On 03/26/13 13:59:
> Hi,
> When I fetch a new structure (1YCR, for example) then run 'h_add 1ycr' 
> the hydrogens are added to the structure as expected, but they are put 
> in the sequence viewer as their own residue with the same chain.
> 
> This is problematic for several reasons, one is that it breaks 
> selections, when I click on a heavy atom of a residue (in residue 
> selection mode) only the heavy atoms are selected and not the 
> hydrogens.  Also, if I save the structure to an pdb file, all of the 
> hydrogens for the whole structure are placed at the beginning or the end 
> of the structure, which makes them difficult to be interpreted by other 
> programs (babel, chimera, namd, etc).
> 
> I am using Pymol 1.5.0.1. (I will be updating to 1.6 soon).
> 
> Any suggestions for settings to change or a workaround (possibly 
> involving other programs, if necessary), would be greatly appreciated.
> 
> Thanks,
> Matt

-- 
Thomas Holder
PyMOL Developer
Schrödinger Contractor

Hi,
When I fetch a new structure (1YCR, for example) then run 'h_add 1ycr' 
the hydrogens are added to the structure as expected, but they are put 
in the sequence viewer as their own residue with the same chain.

This is problematic for several reasons, one is that it breaks 
selections, when I click on a heavy atom of a residue (in residue 
selection mode) only the heavy atoms are selected and not the 
hydrogens.  Also, if I save the structure to an pdb file, all of the 
hydrogens for the whole structure are placed at the beginning or the end 
of the structure, which makes them difficult to be interpreted by other 
programs (babel, chimera, namd, etc).

I am using Pymol 1.5.0.1. (I will be updating to 1.6 soon).

Any suggestions for settings to change or a workaround (possibly 
involving other programs, if necessary), would be greatly appreciated.

Thanks,
Matt

-- 

Hi Christoph,

thanks a lot for the patches.

Regarding your suggestion for pymol.bat: I guess this will not work if
you install with a custom prefix, since you make assumptions where to
find pythonw.exe and the pymol module.

I suggest to discuss this off-list, since it's quite specific.

Cheers,
  Thomas

Christoph Gohlke wrote, On 03/25/13 18:11:
> On 3/24/2013 3:02 AM, Thomas Holder wrote:
>> Dear PyMOL users,
>>
>> The pre-release version of PyMOL 1.6 has been pushed to the open
>> source repository on SourceForge. Besides several minor fixes and
>> improvements, this version should complete the transition to
>> shader-based rendering for all on-screen drawing. For non-integrated
>> chipsets this typically means higher quality and quicker rendering.
>>
>> Please also note that the URL of the SVN repository changed due to an
>> upgrade of the SourceForge website:
>>
>>    svn co svn://svn.code.sf.net/p/pymol/code/trunk/pymol
>>
>> As always, we welcome bug reports and positive feedback.
>>
>> Cheers,
>>
>> - The PyMOL Team at Schrödinger
>>
> 
> Hello,
> 
> Please consider the attached changes for building with msvc on Windows.
> 
> Also, the latest changes to vmdir.h don't compile with msvc.
> <" rel="nofollow">http://sourceforge.net/p/pymol/code/4025/tree//trunk/pymol/contrib/uiuc/plugins/molfile_plugin/src/vmddir.h?diff=50c0fc56e88f3d0bdf694277:4024>
> 
> 
> Opening absolute paths does not work on Windows (e.g. C:\1bna.pdb):
> 
> Index: pymol/modules/pymol/internal.py
> ===================================================================
> --- pymol/modules/pymol/internal.py    (revision 4025)
> +++ pymol/modules/pymol/internal.py    (working copy)
> @@ -303,7 +303,7 @@
>      try:
>          if not isinstance(finfo, basestring):
>              handle = finfo
> -        elif ':' in finfo:
> +        elif '://' in finfo:
>              import urllib
>              handle = urllib.urlopen(finfo)
>          else:
> 
> 
> The launch script, Scripts\pymol.bat, seems overly complicated and
> doesn't always work for binary installers. Suggestion:
> 
> Index: pymol/setup.py
> ===================================================================
> --- pymol/setup.py    (revision 4025)
> +++ pymol/setup.py    (working copy)
> @@ -119,9 +119,7 @@
> 
>          with open(launch_script, 'w') as out:
>              if sys.platform.startswith('win'):
> -                out.write('set PYMOL_PATH=' + pymol_path + os.linesep)
> -                out.write('"%s" "%s"' % (python_exe, pymol_file))
> -                out.write(' %1 %2 %3 %4 %5 %6 %7 %8 %9' + os.linesep)
> +                out.write(r'@%~dp0\..\pythonw.exe -m pymol.__init__ %*')
>              else:
>                  out.write('#!/bin/sh' + os.linesep)
>                  if sys.platform.startswith('darwin'):
> 
> 
> Thanks,
> 
> Christoph

-- 
Thomas Holder
PyMOL Developer
Schrödinger Contractor

Hi Max,

you use a named color "newcolor" and change it's values at each
iteration, but all states refer to this same color. Before I show you
how to fix your script, could you give "spectrum_states" from the
PyMOLWiki a try? It's a script which does exactly what you want:

http://pymolwiki.org/index.php/Spectrum_states

PyMOL> run spectrum_states.py
PyMOL> spectrum_states resi 430-572, surface sphere, green magenta

Cheers,
  Thomas

Max NANAO wrote, On 03/25/13 21:27:
> Hi All,
> Can anyone tell me how I might change the colors of a specific 
> selection during the course of a rigimol generated morph?  I would like 
> one domain to go from purple to green, and have so far been unable to 
> figure out how to do it.  I tried coloring the different start/final 
> states before rigimol-ing but that did not work.  I have also tried to 
> script the state coloring, as described 
> here:http://www.pymolwiki.org/index.php/Color#Color_States_Individually. 
> The problem is that cmd.set("surface_color", "newcolor", "resi 
> 430:572", a) for example, where a is the state, does not seem to work at 
> all.  i.e. the color is not changed.  The idea was to change the colors 
> as follows:
> 
> states = 30
> for a in range(0,states):
>      incr = 1.0/(states-1)
>      r = 1.0-a*incr
>      g = a*incr
>      b = 1.0-a*incr
>      col = "["+str(r)+","+str(g)+","+str(b)+"]"
>      cmd.set_color("newcolor",col)
>      print "COL state "+str(a+1)+": "+col
>      cmd.set("surface_color", "newcolor", "resi 430:572", a)
>      cmd.set("sphere_color","newcolor", "resi 430:572", a)
>      cmd.recolor()
> 
> ugly, I know!  this is 64 bit pymol 1.5.0.6 eval for linux.  Thanks in 
> advance,
> 
> Max

-- 
Thomas Holder
PyMOL Developer
Schrödinger Contractor

Hi All,
Can anyone tell me how I might change the colors of a specific 
selection during the course of a rigimol generated morph?  I would like 
one domain to go from purple to green, and have so far been unable to 
figure out how to do it.  I tried coloring the different start/final 
states before rigimol-ing but that did not work.  I have also tried to 
script the state coloring, as described 
here:http://www.pymolwiki.org/index.php/Color#Color_States_Individually. 
The problem is that cmd.set("surface_color", "newcolor", "resi 
430:572", a) for example, where a is the state, does not seem to work at 
all.  i.e. the color is not changed.  The idea was to change the colors 
as follows:

states = 30
for a in range(0,states):
     incr = 1.0/(states-1)
     r = 1.0-a*incr
     g = a*incr
     b = 1.0-a*incr
     col = "["+str(r)+","+str(g)+","+str(b)+"]"
     cmd.set_color("newcolor",col)
     print "COL state "+str(a+1)+": "+col
     cmd.set("surface_color", "newcolor", "resi 430:572", a)
     cmd.set("sphere_color","newcolor", "resi 430:572", a)
     cmd.recolor()

ugly, I know!  this is 64 bit pymol 1.5.0.6 eval for linux.  Thanks in 
advance,

Max

On Mon, 25 Mar 2013 18:47:27 +0100
Michael Banck <mb...@de...> wrote:

> Hi Stephen,
> 
> On Mon, Mar 25, 2013 at 01:33:16PM -0400, Stephen P. Molnar wrote:
> > On Sun, 24 Mar 2013 11:02:08 +0100
> > Thomas Holder <tho...@sc...> wrote:
> > > The pre-release version of PyMOL 1.6 has been pushed to the open
> > > source repository on SourceForge. Besides several minor fixes and
> > > improvements, this version should complete the transition to
> > > shader-based rendering for all on-screen drawing. For
> > > non-integrated chipsets this typically means higher quality and
> > > quicker rendering.
> > > 
> > > Please also note that the URL of the SVN repository changed due
> > > to an upgrade of the SourceForge website:
> > > 
> > >   svn co svn://svn.code.sf.net/p/pymol/code/trunk/pymol
> > > 
> > > As always, we welcome bug reports and positive feedback.
> > > 
> > > Cheers,
> > > 
> > > - The PyMOL Team at Schrödinger
> > > 
> > 
> > I managed to download the source code.  There were a lot of warnings
> > during the compilation and I got the following error message:
> > 
> > usr/include/python2.7 -c layer1/TypeFace.c -o
> > build/temp.linux-x86_64-2.7/layer1/TypeFace.o -ffast-math
> > -funroll-loops -O3 -fcommon layer1/TypeFace.c:25:22: fatal error:
> > ft2build.h: No such file or directory compilation terminated.
> > 
> > I don't have the faintest idea as to what supplies ft2build.h and
> > would appreciate a point in the correct direction.
> 
> It's shipped by the libfreetype development package.
> 
> 
> Michael
> 
> ------------------------------------------------------------------------------
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
> http://p.sf.net/sfu/appdyn_d2d_mar
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives:
> http://www.mail-archive.com/pym...@li...

Many thanks,  That solved the problem! v1.6.0 is now compiled and
installed.

Hi Stephen,

On Mon, Mar 25, 2013 at 01:33:16PM -0400, Stephen P. Molnar wrote:
> On Sun, 24 Mar 2013 11:02:08 +0100
> Thomas Holder <tho...@sc...> wrote:
> > The pre-release version of PyMOL 1.6 has been pushed to the open
> > source repository on SourceForge. Besides several minor fixes and
> > improvements, this version should complete the transition to
> > shader-based rendering for all on-screen drawing. For non-integrated
> > chipsets this typically means higher quality and quicker rendering.
> > 
> > Please also note that the URL of the SVN repository changed due to an
> > upgrade of the SourceForge website:
> > 
> >   svn co svn://svn.code.sf.net/p/pymol/code/trunk/pymol
> > 
> > As always, we welcome bug reports and positive feedback.
> > 
> > Cheers,
> > 
> > - The PyMOL Team at Schrödinger
> > 
> 
> I managed to download the source code.  There were a lot of warnings
> during the compilation and I got the following error message:
> 
> usr/include/python2.7 -c layer1/TypeFace.c -o
> build/temp.linux-x86_64-2.7/layer1/TypeFace.o -ffast-math
> -funroll-loops -O3 -fcommon layer1/TypeFace.c:25:22: fatal error:
> ft2build.h: No such file or directory compilation terminated.
> 
> I don't have the faintest idea as to what supplies ft2build.h and would
> appreciate a point in the correct direction.

It's shipped by the libfreetype development package.


Michael

On Sun, 24 Mar 2013 11:02:08 +0100
Thomas Holder <tho...@sc...> wrote:

> Dear PyMOL users,
> 
> The pre-release version of PyMOL 1.6 has been pushed to the open
> source repository on SourceForge. Besides several minor fixes and
> improvements, this version should complete the transition to
> shader-based rendering for all on-screen drawing. For non-integrated
> chipsets this typically means higher quality and quicker rendering.
> 
> Please also note that the URL of the SVN repository changed due to an
> upgrade of the SourceForge website:
> 
>   svn co svn://svn.code.sf.net/p/pymol/code/trunk/pymol
> 
> As always, we welcome bug reports and positive feedback.
> 
> Cheers,
> 
> - The PyMOL Team at Schrödinger
> 

I managed to download the source code.  There were a lot of warnings
during the compilation and I got the following error message:

usr/include/python2.7 -c layer1/TypeFace.c -o
build/temp.linux-x86_64-2.7/layer1/TypeFace.o -ffast-math
-funroll-loops -O3 -fcommon layer1/TypeFace.c:25:22: fatal error:
ft2build.h: No such file or directory compilation terminated.

I don't have the faintest idea as to what supplies ft2build.h and would
appreciate a point in the correct direction.

Thanks in advance.

On 3/24/2013 3:02 AM, Thomas Holder wrote:
> Dear PyMOL users,
>
> The pre-release version of PyMOL 1.6 has been pushed to the open source repository on SourceForge. Besides several minor fixes and improvements, this version should complete the transition to shader-based rendering for all on-screen drawing. For non-integrated chipsets this typically means higher quality and quicker rendering.
>
> Please also note that the URL of the SVN repository changed due to an upgrade of the SourceForge website:
>
>    svn co svn://svn.code.sf.net/p/pymol/code/trunk/pymol
>
> As always, we welcome bug reports and positive feedback.
>
> Cheers,
>
> - The PyMOL Team at Schrödinger
>

Hello,

Please consider the attached changes for building with msvc on Windows.

Also, the latest changes to vmdir.h don't compile with msvc.
<" rel="nofollow">http://sourceforge.net/p/pymol/code/4025/tree//trunk/pymol/contrib/uiuc/plugins/molfile_plugin/src/vmddir.h?diff=50c0fc56e88f3d0bdf694277:4024>

Opening absolute paths does not work on Windows (e.g. C:\1bna.pdb):

Index: pymol/modules/pymol/internal.py
===================================================================
--- pymol/modules/pymol/internal.py	(revision 4025)
+++ pymol/modules/pymol/internal.py	(working copy)
@@ -303,7 +303,7 @@
      try:
          if not isinstance(finfo, basestring):
              handle = finfo
-        elif ':' in finfo:
+        elif '://' in finfo:
              import urllib
              handle = urllib.urlopen(finfo)
          else:


The launch script, Scripts\pymol.bat, seems overly complicated and 
doesn't always work for binary installers. Suggestion:

Index: pymol/setup.py
===================================================================
--- pymol/setup.py	(revision 4025)
+++ pymol/setup.py	(working copy)
@@ -119,9 +119,7 @@

          with open(launch_script, 'w') as out:
              if sys.platform.startswith('win'):
-                out.write('set PYMOL_PATH=' + pymol_path + os.linesep)
-                out.write('"%s" "%s"' % (python_exe, pymol_file))
-                out.write(' %1 %2 %3 %4 %5 %6 %7 %8 %9' + os.linesep)
+                out.write(r'@%~dp0\..\pythonw.exe -m pymol.__init__ %*')
              else:
                  out.write('#!/bin/sh' + os.linesep)
                  if sys.platform.startswith('darwin'):


Thanks,

Christoph

Hi Thomas - Thanks!  That's exactly what I wanted.

Cheers,
Jared
--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
Old Public Health Building, Room 610
341 East 25th Street
New York, NY 10016
212-263-7898
http://kong.med.nyu.edu/




On Mar 23, 2013, at 5:31 AM, Thomas Holder <tho...@sc...<mailto:tho...@sc...>>
 wrote:

Hi Jared,

how about:

PyMOL> as surface
PyMOL> set surface_cavity_mode, 1
PyMOL> set surface_type, 2

Cheers,
 Thomas

Sampson, Jared wrote, On 03/22/13 23:31:
Hi all -

Is there a way to show internal cavities as meshes instead of surfaces?
Something like `set surface_cavity_mode, 1` except with mesh?

Thanks in advance for responses.

Cheers,
Jared

--
Thomas Holder
PyMOL Developer
Schrödinger Contractor

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Hi,

On Sun, Mar 24, 2013 at 11:02:08AM +0100, Thomas Holder wrote:
> The pre-release version of PyMOL 1.6 has been pushed to the open
> source repository on SourceForge. Besides several minor fixes and
> improvements, this version should complete the transition to
> shader-based rendering for all on-screen drawing. For non-integrated
> chipsets this typically means higher quality and quicker rendering.
 
[...]

> As always, we welcome bug reports and positive feedback.

Works fine for me so far, I noticed one thing though: In Wizard -> Demo
-> Sculpting, the protein backbone mostly disappears if I rotate a bond,
I just see the angle and the spheres, while the backbone is almost
invisible.  This does not seem to happen if I rotate around a bond at
the outside of the protein.

In 1.5.0.1, the appearance does not change between dragging atoms and
rotating bonds which made it easier to rotate around bonds.

This is with a Lenovo T400 and internal Intel Graphics.


Michael

Matthias,

As David said, try setting internal_gui to 0.

Or, try saving your session as a .psw instead of .pse.

Cheers,

Jason

Sent from my Android. Please excuse the concision and any typos.
On Mar 24, 2013 6:55 PM, "Matthias Haffke" <mat...@ho...> wrote:

> Dear all,
>
> this might be a simple question, but I would like to know how to hide the
> object control panel on the right side in the PyMol window.
> I would like to give a full screen presentation using scenes and it would
> be nice to have "more space" and remove the object control panel. Switching
> "full_screen on" does not do the job unfortunately - the object control
> panel remains visible.
>
> Many thanks already if anyone knows the solution,
>
> Matthias
>
>
> ------------------------------------------------------------------------------
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
> http://p.sf.net/sfu/appdyn_d2d_mar
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>

http://pymolwiki.org/index.php/Internal_gui

-David


On Sunday, March 24, 2013 at 7:54 PM, Matthias Haffke wrote:

> Dear all,
> 
> this might be a simple question, but I would like to know how to hide the object control panel on the right side in the PyMol window.
> I would like to give a full screen presentation using scenes and it would be nice to have "more space" and remove the object control panel. Switching "full_screen on" does not do the job unfortunately - the object control panel remains visible.
> 
> Many thanks already if anyone knows the solution,
> 
> Matthias
> ------------------------------------------------------------------------------
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
> http://p.sf.net/sfu/appdyn_d2d_mar
> 
> _______________________________________________
> PyMOL-users mailing list (PyM...@li... (mailto:PyM...@li...))
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
> 
> 

Dear all,

this might be a simple question, but I would like to know how to hide the object control panel on the right side in the PyMol window.
I would like to give a full screen presentation using scenes and it would be nice to have "more space" and remove the object control panel. Switching "full_screen on" does not do the job unfortunately - the object control panel remains visible.

Many thanks already if anyone knows the solution,

Matthias
 		 	   		  

Hi Michael,

I haven't tagged that commit. It's svn revision 4025. For the final 1.6.0 version we will upload a tar.gz archive to sourceforge.

Cheers,
  Thomas

On Mar 24, 2013, at 1:18 PM, Michael Banck <mb...@de...> wrote:
> Hi,
> 
> On Sun, Mar 24, 2013 at 11:02:08AM +0100, Thomas Holder wrote:
>> The pre-release version of PyMOL 1.6 has been pushed to the open
>> source repository on SourceForge. Besides several minor fixes and
>> improvements, this version should complete the transition to
>> shader-based rendering for all on-screen drawing. For non-integrated
>> chipsets this typically means higher quality and quicker rendering.
>> 
>> Please also note that the URL of the SVN repository changed due to an
>> upgrade of the SourceForge website:
>> 
>>  svn co svn://svn.code.sf.net/p/pymol/code/trunk/pymol
>> 
>> As always, we welcome bug reports and positive feedback.
> 
> Great!  Is there some pre-release version number assigned to that
> commit, like "1.6.0pre1" or "1.6.0rc1", assuming a final 1.6.0 will
> follow at some point?
> 
> Best regards,
> 
> Michael

-- 
Thomas Holder
PyMOL Developer
Schrödinger Contractor

Hi,

On Sun, Mar 24, 2013 at 11:02:08AM +0100, Thomas Holder wrote:
> The pre-release version of PyMOL 1.6 has been pushed to the open
> source repository on SourceForge. Besides several minor fixes and
> improvements, this version should complete the transition to
> shader-based rendering for all on-screen drawing. For non-integrated
> chipsets this typically means higher quality and quicker rendering.
> 
> Please also note that the URL of the SVN repository changed due to an
> upgrade of the SourceForge website:
> 
>   svn co svn://svn.code.sf.net/p/pymol/code/trunk/pymol
> 
> As always, we welcome bug reports and positive feedback.

Great!  Is there some pre-release version number assigned to that
commit, like "1.6.0pre1" or "1.6.0rc1", assuming a final 1.6.0 will
follow at some point?


Best regards,

Michael