pymol-users Mailing List for PyMOL Molecular Graphics System

To quote Warren L. DeLano on building PyMOL on Windows: "Given enough
effort, native compilation is certainly do-able, but it is not intended
to be easy... nor commonplace." See
<" rel="nofollow">http://www.mail-archive.com/pym...@li.../msg05696.html>
and
<." rel="nofollow">http://www.mail-archive.com/pym...@li.../msg06761.html>.
Interesting read... Is this also Schrodinger's opinion?


On 1/30/2010 12:24 PM, Nikola Wenta wrote:
> Hello all!
> I became aware that Pymol, a nice x-ray structure viewer, is no longer
> available as  binary but rather needs to be compiled from source code.
> While the setup under (Slackware 12.2-) Linux ran smootly with "python
> setup.py install" and "python setup2.py install", the same attempt
> didn't work under Windows. Under Windows XP, I have tried it first
> with Python 2.4, but I didn't have a C++ compiler installed. Then I
> installed Visual C++ 2008 Express, but it didn't work either. I then
> found the "build -C mingw32" for MingW32/MSYS installation suggestion
> which also didn't work. At last I have tried to compile Pymol within
> CygWin. All attempts under Windows failed. Did someone succeed with
> generating Windows binaries for Pymol 1.2.x (build 3887) and is
> willing to share the binaries and a working procedure for their
> generation with the Pymol-under-Windows community?
> Thank you very much for any helpful suggestions!
> Niko 

Unofficial binaries are at
<." rel="nofollow">http://www.lfd.uci.edu/~gohlke/pythonlibs/#pymol>.

Christoph

On 1/30/2010 12:24 PM, Nikola Wenta wrote:
> Hello all!
> I became aware that Pymol, a nice x-ray structure viewer, is no longer
> available as  binary but rather needs to be compiled from source code.
> While the setup under (Slackware 12.2-) Linux ran smootly with "python
> setup.py install" and "python setup2.py install", the same attempt
> didn't work under Windows. Under Windows XP, I have tried it first
> with Python 2.4, but I didn't have a C++ compiler installed. Then I
> installed Visual C++ 2008 Express, but it didn't work either. I then
> found the "build -C mingw32" for MingW32/MSYS installation suggestion
> which also didn't work. At last I have tried to compile Pymol within
> CygWin. All attempts under Windows failed. Did someone succeed with
> generating Windows binaries for Pymol 1.2.x (build 3887) and is
> willing to share the binaries and a working procedure for their
> generation with the Pymol-under-Windows community?
> Thank you very much for any helpful suggestions!
> Niko 
> This message has been checked for viruses but the contents of an attachment
> may still contain software viruses which could damage your computer system:
> you are advised to perform your own checks. Email communications with the
> University of Nottingham may be monitored as permitted by UK legislation.
> ------------------------------------------------------------------------------
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> Stay online with enterprise data centers and the best network in the business
> Choose flexible plans and management services without long-term contracts
> Personal 24x7 support from experience hosting pros just a phone call away.
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> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
> 
> 

Hello all!
I became aware that Pymol, a nice x-ray structure viewer, is no longer
available as  binary but rather needs to be compiled from source code.
While the setup under (Slackware 12.2-) Linux ran smootly with "python
setup.py install" and "python setup2.py install", the same attempt
didn't work under Windows. Under Windows XP, I have tried it first
with Python 2.4, but I didn't have a C++ compiler installed. Then I
installed Visual C++ 2008 Express, but it didn't work either. I then
found the "build -C mingw32" for MingW32/MSYS installation suggestion
which also didn't work. At last I have tried to compile Pymol within
CygWin. All attempts under Windows failed. Did someone succeed with
generating Windows binaries for Pymol 1.2.x (build 3887) and is
willing to share the binaries and a working procedure for their
generation with the Pymol-under-Windows community?
Thank you very much for any helpful suggestions!
Niko 
This message has been checked for viruses but the contents of an attachment
may still contain software viruses which could damage your computer system:
you are advised to perform your own checks. Email communications with the
University of Nottingham may be monitored as permitted by UK legislation.

+1 from me



-- 
Justin Lecher
Institute for Neuroscience and Biophysics
ISB 3 - Institute for structural biochemistry
Research Centre Juelich GmbH,
52425 Juelich,Germany
phone: +49 2461 61 5385

 
Several +1s from all the people here....  !!
-Tom

________________________________

From: Sean Law [mailto:mag...@ho...] 
Sent: Thursday, January 28, 2010 12:47 PM
To: pym...@li...
Subject: [PyMOL] CEalign - PyMOL Build


Jason,

I would LOVE to see CEalign built along with PyMOL.  +1

Sean 


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> Dear Jason,
>
> ""super" does pairwise residue alignments followed by a superposition.
> It also does refinements to improve the overall quality."
>
> Could you elaborate a little more on this?  Do you mean that it
> calculates all pairwise distances and does a least squares fit with
> refinement steps that toss out any atoms that are more than 2 standard
> deviations from the mean residue-residue rmsd, or something more
> complex?
>
> Thank you,


Michael,

"Super" does pairwise residue comparisons using a difference of
distance matrices (as is common in other methods).  It then builds the
highest scoring alignment by taking the best scoring match, with or
without gaps, and window averaging, using a dynamic programming style
search for all possible pairs.  Think of doing a Needleman-Wunsch, but
on structural scores instead of a sequence scoring matrix (BLOSUM62).

FYI, there is an infrequently discussed "window" parameter which will
consider not just diff(atomA, atomB) but considers local substructure
as large as the window you provide:

fetch 1rlw 1rsy, async=0
super 1rlw, 1rsy, window=0

# now compare to
super 1rlw, 1rsy, window=8

This window feature is used in other algorithms for considering
average substructure, not just pairwise scores.

Try "help super" for more information on the parameters.

Hope this helps,

-- Jason




-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

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

On 28/01/10 21:31, Michael Lerner wrote:
> Hi all,
> 
> I've been working with Jason Vertrees on a new version of the PyMOL-APBS
> plugin and it's now ready for pre-release.

Hi,

that's really good news, that you are going to develop the plugin in a
more public accessible manner!

For all gentoo user, you can find the plugin in the sci overlay as

sci-chemistry/pymol-apbs-plugin.

There is a version for revision 11 as well as a live ebuild available.

Thanks justin

-- 
Justin Lecher
Institute for Neuroscience and Biophysics
ISB 3 - Institute for structural biochemistry
Research Centre Juelich GmbH,
52425 Juelich,Germany
phone: +49 2461 61 5385

Jason,

I would LOVE to see CEalign built along with PyMOL.  +1

Sean 
 		 	   		  
_________________________________________________________________
Say Happy New Year with Messenger for Mobile.
http://go.microsoft.com/?linkid=9706117

Hi all,

I've been working with Jason Vertrees on a new version of the PyMOL-APBS
plugin and it's now ready for pre-release. There are three big advantages of
the new version:

* It's been tested modern OS X, Windows and Linux systems and fixes several
long-standing bugs.
* It allows you to call through to PDB2PQR directly.
* It has two visualization panels to aid in showing multiple potential
surfaces at once.

I've also upped the default maximum allowed memory since typical users have
bigger and faster computers these days.

The main reason that I'm sending this out now is to get bug reports. I think
it runs everywhere, but *please* let me know if you have problems with it.
Once it's shown to be stable, it'll be included in the next PyMOL release.

A slightly longer list of changes is included below.

== How to get it ==

There are two ways to get the new plugin

* If you have subversion installed, you can always get the latest version
via

svn co
https://pymolapbsplugin.svn.sourceforge.net/svnroot/pymolapbsplugin/trunk/pymolapbsplugin

* You can download the it from
http://pymolapbsplugin.svn.sourceforge.net/viewvc/pymolapbsplugin/trunk/src/apbsplugin.py

That should give you a file called apbsplugin.py

Once you have the plugin, you can install it via PyMOL's plugin installer:
Plugin --> Manage Plugins --> Install

Note that the plugin will be installed as "APBS Tools2" so that you can
continue to use your old version.

== Longer feature list ==

* The ability to call through directly to PDB2PQR
* More modern apbs input files
* Two visualization panels. It's often quite useful to look at two different
electrostatic potentials at once. It's also quite useful to look at
electrostatic potentials mapped onto two different surfaces at once.
Multiple visualization panels makes this a snap: just set up one surface on
panel 1 and another surface on panel 2.
* Fixes several bugs that caused crashes on both OS X and Linux systems
* Increased maximum allowed memory
* Switch from os.system to subprocess for running external programs
* Deals with paths on Windows properly
* Gives better diagnostic information so that PyMOL/APBS developers can find
bugs more easily
* Lots of internal code cleanup

You can find this same information on the PyMOL wiki:
http://pymolwiki.org/index.php/User:Mglerner

Thanks,

-Michael

-- 
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)

Hi All,

I'd like to be able to find the coordinates of a cgo object on the pymol screen. 

Here's my workflow:

1. I generate a cgo object (a criss-cross) at a defined coordinate, and then drag it to a new coordinate. 

2. I'd like to find the xyz coordinates of the new location.

Could anyone tell me the commands needed to query the new location of the center of the crisscross?

Thanks! and all the best,

--Buz

Hi Mike,

PyMOL has quite a few structure alignment and structure fitting
options.  If you want CE, check out CEalign on the PyMOLWiki
(http://www.pymolwiki.org/index.php/Cealign).  It's a script for
PyMOL.  I might build it into newer releases of PyMOL, if anyone's
interested (let me know).

"align" performs a sequence alignment and then a structure
superposition.  After that, it goes through refinement cycles to
improve the result.  Align is fast and returns quality alignments for
two sequences of high seq id.

"super" does pairwise residue alignments followed by a superposition.
It also does refinements to improve the overall quality.

"optAlign," "fit" and others are just least square fitting routines
once the atom correspondence is determined.

Regards,

-- Jason


On Wed, Jan 27, 2010 at 5:55 PM, Michael Zimmermann
<mic...@ia...> wrote:
> Dear PyMOL users,
>
> I have browsed the wiki and the first 300 mailing list messages in the
> archive (the sourceforge archive does not seem to have a search set up
> for the archive... arg!), but did not find any details about the
> algorithms behind 'fit' and 'super.'  I understand how align works,
> and it sounds like fit is align but without the processing steps
> (assumes 1:1 correspondence).  Super, on the other hand, sounds more
> like CE since it is sequence independent, but I cannot find any
> corroboration on this.
>
> I want to run CE or a like algorithm (sequence independent - only
> concerned with spacial arrangement of alpha carbons) on a large
> dataset and want to know my options in terms of speed and accuracy.
>
> Sincerely,
> Mike Z
>
> ------------------------------------------------------------------------------
> The Planet: dedicated and managed hosting, cloud storage, colocation
> Stay online with enterprise data centers and the best network in the business
> Choose flexible plans and management services without long-term contracts
> Personal 24x7 support from experience hosting pros just a phone call away.
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> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>



-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

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

Dear PyMOL users,

I have browsed the wiki and the first 300 mailing list messages in the
archive (the sourceforge archive does not seem to have a search set up
for the archive... arg!), but did not find any details about the
algorithms behind 'fit' and 'super.'  I understand how align works,
and it sounds like fit is align but without the processing steps
(assumes 1:1 correspondence).  Super, on the other hand, sounds more
like CE since it is sequence independent, but I cannot find any
corroboration on this.

I want to run CE or a like algorithm (sequence independent - only
concerned with spacial arrangement of alpha carbons) on a large
dataset and want to know my options in terms of speed and accuracy.

Sincerely,
Mike Z

Hi,

On Tue, 26 Jan 2010 10:48:58 -0600 Michael Zimmermann <mic...@ia...>
wrote:

> If you have a lot of files to do this to, I would suggest learning at
> least a little bit of perl.  It might not be as nice an option as a
> python tab manager (depending on your point of view), though.

Or even better, try sed (the following is in a bash-type shell)!

for file in *.py; sed 's/	/  /g' < $file >${file}.notab

In order to type the "tab" key in the command line, type the key combination
"CTRL-V" followed by the Tab key.

I use vim as my editor and I have it set to always use spaces and not tabs
using the "expandtab" setting, so when I hit the "Tab" key, it just inserts
two spaces for me.

Cheers,
Rob
-- 
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor 
Botterell Hall Rm 644
Department of Biochemistry, Queen's University, 
Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821            Fax: 613-533-2497
<rob...@qu...>    http://pldserver1.biochem.queensu.ca/~rlc

Try the expand command on linux or google for "sed tab to space
replacement".
Marius

On Tue, Jan 26, 2010 at 5:48 PM, Michael Zimmermann <mic...@ia...>wrote:

> If you have a lot of files to do this to, I would suggest learning at
> least a little bit of perl.  It might not be as nice an option as a
> python tab manager (depending on your point of view), though.
>
> Perl uses regular expressions.  In case you'd like to see how to do
> your tab-space replacement, the following bit of code would convert
> tabs to 4 spaces.
>
> Take care,
>
> Mike Z
>
> #----------------------------------
> use strict;
> use warnings;
> my $file = $ARGV[0];
> open(IN,$file) or die $!;
> open(OUT,">".$file."notab") or die $!;
> while(<IN>){
>   $_ =~ s/\t/    /g;
>   print OUT $_;
> }
> close(IN);
> close(OUT);
> exit;
> #----------------------------------
>
> On Tue, Jan 26, 2010 at 9:09 AM, Jason Vertrees
> <jas...@sc...> wrote:
> > David,
> >
> > Oh, the joys of open-source.  Here's my solution for you:
> >  (1) load your file in your favorite editor
> >  (2) determine user-desired tab stop setting
> >  (3) convert all tabs to spaces in your editor (or search replace tabs
> > with X-spaces)
> >  (4) save your file
> >
> > One warning though, I have seen some interpreters crash when they
> > encounter spaces over tabs.
> >
> > -- Jason
> >
> > On Tue, Jan 26, 2010 at 9:12 AM, David Hall <li...@co...>
> wrote:
> >> During my editing of dynoplot.py, I noticed that there were some
> >> whitespace issues.  Normally I consider whitespace a bikeshedding
> >> topic, but in python, it is significant, so it matters.  When tabs and
> >> spaces are mixed, our own personal settings for how tabs are displayed
> >> in an editor makes a huge difference in whether the script is
> >> understandable.
> >>
> >> I checked out the git repo of pymol scripts (
> >> http://github.com/jlec/Pymol-script-repo/ ) and did some analysis
> >>
> >> First, these files switch between some lines where all indenting is
> >> tabs to lines where all indenting is spaces:
> >> Objects_and_Selections/color_objects.py has 8 tab lines and 34 space
> lines
> >> ThirdParty_Scripts/WFMesh.py has 52 tab lines and 21 space lines
> >> biochemical_scripts/pucker.py has 167 tab lines and 5 space lines
> >> math_geo_cgo/modevectors.py has 160 tab lines and 2 space lines
> >> structural_biology_scripts/DynoPlot.py has 82 tab lines and 27 space
> lines
> >> structural_biology_scripts/Rotamers.py has 86 tab lines and 22 space
> lines
> >> structural_biology_scripts/kabsch.py has 51 tab lines and 4 space lines
> >>
> >> Second, there are files where the indenting inside a line switches
> >> back and forth (numbers are the counts of lines that have both tabs
> >> and spaces in indenting):
> >> Objects_and_Selections/color_objects.py: 19
> >> ThirdParty_Scripts/WFMesh.py: 29
> >> ThirdParty_Scripts/transform_odb.py: 6
> >> math_geo_cgo/modevectors.py: 12
> >> structural_biology_scripts/DynoPlot.py: 83
> >> structural_biology_scripts/Rotamers.py: 86
> >> structural_biology_scripts/kabsch.py: 1
> >>
> >> I've tried using pindent.py (
> >> http://svn.python.org/projects/python/trunk/Tools/scripts/pindent.py )
> >> and PythonTidy ( http://pypi.python.org/pypi/PythonTidy/ ) to
> >> generally fix these, but they both run into problems.  Is there a
> >> general solution out in the python world to automatically fix this?  I
> >> don't care whether it produces tabs or spaces.  I just want one or the
> >> other.  If someone points me to something, I'm more than willing to
> >> run it on these scripts, push them back to github and copy them back
> >> onto the wiki.
> >>
> >> -David
> >>
> >>
> ------------------------------------------------------------------------------
> >> The Planet: dedicated and managed hosting, cloud storage, colocation
> >> Stay online with enterprise data centers and the best network in the
> business
> >> Choose flexible plans and management services without long-term
> contracts
> >> Personal 24x7 support from experience hosting pros just a phone call
> away.
> >> http://p.sf.net/sfu/theplanet-com
> >> _______________________________________________
> >> PyMOL-users mailing list (PyM...@li...)
> >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> >> Archives: http://www.mail-archive.com/pym...@li...
> >>
> >
> >
> >
> > --
> > Jason Vertrees, PhD
> > PyMOL Product Manager
> > Schrodinger, LLC
> >
> > (e) Jas...@sc...
> > (o) +1 (603) 374-7120
> >
> >
> ------------------------------------------------------------------------------
> > The Planet: dedicated and managed hosting, cloud storage, colocation
> > Stay online with enterprise data centers and the best network in the
> business
> > Choose flexible plans and management services without long-term contracts
> > Personal 24x7 support from experience hosting pros just a phone call
> away.
> > http://p.sf.net/sfu/theplanet-com
> > _______________________________________________
> > PyMOL-users mailing list (PyM...@li...)
> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> > Archives: http://www.mail-archive.com/pym...@li...
> >
>
>
> ------------------------------------------------------------------------------
> The Planet: dedicated and managed hosting, cloud storage, colocation
> Stay online with enterprise data centers and the best network in the
> business
> Choose flexible plans and management services without long-term contracts
> Personal 24x7 support from experience hosting pros just a phone call away.
> http://p.sf.net/sfu/theplanet-com
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>

If you have a lot of files to do this to, I would suggest learning at
least a little bit of perl.  It might not be as nice an option as a
python tab manager (depending on your point of view), though.

Perl uses regular expressions.  In case you'd like to see how to do
your tab-space replacement, the following bit of code would convert
tabs to 4 spaces.

Take care,

Mike Z

#----------------------------------
use strict;
use warnings;
my $file = $ARGV[0];
open(IN,$file) or die $!;
open(OUT,">".$file."notab") or die $!;
while(<IN>){
   $_ =~ s/\t/    /g;
   print OUT $_;
}
close(IN);
close(OUT);
exit;
#----------------------------------

On Tue, Jan 26, 2010 at 9:09 AM, Jason Vertrees
<jas...@sc...> wrote:
> David,
>
> Oh, the joys of open-source.  Here's my solution for you:
>  (1) load your file in your favorite editor
>  (2) determine user-desired tab stop setting
>  (3) convert all tabs to spaces in your editor (or search replace tabs
> with X-spaces)
>  (4) save your file
>
> One warning though, I have seen some interpreters crash when they
> encounter spaces over tabs.
>
> -- Jason
>
> On Tue, Jan 26, 2010 at 9:12 AM, David Hall <li...@co...> wrote:
>> During my editing of dynoplot.py, I noticed that there were some
>> whitespace issues.  Normally I consider whitespace a bikeshedding
>> topic, but in python, it is significant, so it matters.  When tabs and
>> spaces are mixed, our own personal settings for how tabs are displayed
>> in an editor makes a huge difference in whether the script is
>> understandable.
>>
>> I checked out the git repo of pymol scripts (
>> http://github.com/jlec/Pymol-script-repo/ ) and did some analysis
>>
>> First, these files switch between some lines where all indenting is
>> tabs to lines where all indenting is spaces:
>> Objects_and_Selections/color_objects.py has 8 tab lines and 34 space lines
>> ThirdParty_Scripts/WFMesh.py has 52 tab lines and 21 space lines
>> biochemical_scripts/pucker.py has 167 tab lines and 5 space lines
>> math_geo_cgo/modevectors.py has 160 tab lines and 2 space lines
>> structural_biology_scripts/DynoPlot.py has 82 tab lines and 27 space lines
>> structural_biology_scripts/Rotamers.py has 86 tab lines and 22 space lines
>> structural_biology_scripts/kabsch.py has 51 tab lines and 4 space lines
>>
>> Second, there are files where the indenting inside a line switches
>> back and forth (numbers are the counts of lines that have both tabs
>> and spaces in indenting):
>> Objects_and_Selections/color_objects.py: 19
>> ThirdParty_Scripts/WFMesh.py: 29
>> ThirdParty_Scripts/transform_odb.py: 6
>> math_geo_cgo/modevectors.py: 12
>> structural_biology_scripts/DynoPlot.py: 83
>> structural_biology_scripts/Rotamers.py: 86
>> structural_biology_scripts/kabsch.py: 1
>>
>> I've tried using pindent.py (
>> http://svn.python.org/projects/python/trunk/Tools/scripts/pindent.py )
>> and PythonTidy ( http://pypi.python.org/pypi/PythonTidy/ ) to
>> generally fix these, but they both run into problems.  Is there a
>> general solution out in the python world to automatically fix this?  I
>> don't care whether it produces tabs or spaces.  I just want one or the
>> other.  If someone points me to something, I'm more than willing to
>> run it on these scripts, push them back to github and copy them back
>> onto the wiki.
>>
>> -David
>>
>> ------------------------------------------------------------------------------
>> The Planet: dedicated and managed hosting, cloud storage, colocation
>> Stay online with enterprise data centers and the best network in the business
>> Choose flexible plans and management services without long-term contracts
>> Personal 24x7 support from experience hosting pros just a phone call away.
>> http://p.sf.net/sfu/theplanet-com
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
>>
>
>
>
> --
> Jason Vertrees, PhD
> PyMOL Product Manager
> Schrodinger, LLC
>
> (e) Jas...@sc...
> (o) +1 (603) 374-7120
>
> ------------------------------------------------------------------------------
> The Planet: dedicated and managed hosting, cloud storage, colocation
> Stay online with enterprise data centers and the best network in the business
> Choose flexible plans and management services without long-term contracts
> Personal 24x7 support from experience hosting pros just a phone call away.
> http://p.sf.net/sfu/theplanet-com
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>

Not much of a help, but WingIDE Professional Edition has a very good indentation manager, which takes care of the mixed/space tab issues. If you are working in python frequently it is a worthwhile investment.

Cheers,

	Carsten


> -----Original Message-----
> From: Jason Vertrees [mailto:jas...@sc...]
> Sent: Tuesday, January 26, 2010 10:10 AM
> To: David Hall
> Cc: pymol-users
> Subject: Re: [PyMOL] Whitespacing?
> 
> David,
> 
> Oh, the joys of open-source.  Here's my solution for you:
>  (1) load your file in your favorite editor
>  (2) determine user-desired tab stop setting
>  (3) convert all tabs to spaces in your editor (or search replace tabs
> with X-spaces)
>  (4) save your file
> 
> One warning though, I have seen some interpreters crash when they
> encounter spaces over tabs.
> 
> -- Jason
> 
> On Tue, Jan 26, 2010 at 9:12 AM, David Hall <li...@co...>
> wrote:
> > During my editing of dynoplot.py, I noticed that there were some
> > whitespace issues.  Normally I consider whitespace a bikeshedding
> > topic, but in python, it is significant, so it matters.  When tabs
> and
> > spaces are mixed, our own personal settings for how tabs are
> displayed
> > in an editor makes a huge difference in whether the script is
> > understandable.
> >
> > I checked out the git repo of pymol scripts (
> > http://github.com/jlec/Pymol-script-repo/ ) and did some analysis
> >
> > First, these files switch between some lines where all indenting is
> > tabs to lines where all indenting is spaces:
> > Objects_and_Selections/color_objects.py has 8 tab lines and 34 space
> lines
> > ThirdParty_Scripts/WFMesh.py has 52 tab lines and 21 space lines
> > biochemical_scripts/pucker.py has 167 tab lines and 5 space lines
> > math_geo_cgo/modevectors.py has 160 tab lines and 2 space lines
> > structural_biology_scripts/DynoPlot.py has 82 tab lines and 27 space
> lines
> > structural_biology_scripts/Rotamers.py has 86 tab lines and 22 space
> lines
> > structural_biology_scripts/kabsch.py has 51 tab lines and 4 space
> lines
> >
> > Second, there are files where the indenting inside a line switches
> > back and forth (numbers are the counts of lines that have both tabs
> > and spaces in indenting):
> > Objects_and_Selections/color_objects.py: 19
> > ThirdParty_Scripts/WFMesh.py: 29
> > ThirdParty_Scripts/transform_odb.py: 6
> > math_geo_cgo/modevectors.py: 12
> > structural_biology_scripts/DynoPlot.py: 83
> > structural_biology_scripts/Rotamers.py: 86
> > structural_biology_scripts/kabsch.py: 1
> >
> > I've tried using pindent.py (
> > http://svn.python.org/projects/python/trunk/Tools/scripts/pindent.py
> )
> > and PythonTidy ( http://pypi.python.org/pypi/PythonTidy/ ) to
> > generally fix these, but they both run into problems.  Is there a
> > general solution out in the python world to automatically fix this?
>  I
> > don't care whether it produces tabs or spaces.  I just want one or
> the
> > other.  If someone points me to something, I'm more than willing to
> > run it on these scripts, push them back to github and copy them back
> > onto the wiki.
> >
> > -David
> >
> > ---------------------------------------------------------------------
> ---------
> > The Planet: dedicated and managed hosting, cloud storage, colocation
> > Stay online with enterprise data centers and the best network in the
> business
> > Choose flexible plans and management services without long-term
> contracts
> > Personal 24x7 support from experience hosting pros just a phone call
> away.
> > http://p.sf.net/sfu/theplanet-com
> > _______________________________________________
> > PyMOL-users mailing list (PyM...@li...)
> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> > Archives: http://www.mail-archive.com/pymol-
> us...@li...
> >
> 
> 
> 
> --
> Jason Vertrees, PhD
> PyMOL Product Manager
> Schrodinger, LLC
> 
> (e) Jas...@sc...
> (o) +1 (603) 374-7120
> 
> -----------------------------------------------------------------------
> -------
> The Planet: dedicated and managed hosting, cloud storage, colocation
> Stay online with enterprise data centers and the best network in the
> business
> Choose flexible plans and management services without long-term
> contracts
> Personal 24x7 support from experience hosting pros just a phone call
> away.
> http://p.sf.net/sfu/theplanet-com
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...

David,

Oh, the joys of open-source.  Here's my solution for you:
 (1) load your file in your favorite editor
 (2) determine user-desired tab stop setting
 (3) convert all tabs to spaces in your editor (or search replace tabs
with X-spaces)
 (4) save your file

One warning though, I have seen some interpreters crash when they
encounter spaces over tabs.

-- Jason

On Tue, Jan 26, 2010 at 9:12 AM, David Hall <li...@co...> wrote:
> During my editing of dynoplot.py, I noticed that there were some
> whitespace issues.  Normally I consider whitespace a bikeshedding
> topic, but in python, it is significant, so it matters.  When tabs and
> spaces are mixed, our own personal settings for how tabs are displayed
> in an editor makes a huge difference in whether the script is
> understandable.
>
> I checked out the git repo of pymol scripts (
> http://github.com/jlec/Pymol-script-repo/ ) and did some analysis
>
> First, these files switch between some lines where all indenting is
> tabs to lines where all indenting is spaces:
> Objects_and_Selections/color_objects.py has 8 tab lines and 34 space lines
> ThirdParty_Scripts/WFMesh.py has 52 tab lines and 21 space lines
> biochemical_scripts/pucker.py has 167 tab lines and 5 space lines
> math_geo_cgo/modevectors.py has 160 tab lines and 2 space lines
> structural_biology_scripts/DynoPlot.py has 82 tab lines and 27 space lines
> structural_biology_scripts/Rotamers.py has 86 tab lines and 22 space lines
> structural_biology_scripts/kabsch.py has 51 tab lines and 4 space lines
>
> Second, there are files where the indenting inside a line switches
> back and forth (numbers are the counts of lines that have both tabs
> and spaces in indenting):
> Objects_and_Selections/color_objects.py: 19
> ThirdParty_Scripts/WFMesh.py: 29
> ThirdParty_Scripts/transform_odb.py: 6
> math_geo_cgo/modevectors.py: 12
> structural_biology_scripts/DynoPlot.py: 83
> structural_biology_scripts/Rotamers.py: 86
> structural_biology_scripts/kabsch.py: 1
>
> I've tried using pindent.py (
> http://svn.python.org/projects/python/trunk/Tools/scripts/pindent.py )
> and PythonTidy ( http://pypi.python.org/pypi/PythonTidy/ ) to
> generally fix these, but they both run into problems.  Is there a
> general solution out in the python world to automatically fix this?  I
> don't care whether it produces tabs or spaces.  I just want one or the
> other.  If someone points me to something, I'm more than willing to
> run it on these scripts, push them back to github and copy them back
> onto the wiki.
>
> -David
>
> ------------------------------------------------------------------------------
> The Planet: dedicated and managed hosting, cloud storage, colocation
> Stay online with enterprise data centers and the best network in the business
> Choose flexible plans and management services without long-term contracts
> Personal 24x7 support from experience hosting pros just a phone call away.
> http://p.sf.net/sfu/theplanet-com
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>



-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

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

During my editing of dynoplot.py, I noticed that there were some
whitespace issues.  Normally I consider whitespace a bikeshedding
topic, but in python, it is significant, so it matters.  When tabs and
spaces are mixed, our own personal settings for how tabs are displayed
in an editor makes a huge difference in whether the script is
understandable.

I checked out the git repo of pymol scripts (
http://github.com/jlec/Pymol-script-repo/ ) and did some analysis

First, these files switch between some lines where all indenting is
tabs to lines where all indenting is spaces:
Objects_and_Selections/color_objects.py has 8 tab lines and 34 space lines
ThirdParty_Scripts/WFMesh.py has 52 tab lines and 21 space lines
biochemical_scripts/pucker.py has 167 tab lines and 5 space lines
math_geo_cgo/modevectors.py has 160 tab lines and 2 space lines
structural_biology_scripts/DynoPlot.py has 82 tab lines and 27 space lines
structural_biology_scripts/Rotamers.py has 86 tab lines and 22 space lines
structural_biology_scripts/kabsch.py has 51 tab lines and 4 space lines

Second, there are files where the indenting inside a line switches
back and forth (numbers are the counts of lines that have both tabs
and spaces in indenting):
Objects_and_Selections/color_objects.py: 19
ThirdParty_Scripts/WFMesh.py: 29
ThirdParty_Scripts/transform_odb.py: 6
math_geo_cgo/modevectors.py: 12
structural_biology_scripts/DynoPlot.py: 83
structural_biology_scripts/Rotamers.py: 86
structural_biology_scripts/kabsch.py: 1

I've tried using pindent.py (
http://svn.python.org/projects/python/trunk/Tools/scripts/pindent.py )
and PythonTidy ( http://pypi.python.org/pypi/PythonTidy/ ) to
generally fix these, but they both run into problems.  Is there a
general solution out in the python world to automatically fix this?  I
don't care whether it produces tabs or spaces.  I just want one or the
other.  If someone points me to something, I'm more than willing to
run it on these scripts, push them back to github and copy them back
onto the wiki.

-David

On 20 Jan 2010, at 22:07, Jason Vertrees wrote:

> PyMOLers,
> 
> I just want to quickly reiterate: PyMOL will still be supported on the
> Mac--no need to worry.  Even though other Schrodinger software doesn't
> run on the Mac, PyMOL will.

Actually, I expect that schrodinger will port their own software to the Mac sooner than later.

PyMOLers,

If any of you want to pay respects to Warren, there is a memorial
service planned for Feb. 7th.  Details copied below.

See you there,

-- Jason


---------- Forwarded message ----------
From: Axel Brunger <br...@st...>
Date: Thu, Jan 21, 2010 at 6:32 PM
Subject: [ccp4bb] Memorial Service for Warren DeLano
To: CC...@ji...



Begin forwarded message:

From: Charles Wolfus <cw...@gm...>
Subject: Memorial Service for Warren DeLano
In case you have not already heard, the DeLano family is having a
memorial service for Warren:

Sunday, February 7th @ 10am
The Lucie Stern Center
1305 Middlefield Road
Palo Alto, 94301

Please join us in remembering Warren, his special gifts, and accomplishments.

Also, please freely forward this message to any others who may want to join us.

Best Regards,

Friends and Family of Warren DeLano


Axel T. Brunger
Investigator,  Howard Hughes Medical Institute
Professor of Molecular and Cellular Physiology
Stanford University
Web:    http://atbweb.stanford.edu
Email:  br...@st...
Phone:  +1 650-736-1031
Fax:    +1 650-745-1463


-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

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

Here's a slightly improved version. It only kicks in if dpi is specified. I
think that you could make the obvious modifications to the help message and
argument list and use it as a replacement for cmd.ray (as long as you're
aware of the fact that the argument list will be different).

#!/usr/bin/env pymol

from pymol import cmd

def rayy(width=-1,height=-1,dpi=-1,units='in',**kwargs):
    """
    Slightly better version of the ray command.
    You can specify width and height in the units of your choice, e.g.

    rayy 3,2,units=in,dpi=300
    rayy 3in,2in
    rayy 1in, 2 cm, dpi=600

    Extra keyword arguments get passed on to the normal ray command.

    Units can be 'in' or 'cm'.

    For backwards compatibility, the conversion to dpi (or dots per
    centimeter) is only performed when dpi is specified.
    """
    if type(dpi) in [type('')]: dpi = int(dpi)
    in_per_cm = 0.393700787
    def todots(x,units,dpi):
        if type(x) in [type('')]:
            x = x.lower()
            if 'in' in x:
                units = 'in'
            elif 'cm' in x:
                units = 'cm'
            x = float(x.replace(units,'').strip())
        if (dpi == -1):
            return x
        if units ==   'cm':   x = x * in_per_cm
        elif units == 'in': pass
        else:         raise ValueError('Unknown units (%s)'%units)
        print '%s%s at %sdpi'%(x,units,dpi)
        return int(x * dpi)
    # How do we get current width/height of viewport? MainSceneGetSize
perhaps
    # But it doesn't matter, as PyMOL will autoscale internally for us when
given -1.
    try:
        width,height = todots(width,units,dpi),todots(height,units,dpi)
    except ValueError:
        print "Unknown units"
        return
    print 'width',width,'height',height
    cmd.ray(width=width,height=height,**kwargs)
cmd.extend('rayy',rayy)


On Thu, Jan 21, 2010 at 2:39 PM, Michael Lerner <
mgl...@gm... <mglerner%2Bs...@gm...>> wrote:

> I think this works. It handles different units (in and cm). If you leave
> out width or height, it gets scaled correctly. If you  leave them both out,
> you get whatever the current viewport size is (is there something better?).
>
> #!/usr/bin/env pymol
>
> from pymol import cmd
>
> def rayy(width=-1,height=-1,dpi=300,units='in',**kwargs):
>     """
>     Slightly better version of the ray command.
>     You can specify width and height in the units of your choice, e.g.
>
>     rayy 3,2,units=in,dpi=300
>     rayy 3in,2in
>     rayy 1in, 2 cm, dpi=600
>
>     Extra keyword arguments get passed on to the normal ray command.
>     """
>     if type(dpi) in [type('')]: dpi = int(dpi)
>     in_per_cm = 0.393700787
>     def todots(x,units,dpi):
>         if type(x) in [type('')]:
>             x = x.lower()
>             if 'in' in x:   units = 'in'
>             elif 'cm' in x: units = 'cm'
>             x = float(x.replace(units,'').strip())
>         if units ==   'cm':   x = x * in_per_cm
>         elif units == 'in': pass
>         else:         raise ValueError('Unknown units (%s)'%units)
>         print x,units,dpi
>         return int(x * dpi)
>     # How do we get current width/height of viewport? MainSceneGetSize
> perhaps
>     # But it doesn't matter, as PyMOL will autoscale internally for us.
>     try:
>         height,width = todots(height,units,dpi),todots(width,units,dpi)
>     except ValueError:
>         print "Unknown units"
>         return
>     print 'width',width,'height',height
>     cmd.ray(width=width,height=height,**kwargs)
>     #cmd.png(self.filename.getvalue(), dpi=int(self.dpi.getvalue()))
> cmd.extend('rayy',rayy)
>
> On Thu, Jan 21, 2010 at 11:52 AM, Michael Lerner <
> mgl...@gm... <mglerner%2Bs...@gm...>> wrote:
>
>> The ray command bugs me, so I'll take a stab at improving it this
>> afternoon.
>>
>> Can someone tell me how to get the size of the current viewport?
>>
>> This solution:
>>
>> http://www.mail-archive.com/pym...@li.../msg05888.html
>>
>> width,height = cmd.get_session()['main'][0:2]
>>
>>
>> doesn't seem to work for me:
>>
>> PyMOL>print sorted(cmd.get_session().keys())
>> ['cache', 'color_ext', 'colors', 'editor', 'movie', 'names', 'scene_dict',
>> 'scene_order', 'selector_secrets', 'session', 'settings', 'unique_settings',
>> 'version', 'view', 'view_dict', 'wizard']
>>
>> -Michael
>>
>> On Wed, Jan 20, 2010 at 3:54 PM, Tsjerk Wassenaar <ts...@gm...>wrote:
>>
>>> Hi,
>>>
>>> > ray 10cm, 20cm, dpi=300?
>>> > ray 2.5in, 5in, dpi=300?
>>>
>>> I'd slightly modify that to read:
>>>
>>> ray 10,10,units=cm,resolution=300
>>>
>>> where units can be pixels (default), cm, inches, meters, yards,
>>> lightyears...
>>>
>>> Cheers,
>>>
>>> Tsjerk
>>>
>>>
>>> --
>>> Tsjerk A. Wassenaar, Ph.D.
>>>
>>> Computational Chemist
>>> Medicinal Chemist
>>> Neuropharmacologist
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Throughout its 18-year history, RSA Conference consistently attracts the
>>> world's best and brightest in the field, creating opportunities for
>>> Conference
>>> attendees to learn about information security's most important issues
>>> through
>>> interactions with peers, luminaries and emerging and established
>>> companies.
>>> http://p.sf.net/sfu/rsaconf-dev2dev
>>> _______________________________________________
>>> PyMOL-users mailing list (PyM...@li...)
>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>>> Archives: http://www.mail-archive.com/pym...@li...
>>>
>>
>>
>>
>> --
>> 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)
>>
>
>
>
> --
> 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)
>



-- 
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)

I think this works. It handles different units (in and cm). If you leave out
width or height, it gets scaled correctly. If you  leave them both out, you
get whatever the current viewport size is (is there something better?).

#!/usr/bin/env pymol

from pymol import cmd

def rayy(width=-1,height=-1,dpi=300,units='in',**kwargs):
    """
    Slightly better version of the ray command.
    You can specify width and height in the units of your choice, e.g.

    rayy 3,2,units=in,dpi=300
    rayy 3in,2in
    rayy 1in, 2 cm, dpi=600

    Extra keyword arguments get passed on to the normal ray command.
    """
    if type(dpi) in [type('')]: dpi = int(dpi)
    in_per_cm = 0.393700787
    def todots(x,units,dpi):
        if type(x) in [type('')]:
            x = x.lower()
            if 'in' in x:   units = 'in'
            elif 'cm' in x: units = 'cm'
            x = float(x.replace(units,'').strip())
        if units ==   'cm':   x = x * in_per_cm
        elif units == 'in': pass
        else:         raise ValueError('Unknown units (%s)'%units)
        print x,units,dpi
        return int(x * dpi)
    # How do we get current width/height of viewport? MainSceneGetSize
perhaps
    # But it doesn't matter, as PyMOL will autoscale internally for us.
    try:
        height,width = todots(height,units,dpi),todots(width,units,dpi)
    except ValueError:
        print "Unknown units"
        return
    print 'width',width,'height',height
    cmd.ray(width=width,height=height,**kwargs)
    #cmd.png(self.filename.getvalue(), dpi=int(self.dpi.getvalue()))
cmd.extend('rayy',rayy)

On Thu, Jan 21, 2010 at 11:52 AM, Michael Lerner <
mgl...@gm... <mglerner%2Bs...@gm...>> wrote:

> The ray command bugs me, so I'll take a stab at improving it this
> afternoon.
>
> Can someone tell me how to get the size of the current viewport?
>
> This solution:
> http://www.mail-archive.com/pym...@li.../msg05888.html
>
> width,height = cmd.get_session()['main'][0:2]
>
>
> doesn't seem to work for me:
>
> PyMOL>print sorted(cmd.get_session().keys())
> ['cache', 'color_ext', 'colors', 'editor', 'movie', 'names', 'scene_dict',
> 'scene_order', 'selector_secrets', 'session', 'settings', 'unique_settings',
> 'version', 'view', 'view_dict', 'wizard']
>
> -Michael
>
> On Wed, Jan 20, 2010 at 3:54 PM, Tsjerk Wassenaar <ts...@gm...>wrote:
>
>> Hi,
>>
>> > ray 10cm, 20cm, dpi=300?
>> > ray 2.5in, 5in, dpi=300?
>>
>> I'd slightly modify that to read:
>>
>> ray 10,10,units=cm,resolution=300
>>
>> where units can be pixels (default), cm, inches, meters, yards,
>> lightyears...
>>
>> Cheers,
>>
>> Tsjerk
>>
>>
>> --
>> Tsjerk A. Wassenaar, Ph.D.
>>
>> Computational Chemist
>> Medicinal Chemist
>> Neuropharmacologist
>>
>>
>> ------------------------------------------------------------------------------
>> Throughout its 18-year history, RSA Conference consistently attracts the
>> world's best and brightest in the field, creating opportunities for
>> Conference
>> attendees to learn about information security's most important issues
>> through
>> interactions with peers, luminaries and emerging and established
>> companies.
>> http://p.sf.net/sfu/rsaconf-dev2dev
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
>>
>
>
>
> --
> 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)
>



-- 
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)

The ray command bugs me, so I'll take a stab at improving it this afternoon.

Can someone tell me how to get the size of the current viewport?

This solution:
http://www.mail-archive.com/pym...@li.../msg05888.html

width,height = cmd.get_session()['main'][0:2]


doesn't seem to work for me:

PyMOL>print sorted(cmd.get_session().keys())
['cache', 'color_ext', 'colors', 'editor', 'movie', 'names', 'scene_dict',
'scene_order', 'selector_secrets', 'session', 'settings', 'unique_settings',
'version', 'view', 'view_dict', 'wizard']

-Michael

On Wed, Jan 20, 2010 at 3:54 PM, Tsjerk Wassenaar <ts...@gm...> wrote:

> Hi,
>
> > ray 10cm, 20cm, dpi=300?
> > ray 2.5in, 5in, dpi=300?
>
> I'd slightly modify that to read:
>
> ray 10,10,units=cm,resolution=300
>
> where units can be pixels (default), cm, inches, meters, yards,
> lightyears...
>
> Cheers,
>
> Tsjerk
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> Computational Chemist
> Medicinal Chemist
> Neuropharmacologist
>
>
> ------------------------------------------------------------------------------
> Throughout its 18-year history, RSA Conference consistently attracts the
> world's best and brightest in the field, creating opportunities for
> Conference
> attendees to learn about information security's most important issues
> through
> interactions with peers, luminaries and emerging and established companies.
> http://p.sf.net/sfu/rsaconf-dev2dev
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>



-- 
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)

On Thu, Jan 21, 2010 at 6:10 AM, Schubert, Carsten [PRDUS] <
CSC...@it...> wrote:

> 4) A better density wizard, let's just copy coot and be done with it.
> Ability to dynamically bind density levels or some other properties to
> the scroll-wheel for that matter.
>

+1


> 6) Integration/bundling of wxPython as an alternative to TCL/Tk??
>

Also +1.  Warren mentioned this last year as a possibility for integrating
PyMOL with the Phenix GUI, and in theory support for embedding a PyMOL view
in wxPython is already present.  However, that code appears to be very old
and not maintained - I couldn't get it to work even after updating it to use
the newer wx modules.  I suspect there is not much work to do in order to
resurrect it, but I don't know enough about PyMOL internals, or have time to
learn.  Note that this feature (if it were open-source) would allow anyone
to make a native Mac PyMOL GUI and distribute that, so it isn't something
I'd ask Schrodinger to subsidize.  (If anyone else is interested in helping
figure this out, however, let me know.)

7) Internal FFT routines to be able to read map-coefficients
>

+2.  I believe the CCP4 libraries for this are open-source, so those are one
option.  CCTBX is another (I have tried this and it works), but this will be
a lot more overhead.

Don't forget the PNG command also takes a "ray" argument:

 png fileName, height=X, width=Y, ray=1, dpi=300

PyMOL will resample in that case.  You always get a ray traced file
from that command.

If you do:
  ray 300, 300
  png fileName.ong, height=1000, width=1000

You get a 1000,1000 non-ray traced image.

-- J

On Thu, Jan 21, 2010 at 11:32 AM, Tsjerk Wassenaar <ts...@gm...> wrote:
> Hi,
>
> So what happens if you try it after ray-tracing?
>
> T.
>
> On Thu, Jan 21, 2010 at 5:17 PM, David Hall <li...@co...> wrote:
>> On Thu, Jan 21, 2010 at 9:46 AM, Tsjerk Wassenaar <ts...@gm...> wrote:
>>>
>>> Errm, that only makes sense if the viewport itself is resampled
>>> somehow when you don't do raytracing, but I don't think it is.
>>
>> I'm pretty sure it is resampled when you specify a width or height.  All
>> this below is with 1.2r1 incentive executable, but I'm pretty sure this also
>> occurs on my trunk builds as well.  Maybe this is some new behavior?
>>
>> I do:
>> viewport 600,400
>> png out.png, 800,800
>>
>> The viewport now looks the way it does if I did ray 800,800 (except not ray
>> traced) and I get an 800x800 picture.
>>
>> Another example:
>> png out.png, 10000,10000
>> Scene-Warning: Maximum OpenGL viewport dimension exceeded. ScenePNG: wrote
>> 8192x8192 pixel image to file "out.png".
>>
>> PyMol seems to be saying to me, "I'm sampling an OpenGL viewport with the
>> dimensions you specified to create this png"
>>
>> -David
>>
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> Computational Chemist
> Medicinal Chemist
> Neuropharmacologist
>
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-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

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