pymol-users Mailing List for PyMOL Molecular Graphics System

Hi Bob,

This is probably not the slickest way to do this but  generally I think it is one surface one object, so in a simple case of a peptide bound to a protein, I would select the peptide chain (right click in the viewer) and extract that selection to a new object and then you can generate two separate surfaces.

Hope this helps
Joel

From: Robert Hanson [mailto:ha...@st...]
Sent: Friday, 31 May 2013 6:26 a.m.
To: pymol-users
Subject: [PyMOL] surfaces involving more than one object

PyMOL questions about surfaces:

Simple enough to create a surface for one object. What about for only a portion of the object? How to do each of these?
  -- closed surface ignoring a selected set of atoms
  -- open surface not ignoring any atoms, but also not displaying their part

Is the rule, "One surface, one object"? That is, all atoms involved in a surface must originate from a single object?

Bob

--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900

But as far as I can tell, in the session file, the coordinates are just
numbers -- no reference to atoms. What am I missing?


On Fri, May 31, 2013 at 8:57 AM, Jason Vertrees <
jas...@sc...> wrote:

> Hi Bob,
>
> We added this a year or two ago:
>
> set dynamic_measures, 1
>
> In newer versions of PyMOL this is enabled by default.
>
> Cheers,
>
> -- Jason
>
>
> On Fri, May 31, 2013 at 8:27 AM, Robert Hanson <ha...@st...> wrote:
>
>> Is there a way to tie measurement ends to specific atoms, so that when
>> the structure is tweaked, those measurements update automatically?
>>
>> --
>> Robert M. Hanson
>> Larson-Anderson Professor of Chemistry
>> Chair, Chemistry Department
>> St. Olaf College
>> Northfield, MN
>> http://www.stolaf.edu/people/hansonr
>>
>>
>> If nature does not answer first what we want,
>> it is better to take what answer we get.
>>
>> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Get 100% visibility into Java/.NET code with AppDynamics Lite
>> It's a free troubleshooting tool designed for production
>> Get down to code-level detail for bottlenecks, with <2% overhead.
>> Download for free and get started troubleshooting in minutes.
>> http://p.sf.net/sfu/appdyn_d2d_ap2
>> _______________________________________________
>> 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
> Director of Core Modeling Products
> Schrödinger, Inc.
>
> (e) Jas...@sc...
> (o) +1 (603) 374-7120
>



-- 
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900

Dear all,

I am trying to run the ABPS plugin with PyMOL Version 1.6.0.0 on Ubuntu
12.10. I have compiled pymol from source (
http://www.pymolwiki.org/index.php/Linux_Install).

When running the plugin, I can set the grid, but after clicking on Run
APBS, I get the following error:

Unexpected error: (<type 'exceptions.ImportError'>, ImportError('No module
named pdb2pqr.pdb2pqr',), <traceback object at 0x7fd130771200>)
<type 'exceptions.UnboundLocalError'> Exception in Tk callback
  Function: <function <lambda> at 0x7fd13078e398> (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 "/home/pymol-svn/modules/pmg_tk/startup/apbs_tools.py", line 1036,
in execute
    good = self.generatePqrFile()
  File "/home/pymol-svn/modules/pmg_tk/startup/apbs_tools.py", line 1007,
in generatePqrFile
    good = self._generatePdb2pqrPqrFile()
  File "/home/pymol-svn/modules/pmg_tk/startup/apbs_tools.py", line 1615,
in _generatePdb2pqrPqrFile
    if retval != 0:
<type 'exceptions.UnboundLocalError'>: local variable 'retval' referenced
before assignment

The first line suggests that the pdb2pqr module cannot be loaded. However,
the grid seems to be set okay. Has anybody encountered this error before
and knows how to solve it?

I have also tried the pymol version that can be installed with apt-get, but
same error.

Thanks for any advice!

Best wishes, Tobias.

Hi Bob,

We added this a year or two ago:

set dynamic_measures, 1

In newer versions of PyMOL this is enabled by default.

Cheers,

-- Jason


On Fri, May 31, 2013 at 8:27 AM, Robert Hanson <ha...@st...> wrote:

> Is there a way to tie measurement ends to specific atoms, so that when the
> structure is tweaked, those measurements update automatically?
>
> --
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> Chair, Chemistry Department
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr
>
>
> If nature does not answer first what we want,
> it is better to take what answer we get.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>
>
>
> ------------------------------------------------------------------------------
> Get 100% visibility into Java/.NET code with AppDynamics Lite
> It's a free troubleshooting tool designed for production
> Get down to code-level detail for bottlenecks, with <2% overhead.
> Download for free and get started troubleshooting in minutes.
> http://p.sf.net/sfu/appdyn_d2d_ap2
> _______________________________________________
> 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
Director of Core Modeling Products
Schrödinger, Inc.

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

Is there a way to tie measurement ends to specific atoms, so that when the
structure is tweaked, those measurements update automatically?

-- 
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900

PyMOL questions about surfaces:

Simple enough to create a surface for one object. What about for only a
portion of the object? How to do each of these?

  -- closed surface ignoring a selected set of atoms
  -- open surface not ignoring any atoms, but also not displaying their part

Is the rule, "One surface, one object"? That is, all atoms involved in a
surface must originate from a single object?

Bob

-- 
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900

Hello, PyMOL users,

The driving force behind these last four months of Jmol/JSmol development
has been e-publication. The goal has been to produce a means of
e-publishing working interactive biomolecular models that are ubiquitously
accessible (i.e. no Java, no  WebGL). We achieved that goal for Jmol late
last year, with the introduction of "JSmol" -- a fully HTML5-based
identical renderer for Jmol. See
http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm

Today, I'm letting you all know that we have that for PyMOL as well,
basically. Authors can produce all the beautiful PyMOL images they want for
regular publication purposes and then have them available for general
viewing on a publisher's web site (if that site is so equipped) or on their
own institutional site.

This works because Jmol now has a pretty decent PyMOL session file reader.
It's a work in progress, but we are reproducing our complete set of test
files (104 to date) fully now, with quite a wide variety of features. It's
a work in progress, of course, and we are handling issues as they arise.
But I think one look at http://ispcsrv3.weizmann.ac.il/a2jmolb/browse will
convince you that we have made some pretty significant progress along these
lines.

[That server is having significant issues just this week, so pardon the
"Failed" signs. Those aren't real problems; just some sort of unidentified
server issue at the Weizmann Institute.]

There are some differences in that test set, but they are only cosmetic --
a few sightly different renderings of cartoons, for instance. Jmol, though
it has a PovRAY interface, doesn't interactively do shadows. Translucency
is handled differently. (PyMOL's translucency is object-based; Jmol's
translucency is pixel-based.) The perspective is exact, though, because
both programs use the same perspective model. Morph-type (not scripted)
movies are no problem. Electron density maps are read. Scenes are
cataloged, reproducible, and easily "discovered" by web page based
JavaScript.

Of course, the JavaScript-only non-WebGL version is slower than Java, which
itself is (sometimes perceptively) slower than C++. That's a given. Don't
expect prime performance on your smart phone.

Surface generation, particularly the PyMOL default solvent-excluded
surface, is considerably slower in JavaScript, but we have a way around
that. There's a way of caching the session files in Jmol that allows them
to be displayed essentially instantly, even in JavaScript.

This will be released as Jmol 13.2.0 sometime next week. In the mean time,
if you want to experiment --- realizing that most of you do not do anything
with Jmol right now, right? -- that's understandable --- the link to the
compiled Java and HTML5 versions are:

http://chemapps.stolaf.edu/jmol/jmol-13.1.16_2013.05.30c.zip
(Java, including stand-alone Jmol.jar and JmolData.jar and applet files)

http://chemapps.stolaf.edu/jmol/jsmol.zip
(HTML5/JavaScript and also applet files, with demo pages)

I'm hoping this will interest some of you, and you might get involved in
future efforts as we develop this connection further.

Bob Hanson

-- 
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900

Hi Jacob,

Use the result from cmd.cealign and an "alignment object". Here's an
example:


# fetch two proteins

fetch 1cll 1ggz, async=0

# use a python block

python

# cealign the two structures and create a corresponding "alignment" object

result = cmd.cealign("1cll", "1ggz", object="aln")

# print out the values from the result

print result.keys()
for key in result:
  print "%s: %s" % (key, result[key])

# end the python block

python end

# now access those atoms in the alignment

select 1cll and aln

# or count the atoms in 1ggz and aln

print cmd.count_atoms("1ggz and aln")

Cheers,

-- Jason




On Thu, May 30, 2013 at 2:07 PM, Jacob Pessin
<Jac...@ei...>wrote:

>  Hi all,
>
> can anyone suggest a straightforward way of collecting the cealign output
> in bulk, (RMS, #atoms compared), using alignto doesn't even print this to
> screen (I tried adjusting quiet=, to no avail).
>
>
> thanks in advance
>
> jacob
>
> <" rel="nofollow">https://owa.einstein.yu.edu/owa/?ae=Item&a=Open&t=IPM.Note&id=RgAAAADDT2ZJXulBTI8H5G%2fACk3UBwBPSkr8RdqeRa4tSfsjXcRlAAAASCziAABPSkr8RdqeRa4tSfsjXcRlAAAPdWInAAAA&s=Draft&pspid=_1369930182703_402002554#>
> <" rel="nofollow">https://owa.einstein.yu.edu/owa/?ae=Item&a=Open&t=IPM.Note&id=RgAAAADDT2ZJXulBTI8H5G%2fACk3UBwBPSkr8RdqeRa4tSfsjXcRlAAAASCziAABPSkr8RdqeRa4tSfsjXcRlAAAPdWInAAAA&s=Draft&pspid=_1369930182703_402002554#>
>
>
> ------------------------------------------------------------------------------
> Introducing AppDynamics Lite, a free troubleshooting tool for Java/.NET
> Get 100% visibility into your production application - at no cost.
> Code-level diagnostics for performance bottlenecks with <2% overhead
> Download for free and get started troubleshooting in minutes.
> http://p.sf.net/sfu/appdyn_d2d_ap1
> _______________________________________________
> 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
Director of Core Modeling Products
Schrödinger, Inc.

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

Hi all,

can anyone suggest a straightforward way of collecting the cealign output in bulk, (RMS, #atoms compared), using alignto doesn't even print this to screen (I tried adjusting quiet=, to no avail).


thanks in advance

jacob
<" rel="nofollow">https://owa.einstein.yu.edu/owa/?ae=Item&a=Open&t=IPM.Note&id=RgAAAADDT2ZJXulBTI8H5G%2fACk3UBwBPSkr8RdqeRa4tSfsjXcRlAAAASCziAABPSkr8RdqeRa4tSfsjXcRlAAAPdWInAAAA&s=Draft&pspid=_1369930182703_402002554#>
<" rel="nofollow">https://owa.einstein.yu.edu/owa/?ae=Item&a=Open&t=IPM.Note&id=RgAAAADDT2ZJXulBTI8H5G%2fACk3UBwBPSkr8RdqeRa4tSfsjXcRlAAAASCziAABPSkr8RdqeRa4tSfsjXcRlAAAPdWInAAAA&s=Draft&pspid=_1369930182703_402002554#>

Hi Thomas,

Probably something like this should do something close to what you need:

sed -n '/^\(ATOM\|HETATM\)/s/^.\{16\}\(.\{10\}\)/\1 \0/p' file.pdb | sort
-n -k 3 | cut -b 11-

Hope it helps,

Tsjerk



On Thu, May 30, 2013 at 10:21 AM, Thomas Evangelidis <te...@gm...>wrote:

> Dear PyMOL users/developers,
>
> Is there any way to rearrange the atom records in a .pdb file according to
> their residue ID? I have run Vina with flexible sidechains and then
> concatenated the rigid receptor part with the sidechain conformations for
> each pose. That resulted to .pdb files where the backbone atoms (apart from
> Ca) occur in the correct order but the flexible sidechain atoms are at the
> end of the file. That leads to some problems in visualization and analysis
> of the protein-ligand complexes that I'd like to overcome. If anyone know
> how to fix that problem either with PyMOL or any other program please let
> me know.
>
> thanks,
> Thomas
>
>
> --
>
> ======================================================================
>
> Thomas Evangelidis
>
> PhD student
> University of Athens
> Faculty of Pharmacy
> Department of Pharmaceutical Chemistry
> Panepistimioupoli-Zografou
> 157 71 Athens
> GREECE
>
> email: te...@ph...
>
>           te...@gm...
>
>
> website: https://sites.google.com/site/thomasevangelidishomepage/
>
>
>
>
> ------------------------------------------------------------------------------
> Introducing AppDynamics Lite, a free troubleshooting tool for Java/.NET
> Get 100% visibility into your production application - at no cost.
> Code-level diagnostics for performance bottlenecks with <2% overhead
> Download for free and get started troubleshooting in minutes.
> http://p.sf.net/sfu/appdyn_d2d_ap1
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>



-- 
Tsjerk A. Wassenaar, Ph.D.

Dear PyMOL users/developers,

Is there any way to rearrange the atom records in a .pdb file according to
their residue ID? I have run Vina with flexible sidechains and then
concatenated the rigid receptor part with the sidechain conformations for
each pose. That resulted to .pdb files where the backbone atoms (apart from
Ca) occur in the correct order but the flexible sidechain atoms are at the
end of the file. That leads to some problems in visualization and analysis
of the protein-ligand complexes that I'd like to overcome. If anyone know
how to fix that problem either with PyMOL or any other program please let
me know.

thanks,
Thomas


-- 

======================================================================

Thomas Evangelidis

PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
Panepistimioupoli-Zografou
157 71 Athens
GREECE

email: te...@ph...

          te...@gm...


website: https://sites.google.com/site/thomasevangelidishomepage/

Dear Pymol Users,

I am very pleased with my Debian system until today I found pymol cannot
run scripts, which work fine on pymol-win.

This is the initialization information:
 Detected OpenGL version 2.0 or greater. Shaders available.
 Detected GLSL version 4.20.
 Adapting to Quadro hardware.
 Detected 8 CPU cores.  Enabled multithreaded rendering.

The message is like this:
 Scene: view updated.
*** glibc detected *** /usr/bin/python: realloc(): invalid next size:
0x0000000003bec340 ***
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(+0x76d76)[0x7f616dcb9d76]
/lib/x86_64-linux-gnu/libc.so.6(+0x7c94c)[0x7f616dcbf94c]
/lib/x86_64-linux-gnu/libc.so.6(realloc+0xf0)[0x7f616dcbfc60]
/usr/lib/x86_64-linux-gnu/libGL.so.1(+0xa90eb)[0x7f616c6750eb]
======= Memory map: ========
00400000-00658000 r-xp 00000000 08:0a 141416
/usr/bin/python2.7
00857000-00858000 r--p 00257000 08:0a 141416
/usr/bin/python2.7
00858000-008c1000 rw-p 00258000 08:0a 141416
/usr/bin/python2.7
008c1000-008d3000 rw-p 00000000 00:00 0
0246a000-03fe6000 rw-p 00000000 00:00 0
[heap]
401b2000-401b4000 r-xs 00000000 08:0a 1849786
/tmp/glHSIYOE (deleted)
401eb000-401ed000 r-xs 00000000 08:0a 1849795
/tmp/glOTvv4v (deleted)
403b2000-403b4000 r-xs 00000000 08:0a 1849785
/tmp/glM0vw4m (deleted)
40b01000-40b03000 r-xs 00000000 08:0a 1849787
/tmp/glgyMszW (deleted)
40ee6000-40ee8000 r-xs 00000000 08:0a 1849788
/tmp/gldriYje (deleted)
41d62000-41de0000 rw-p 00000000 00:00 0
7f615c000000-7f615c021000 rw-p 00000000 00:00 0
7f615c021000-7f6160000000 ---p 00000000 00:00 0
7f6162573000-7f61625c6000 rw-p 00000000 00:00 0
7f6162793000-7f616279b000 rw-p 00000000 00:00 0
7f6162b05000-7f6162b0d000 rw-p 00000000 00:00 0
7f6162c6d000-7f6162da2000 rw-p 00000000 00:00 0
7f6162ecf000-7f6162ed7000 r-xp 00000000 08:0a 141573
/usr/lib/python2.7/lib-dynload/_ssl.so
7f6162ed7000-7f61630d6000 ---p 00008000 08:0a 141573
/usr/lib/python2.7/lib-dynload/_ssl.so
7f61630d6000-7f61630d7000 r--p 00007000 08:0a 141573
/usr/lib/python2.7/lib-dynload/_ssl.so
7f61630d7000-7f61630d8000 rw-p 00008000 08:0a 141573
/usr/lib/python2.7/lib-dynload/_ssl.so
7f61630d8000-7f61630e3000 r-xp 00000000 08:0a 2490381
/lib/x86_64-linux-gnu/libnss_files-2.13.so
7f61630e3000-7f61632e2000 ---p 0000b000 08:0a 2490381
/lib/x86_64-linux-gnu/libnss_files-2.13.so
7f61632e2000-7f61632e3000 r--p 0000a000 08:0a 2490381
/lib/x86_64-linux-gnu/libnss_files-2.13.so
7f61632e3000-7f61632e4000 rw-p 0000b000 08:0a 2490381
/lib/x86_64-linux-gnu/libnss_files-2.13.so
7f61632e4000-7f61632ee000 r-xp 00000000 08:0a 2490393
/lib/x86_64-linux-gnu/libnss_nis-2.13.so
7f61632ee000-7f61634ed000 ---p 0000a000 08:0a 2490393
/lib/x86_64-linux-gnu/libnss_nis-2.13.so
7f61634ed000-7f61634ee000 r--p 00009000 08:0a 2490393
/lib/x86_64-linux-gnu/libnss_nis-2.13.so
7f61634ee000-7f61634ef000 rw-p 0000a000 08:0a 2490393
/lib/x86_64-linux-gnu/libnss_nis-2.13.so
7f61634ef000-7f61634f6000 r-xp 00000000 08:0a 2490383
/lib/x86_64-linux-gnu/libnss_compat-2.13.so
7f61634f6000-7f61636f5000 ---p 00007000 08:0a 2490383
/lib/x86_64-linux-gnu/libnss_compat-2.13.so
7f61636f5000-7f61636f6000 r--p 00006000 08:0a 2490383
/lib/x86_64-linux-gnu/libnss_compat-2.13.so
7f61636f6000-7f61636f7000 rw-p 00007000 08:0a 2490383
/lib/x86_64-linux-gnu/libnss_compat-2.13.so
7f61636f7000-7f61636f8000 ---p 00000000 00:00 0
7f61636f8000-7f6163ef8000 rw-p 00000000 00:00 0
7f6163ef8000-7f6163ef9000 ---p 00000000 00:00 0
7f6163ef9000-7f61646f9000 rw-p 00000000 00:00 0
7f61646f9000-7f6164720000 r-xp 00000000 08:0a 2494127
/lib/x86_64-linux-gnu/libexpat.so.1.6.0
7f6164720000-7f6164920000 ---p 00027000 08:0a 2494127
/lib/x86_64-linux-gnu/libexpat.so.1.6.0
7f6164920000-7f6164922000 r--p 00027000 08:0a 2494127
/lib/x86_64-linux-gnu/libexpat.so.1.6.0
7f6164922000-7f6164923000 rw-p 00029000 08:0a 2494127
/lib/x86_64-linux-gnu/libexpat.so.1.6.0
7f6164923000-7f616492c000 r-xp 00000000 08:0a 139229
/usr/lib/x86_64-linux-gnu/libXrender.so.1.3.0
7f616492c000-7f6164b2b000 ---p 00009000 08:0a 139229
/usr/lib/x86_64-linux-gnu/libXrender.so.1.3.0
7f6164b2b000-7f6164b2c000 rw-p 00008000 08:0a 139229
/usr/lib/x86_64-linux-gnu/libXrender.so.1.3.0
7f6164b2c000-7f6164b61000 r-xp 00000000 08:0a 138977
/usr/lib/x86_64-linux-gnu/libfontconfig.so.1.5.0
7f6164b61000-7f6164d61000 ---p 00035000 08:0a 138977
/usr/lib/x86_64-linux-gnu/libfontconfig.so.1.5.0
7f6164d61000-7f6164d62000 r--p 00035000 08:0a 138977
/usr/lib/x86_64-linux-gnu/libfontconfig.so.1.5.0
7f6164d62000-7f6164d63000 rw-p 00036000 08:0a 138977
/usr/lib/x86_64-linux-gnu/libfontconfig.so.1.5.0
7f6164d63000-7f6164d77000 r-xp 00000000 08:0a 139675
/usr/lib/x86_64-linux-gnu/libXft.so.2.3.1
7f6164d77000-7f6164f77000 ---p 00014000 08:0a 139675
/usr/lib/x86_64-linux-gnu/libXft.so.2.3.1
7f6164f77000-7f6164f78000 rw-p 00014000 08:0a 139675
/usr/lib/x86_64-linux-gnu/libXft.so.2.3.1
7f6164f78000-7f6164f7a000 r-xp 00000000 08:0a 146371
/usr/lib/x86_64-linux-gnu/libXss.so.1.0.0
7f6164f7a000-7f616517a000 ---p 00002000 08:0a 146371
/usr/lib/x86_64-linux-gnu/libXss.so.1.0.0
7f616517a000-7f616517b000 rw-p 00002000 08:0a 146371
/usr/lib/x86_64-linux-gnu/libXss.so.1.0.0
7f616517b000-7f6165190000 r-xp 00000000 08:0a 2490391
/lib/x86_64-linux-gnu/libnsl-2.13.so
7f6165190000-7f616538f000 ---p 00015000 08:0a 2490391
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7f616538f000-7f6165390000 r--p 00014000 08:0a 2490391
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7f6165390000-7f6165391000 rw-p 00015000 08:0a 2490391
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7f6165391000-7f6165393000 rw-p 00000000 00:00 0
7f6165393000-7f61654a7000 r-xp 00000000 08:0a 161724
/usr/lib/libtcl8.5.so.0
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7f61656aa000-7f61656b2000 rw-p 00117000 08:0a 161724
/usr/lib/libtcl8.5.so.0
7f61656b2000-7f61656b3000 rw-p 00000000 00:00 0
7f61656b3000-7f61657de000 r-xp 00000000 08:0a 161729
/usr/lib/libtk8.5.so.0
7f61657de000-7f61659dd000 ---p 0012b000 08:0a 161729
/usr/lib/libtk8.5.so.0
7f61659dd000-7f61659e8000 r--p 0012a000 08:0a 161729
/usr/lib/libtk8.5.so.0
7f61659e8000-7f61659fc000 rw-p 00135000 08:0a 161729
/usr/lib/libtk8.5.so.0
7f61659fc000-7f61659fd000 rw-p 00000000 00:00 0
7f61659fd000-7f6165b00000 r-xp 00000000 08:0a 161731
/usr/lib/libBLT.2.4.so.8.5
7f6165b00000-7f6165d00000 ---p 00103000 08:0a 161731
/usr/lib/libBLT.2.4.so.8.5
7f6165d00000-7f6165d1d000 rw-p 00103000 08:0a 161731
/usr/lib/libBLT.2.4.so.8.5
7f6165d1d000-7f6165d1e000 rw-p 00000000 00:00 0
7f6165d1e000-7f6165d2a000 r-xp 00000000 08:0a 161760
/usr/lib/python2.7/lib-dynload/_tkinter.so
7f6165d2a000-7f6165f29000 ---p 0000c000 08:0a 161760
/usr/lib/python2.7/lib-dynload/_tkinter.so
7f6165f29000-7f6165f2a000 r--p 0000b000 08:0a 161760
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7f6165f2a000-7f6165f2c000 rw-p 0000c000 08:0a 161760
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7f6165f2c000-7f616612c000 rw-s 165d2f000 00:05 10285
/dev/nvidia0
7f616612c000-7f6166235000 rw-p 00000000 00:00 0
7f6166327000-7f616632f000 rw-p 00000000 00:00 0
7f616632f000-7f6166336000 r--s 00000000 08:0a 131134
/usr/lib/x86_64-linux-gnu/gconv/gconv-modules.cache
7f6166336000-7f6166347000 rw-p 00000000 00:00 0
7f6166347000-7f6166747000 rw-s 14fcfb000 00:05 10285
/dev/nvidia0
7f6166747000-7f6166b47000 rw-s 165fe6000 00:05 10285
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7f6166b47000-7f6166f47000 rw-s 14dc8b000 00:05 10285
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7f6166f4b000-7f6166f6b000 rw-s e00c0000 00:05 10285
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7f616702c000-7f6167193000 rw-p 00000000 00:00 0
7f6167193000-7f61671b2000 r-xp 00000000 08:0a 141899
/usr/lib/python2.7/lib-dynload/_io.so
7f61671b2000-7f61673b1000 ---p 0001f000 08:0a 141899
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7f61673b1000-7f61673b2000 r--p 0001e000 08:0a 141899
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7f61673b2000-7f61673bb000 rw-p 0001f000 08:0a 141899
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7f61673bb000-7f616747c000 rw-p 00000000 00:00 0
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7f6167633000-7f6167832000 ---p 001b7000 08:0a 135409
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7f616784d000-7f616785c000 rw-p 001d1000 08:0a 135409
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7f616785c000-7f6167860000 rw-p 00000000 00:00 0
7f6167860000-7f61678b6000 r-xp 00000000 08:0a 135410
/usr/lib/x86_64-linux-gnu/libssl.so.1.0.0
7f61678b6000-7f6167ab5000 ---p 00056000 08:0a 135410
/usr/lib/x86_64-linux-gnu/libssl.so.1.0.0
7f6167ab5000-7f6167ab8000 r--p 00055000 08:0a 135410
/usr/lib/x86_64-linux-gnu/libssl.so.1.0.0
7f6167ab8000-7f6167abf000 rw-p 00058000 08:0a 135410
/usr/lib/x86_64-linux-gnu/libssl.so.1.0.0
7f6167abf000-7f6167ac2000 r-xp 00000000 08:0a 141574
/usr/lib/python2.7/lib-dynload/_hashlib.so
7f6167ac2000-7f6167cc2000 ---p 00003000 08:0a 141574
/usr/lib/python2.7/lib-dynload/_hashlib.so
7f6167cc2000-7f6167cc3000 r--p 00003000 08:0a 141574
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7f6167cc3000-7f6167cc4000 rw-p 00004000 08:0a 141574
/usr/lib/python2.7/lib-dynload/_hashlib.so
7f6167cc4000-7f6167d85000 rw-p 00000000 00:00 0
7f6167d85000-7f6167d89000 r-xp 00000000 08:0a 2490437
/lib/x86_64-linux-gnu/libuuid.so.1.3.0
7f6167d89000-7f6167f88000 ---p 00004000 08:0a 2490437
/lib/x86_64-linux-gnu/libuuid.so.1.3.0
7f6167f88000-7f6167f89000 r--p 00003000 08:0a 2490437
/lib/x86_64-linux-gnu/libuuid.so.1.3.0
7f6167f89000-7f6167f8a000 rw-p 00004000 08:0a 2490437
/lib/x86_64-linux-gnu/libuuid.so.1.3.0
7f6167f8a000-7f6167fa1000 r-xp 00000000 08:0a 141031
/usr/lib/x86_64-linux-gnu/libICE.so.6.3.0
7f6167fa1000-7f61681a0000 ---p 00017000 08:0a 141031
/usr/lib/x86_64-linux-gnu/libICE.so.6.3.0
7f61681a0000-7f61681a2000 rw-p 00016000 08:0a 141031
/usr/lib/x86_64-linux-gnu/libICE.so.6.3.0
7f61681a2000-7f61681a5000 rw-p 00000000 00:00 0
7f61681a5000-7f61681ac000 r-xp 00000000 08:0a 141033
/usr/lib/x86_64-linux-gnu/libSM.so.6.0.1
7f61681ac000-7f61683ab000 ---p 00007000 08:0a 141033
/usr/lib/x86_64-linux-gnu/libSM.so.6.0.1
7f61683ab000-7f61683ac000 rw-p 00006000 08:0a 141033
/usr/lib/x86_64-linux-gnu/libSM.so.6.0.1Aborted

Does anybody have any ideas?

Thank you so much!

Best,
Chen

Hi Yarrow,

I've played with POV-Ray for years now on and off. The reasons to use POV-Ray are mostly for transparency and cool shadows. However, I have found that for most renders, the engine in PyMOL or those in VMD produce more intelligible and intuitive pictures than POV-Ray, even though the shadowing and transparency calculations in POV-Ray are more sophisticated and "accurate".

By all means, play with POV-Ray, but it is a deep rabbit hole that may take more time than you may eventually find it will be worth.

FWIW,
Darrell 


Darrell Hurt, Ph.D.
Section Head, Computational Biology
Bioinformatics and Computational Biosciences Branch (BCBB)
OCICB/OSMO/OD/NIAID/NIH

31 Center Drive, Room 3B62B, MSC 2135
Bethesda, MD 20892-2135

Office  301-402-0095
Mobile 301-758-3559
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----- Original Message -----
From: Yarrow Madrona [mailto:ama...@uc...]
Sent: Wednesday, May 29, 2013 01:41 PM
To: Patrice Peterson <pat...@st...>
Cc: pym...@li... <pym...@li...>
Subject: Re: [PyMOL] internal cavity lighting

Thanks Patrice,

I have used VMD mostly to look at trajectories. I should delve into in a
bit more. I really like having a one stop-shop for illustration which is
why I like pymol. However, I have heard a lot about POV-ray and want to
explore it. I have also heard that it is a "black-hole" and very
difficult. Still maybe worth it.

-Yarrow


> On 13-05-28 14:11, Yarrow Madrona wrote:
>> Hi,
>>
>> I saw a post on this sight a while back about how to move the
>> lighting.  However, I have not seen any information on how to change
>> the lighting of an internal cavity. I want the internal cavity to
>> appear darker as it would be more realistic. However, it is almost
>> like there is a light source coming from inside the object that
>> brightens it up.
>>
>> Does anyone know how to change the internal lighting of a cavity when
>> shown in surface representation?
>>
>> Thanks.
>
> Hey,
>
> What you probably want is some kind of ambient occlusion. The tachyon
> rendering library (which is used with VMD) can do that. However, you can
> get a similar effect in PyMOL using the POV-Ray renderer with
> appropriate radiosity settings. I'm using a modified make_pov.py script
> to do something similar [1], but the POV-Ray settings are not yet
> finalized (I'm very new to POV-Ray myself). I'd also suggest using
> POV-Ray 3.7 to allow the use of multiple cores, as radiosity can
> increase rendering time quite significantly.
>
> The file I posted does not yet have the correct field of view. I'll
> update the Gist once I've found the correct value.
>
> Cheers,
> Patrice
>
> [1] https://gist.github.com/runiq/5669624
>
>>--
>>Yarrow Madrona
>>
>>Graduate Student
>>Molecular Biology and Biochemistry Dept.
>>University of California, Irvine
>>Natural Sciences I, Rm 2403
>>Irvine, CA 92697
> ------------------------------------------------------------------------------
> Introducing AppDynamics Lite, a free troubleshooting tool for Java/.NET
> Get 100% visibility into your production application - at no cost.
> Code-level diagnostics for performance bottlenecks with <2% overhead
> Download for free and get started troubleshooting in minutes.
> http://p.sf.net/sfu/appdyn_d2d_ap1_______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...


-- 
Yarrow Madrona

Graduate Student
Molecular Biology and Biochemistry Dept.
University of California, Irvine
Natural Sciences I, Rm 2403
Irvine, CA 92697




------------------------------------------------------------------------------
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Get 100% visibility into your production application - at no cost.
Code-level diagnostics for performance bottlenecks with <2% overhead
Download for free and get started troubleshooting in minutes.
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_______________________________________________
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Thanks Patrice,

I have used VMD mostly to look at trajectories. I should delve into in a
bit more. I really like having a one stop-shop for illustration which is
why I like pymol. However, I have heard a lot about POV-ray and want to
explore it. I have also heard that it is a "black-hole" and very
difficult. Still maybe worth it.

-Yarrow


> On 13-05-28 14:11, Yarrow Madrona wrote:
>> Hi,
>>
>> I saw a post on this sight a while back about how to move the
>> lighting.  However, I have not seen any information on how to change
>> the lighting of an internal cavity. I want the internal cavity to
>> appear darker as it would be more realistic. However, it is almost
>> like there is a light source coming from inside the object that
>> brightens it up.
>>
>> Does anyone know how to change the internal lighting of a cavity when
>> shown in surface representation?
>>
>> Thanks.
>
> Hey,
>
> What you probably want is some kind of ambient occlusion. The tachyon
> rendering library (which is used with VMD) can do that. However, you can
> get a similar effect in PyMOL using the POV-Ray renderer with
> appropriate radiosity settings. I'm using a modified make_pov.py script
> to do something similar [1], but the POV-Ray settings are not yet
> finalized (I'm very new to POV-Ray myself). I'd also suggest using
> POV-Ray 3.7 to allow the use of multiple cores, as radiosity can
> increase rendering time quite significantly.
>
> The file I posted does not yet have the correct field of view. I'll
> update the Gist once I've found the correct value.
>
> Cheers,
> Patrice
>
> [1] https://gist.github.com/runiq/5669624
>
>>--
>>Yarrow Madrona
>>
>>Graduate Student
>>Molecular Biology and Biochemistry Dept.
>>University of California, Irvine
>>Natural Sciences I, Rm 2403
>>Irvine, CA 92697
> ------------------------------------------------------------------------------
> Introducing AppDynamics Lite, a free troubleshooting tool for Java/.NET
> Get 100% visibility into your production application - at no cost.
> Code-level diagnostics for performance bottlenecks with <2% overhead
> Download for free and get started troubleshooting in minutes.
> http://p.sf.net/sfu/appdyn_d2d_ap1_______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...


-- 
Yarrow Madrona

Graduate Student
Molecular Biology and Biochemistry Dept.
University of California, Irvine
Natural Sciences I, Rm 2403
Irvine, CA 92697

Thanks Thomas!

This is exactly what I was looking for.

-Yarrow


> Hi Yarrow and Patrice,
>
> PyMOL introduced ambient occlusion in version 1.5.0 for surface
> rendering. Try this:
>
> fetch 1rx1, async=0
> as surface
> set ambient_occlusion_mode
>
> If you are a pymol sponsor, visit this page:
> http://pymol.org/dsc/dokuwiki/doku.php?id=media:ambient_occlusion
>
> Hope that helps.
>
> Cheers,
>   Thomas
>
> Patrice Peterson wrote, On 05/29/13 13:37:
>> On 13-05-28 14:11, Yarrow Madrona wrote:
>>> Hi,
>>>
>>> I saw a post on this sight a while back about how to move the
>>> lighting.  However, I have not seen any information on how to change
>>> the lighting of an internal cavity. I want the internal cavity to
>>> appear darker as it would be more realistic. However, it is almost
>>> like there is a light source coming from inside the object that
>>> brightens it up.
>>>
>>> Does anyone know how to change the internal lighting of a cavity when
>>> shown in surface representation?
>>>
>>> Thanks.
>>
>> Hey,
>>
>> What you probably want is some kind of ambient occlusion. The tachyon
>> rendering library (which is used with VMD) can do that. However, you can
>> get a similar effect in PyMOL using the POV-Ray renderer with
>> appropriate radiosity settings. I'm using a modified make_pov.py script
>> to do something similar [1], but the POV-Ray settings are not yet
>> finalized (I'm very new to POV-Ray myself). I'd also suggest using
>> POV-Ray 3.7 to allow the use of multiple cores, as radiosity can
>> increase rendering time quite significantly.
>>
>> The file I posted does not yet have the correct field of view. I'll
>> update the Gist once I've found the correct value.
>>
>> Cheers,
>> Patrice
>>
>> [1] https://gist.github.com/runiq/5669624
>>
>>> --
>>> Yarrow Madrona
>>>
>>> Graduate Student
>>> Molecular Biology and Biochemistry Dept.
>>> University of California, Irvine
>>> Natural Sciences I, Rm 2403
>>> Irvine, CA 92697
>
> --
> Thomas Holder
> PyMOL Developer
> Schrödinger Contractor
>
> ------------------------------------------------------------------------------
> Introducing AppDynamics Lite, a free troubleshooting tool for Java/.NET
> Get 100% visibility into your production application - at no cost.
> Code-level diagnostics for performance bottlenecks with <2% overhead
> Download for free and get started troubleshooting in minutes.
> http://p.sf.net/sfu/appdyn_d2d_ap1
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>
>


-- 
Yarrow Madrona

Graduate Student
Molecular Biology and Biochemistry Dept.
University of California, Irvine
Natural Sciences I, Rm 2403
Irvine, CA 92697

Hi Yarrow and Patrice,

PyMOL introduced ambient occlusion in version 1.5.0 for surface
rendering. Try this:

fetch 1rx1, async=0
as surface
set ambient_occlusion_mode

If you are a pymol sponsor, visit this page:
http://pymol.org/dsc/dokuwiki/doku.php?id=media:ambient_occlusion

Hope that helps.

Cheers,
  Thomas

Patrice Peterson wrote, On 05/29/13 13:37:
> On 13-05-28 14:11, Yarrow Madrona wrote:
>> Hi,
>>
>> I saw a post on this sight a while back about how to move the
>> lighting.  However, I have not seen any information on how to change
>> the lighting of an internal cavity. I want the internal cavity to
>> appear darker as it would be more realistic. However, it is almost
>> like there is a light source coming from inside the object that
>> brightens it up.
>>
>> Does anyone know how to change the internal lighting of a cavity when
>> shown in surface representation?
>>
>> Thanks.
> 
> Hey,
> 
> What you probably want is some kind of ambient occlusion. The tachyon
> rendering library (which is used with VMD) can do that. However, you can
> get a similar effect in PyMOL using the POV-Ray renderer with
> appropriate radiosity settings. I'm using a modified make_pov.py script
> to do something similar [1], but the POV-Ray settings are not yet
> finalized (I'm very new to POV-Ray myself). I'd also suggest using
> POV-Ray 3.7 to allow the use of multiple cores, as radiosity can
> increase rendering time quite significantly.
> 
> The file I posted does not yet have the correct field of view. I'll
> update the Gist once I've found the correct value.
> 
> Cheers,
> Patrice
> 
> [1] https://gist.github.com/runiq/5669624
> 
>> -- 
>> Yarrow Madrona
>>
>> Graduate Student
>> Molecular Biology and Biochemistry Dept.
>> University of California, Irvine
>> Natural Sciences I, Rm 2403
>> Irvine, CA 92697

-- 
Thomas Holder
PyMOL Developer
Schrödinger Contractor

On 13-05-28 14:11, Yarrow Madrona wrote:
> Hi,
> 
> I saw a post on this sight a while back about how to move the 
> lighting.  However, I have not seen any information on how to change 
> the lighting of an internal cavity. I want the internal cavity to 
> appear darker as it would be more realistic. However, it is almost 
> like there is a light source coming from inside the object that 
> brightens it up.
> 
> Does anyone know how to change the internal lighting of a cavity when 
> shown in surface representation?
> 
> Thanks.

Hey,

What you probably want is some kind of ambient occlusion. The tachyon 
rendering library (which is used with VMD) can do that. However, you can 
get a similar effect in PyMOL using the POV-Ray renderer with 
appropriate radiosity settings. I'm using a modified make_pov.py script 
to do something similar [1], but the POV-Ray settings are not yet 
finalized (I'm very new to POV-Ray myself). I'd also suggest using 
POV-Ray 3.7 to allow the use of multiple cores, as radiosity can 
increase rendering time quite significantly.

The file I posted does not yet have the correct field of view. I'll 
update the Gist once I've found the correct value.

Cheers,
Patrice

[1] https://gist.github.com/runiq/5669624

>--
>Yarrow Madrona
>
>Graduate Student
>Molecular Biology and Biochemistry Dept.
>University of California, Irvine
>Natural Sciences I, Rm 2403
>Irvine, CA 92697

Hi,

I saw a post on this sight a while back about how to move the lighting.
However, I have not seen any information on how to change the lighting of
an internal cavity. I want the internal cavity to appear darker as it
would be more realistic. However, it is almost like there is a light
source coming from inside the object that brightens it up.

Does anyone know how to change the internal lighting of a cavity when
shown in surface representation?

Thanks.

-- 
Yarrow Madrona

Graduate Student
Molecular Biology and Biochemistry Dept.
University of California, Irvine
Natural Sciences I, Rm 2403
Irvine, CA 92697

Thank you, Tsjerk, that's helpful.

To date, we are successfully interpreting all of the following:

     -- atoms with labels
     -- bonds
     -- standard PyMOL rendering, including:
        -- lines
        -- sticks
        -- nonbonded (stars)
        -- nb_spheres
        -- cartoons of various types (not plank)
        -- rockets
        -- ribbon (as Jmol backbone or trace)
        -- putty (trace)
        -- dots
        -- surfaces (molecular)
     -- measures
     -- simple CGO objects
     -- electron density as points and meshes
     -- custom colors
     -- fog and slab
     -- morphing movies (not scripted movies)
     -- JVXL caching of isosurfaces

I'm interested in any PyMOL session files that go beyond that or implement
CGOs in more than just a "demo" mode. In other words, actual figures used
in publication or research.

I am working on scenes now and will have some programming questions.

Bob

-- 
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900

Hi Bob,

I notice that this question has not yet been answered, unless you have
received private answers. To start with the second question, this list is
followed by those who are most involved in the code, and, AFAIK, there is
no specific developers list (I do care to know if there is :P). Also for
general how-to questions, this is the place to be.

As for the first question, I would say that it would be valuable to have a
way to communicate not only a static picture with caption, but also an
annotated, interactive view.

Finally, I don't think there's a repository of session files. Are there
specific things that you're missing in the set you have? I can probably
provide some examples with various classes of CGO objects.

Hope it helps,

Tsjerk



On Fri, May 24, 2013 at 9:59 PM, Robert Hanson <ha...@st...> wrote:

> Hello, PyMOL users!
>
> I'm new to this list. Some may recognize me as the current principal
> developer of Jmol. Until recently I hadn't explored PyMOL much, mostly
> because I'm not myself a biochemist. For about three months now, though,
> Jaime Prilusky (Weizmann Institute) and I have been working on a PSE file
> reader for Jmol, and I think we're just about ready to roll that out, at
> least in a preliminary version.
>
> A few questions:
>
> Q: Does the availability of a way to manipulate PyMOL models on the web
> using Java or just HTML5 interest this crowd? Or are people more focused
> specifically on journal image production or stand-alone PyMOL application
> use?
>
> Q: Are there people on this list who can answer fundamental PyMOL
> programming issues, or is that another list? I'm pretty much a autodidact,
> but there are some nuances that I don't understand. I don't want to waste
> this list's bytes if questions like "Is the second array in a scene color
> definition list always just a list of 1s?" are inappropriate.
>
> Q: I also have lots of questions relating to how you go about doing things
> in PyMOL. (Getting a list of all defined scenes, for example.) OK to ask
> those here?
>
> Q: Now that we have a pretty good handle on how PyMOL is organized and
> most of the basic data structures, and with all the *basic* modeling
> options reproducible in Jmol, we need more examples. More interesting CGOs
> than "Hello, World," examples of various specific objects such as Surface
> object, that sort of thing. I think I'm just about done with our current
> sample set of about 100 PSE files. Anyone interested in contributing PSE
> files to the Jmol project? Is there a repository somewhere of those?
>
>
> Thanks in advance,
>
> Bob Hanson
>
> --
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> Chair, Chemistry Department
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr
>
>
> If nature does not answer first what we want,
> it is better to take what answer we get.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>
>
>
> ------------------------------------------------------------------------------
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> Archives: http://www.mail-archive.com/pym...@li...
>



-- 
Tsjerk A. Wassenaar, Ph.D.

Hello, PyMOL users!

I'm new to this list. Some may recognize me as the current principal
developer of Jmol. Until recently I hadn't explored PyMOL much, mostly
because I'm not myself a biochemist. For about three months now, though,
Jaime Prilusky (Weizmann Institute) and I have been working on a PSE file
reader for Jmol, and I think we're just about ready to roll that out, at
least in a preliminary version.

A few questions:

Q: Does the availability of a way to manipulate PyMOL models on the web
using Java or just HTML5 interest this crowd? Or are people more focused
specifically on journal image production or stand-alone PyMOL application
use?

Q: Are there people on this list who can answer fundamental PyMOL
programming issues, or is that another list? I'm pretty much a autodidact,
but there are some nuances that I don't understand. I don't want to waste
this list's bytes if questions like "Is the second array in a scene color
definition list always just a list of 1s?" are inappropriate.

Q: I also have lots of questions relating to how you go about doing things
in PyMOL. (Getting a list of all defined scenes, for example.) OK to ask
those here?

Q: Now that we have a pretty good handle on how PyMOL is organized and most
of the basic data structures, and with all the *basic* modeling options
reproducible in Jmol, we need more examples. More interesting CGOs than
"Hello, World," examples of various specific objects such as Surface
object, that sort of thing. I think I'm just about done with our current
sample set of about 100 PSE files. Anyone interested in contributing PSE
files to the Jmol project? Is there a repository somewhere of those?


Thanks in advance,

Bob Hanson

-- 
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900

Hi Daniel,

this memory leak is fixed in PyMOL 1.6 (latest open-source).

Cheers,
  Thomas

Daniel Mann wrote, On 05/23/13 17:56:
> Hello,
> I just wanted to leave a short note on a possible bug I've observed.
> When I stop PyMOL from caching the geometry of my trajectory in RAM by
> set_defer_builds_mode, 3
> and load a rather short trajectory (ca. 100 frames) of a protein that is 
> shown in Cartoon-representation PyMOL starts eating my RAM gradually.
> As the trajectory loops several times more and more is stored to RAM, 
> even worse the "reinit" command doesn't get rid of the cache, whatever 
> is cached to RAM there...
> This doesn't seem to happen in lines-representation, but also for sticks.
> (PyMOL 1.5.0.4, Ubuntu 12.04 64-bit)
> 
> Regards,
> Daniel

-- 
Thomas Holder
PyMOL Developer
Schrödinger Contractor

Hello,
I just wanted to leave a short note on a possible bug I've observed.
When I stop PyMOL from caching the geometry of my trajectory in RAM by
set_defer_builds_mode, 3
and load a rather short trajectory (ca. 100 frames) of a protein that is 
shown in Cartoon-representation PyMOL starts eating my RAM gradually.
As the trajectory loops several times more and more is stored to RAM, 
even worse the "reinit" command doesn't get rid of the cache, whatever 
is cached to RAM there...
This doesn't seem to happen in lines-representation, but also for sticks.
(PyMOL 1.5.0.4, Ubuntu 12.04 64-bit)

Regards,
Daniel

-- 
Daniel Mann, M.Sc
Department of Biophysics
Ruhr-University Bochum

Great, that seems to have fixed the problem.

Thanks for your help,

Dan

From: jas...@sc...
Date: Mon, 20 May 2013 10:25:14 -0500
Subject: Re: [PyMOL] Discrepancy between select within and distance?
To: psd...@ou...
CC: pym...@li...

Hi,
Folmer is correct on both accounts. 
First, "select" was selecting across various states into one multistate selection. Then, the distance command was operating on the first state, which is its default behavior. So, replace 


    select asdf, 1MM2////CA w. 5 of 2kgi///22/CA

with 
    select asdf, 1MM2////CA w. 5 of 2kgi///22/CA, state=1


or whichever state you want and try again. (Or use Folmer's suggestion of splitting out the states.)
Second, please don't hind behind a pseudonym. We don't bite.


Cheers,
-- Jason

On Sun, May 19, 2013 at 4:55 PM, asdf asdf <psd...@ou...> wrote:





Hello,

I'm measuring the distance between certain residues in an alignment and I've noticed a discrepancy in the selections returned by the "select within command" and the actual distances measured to the atoms returned by the selection.  I was wondering if maybe somebody knew where I was going wrong.



When I run the following commands

> fetch 1MM2
> fetch 2kgi
> align 2kgi, 1MM2
> select asdf, 1MM2////CA w. 5 of 2kgi///22/CA
> iterate asdf, print(resi + " " + resn + " " + name + " " + str(cmd.distance("tmp", "2kgi///22/CA", "1MM2///" + resi + "/CA")))



I get this output:

24 CYS CA 5.15101623535
25 ASP CA 3.34501266479
26 THR CA 6.03605747223
47 GLU CA 3.80576062202
48 TRP CA 3.85521435738
49 LEU CA 4.28281402588

I'm just a little confused about why atoms that are further than 5 angstroms away from the atom I specified in the select command are returned.  Is there some difference in the way "select within" and "cmd.distance", or have a confused some of the commands?



Any suggestions are appreciated
 		 	   		  

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

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


 		 	   		  

Hi Jordan,

use the "first" operator:

PyMOL> label first foo, "foo"

or for the first CA atom in foo:

PyMOL> label first (foo and guide), "foo"

Cheers,
  Thomas

Jordan Willis wrote, On 05/21/13 11:07:
> Yes thank you!
> 
> I meant to post that as my solution considering it works pretty good.
> It preserves depth and position.
> 
> Jordan
> 
> On May 21, 2013, at 3:45 AM, Folmer Fredslund wrote:
> 
>> Hi Jordan,
>>
>> As a workaround you can label just the CA's (so this doesn't answer
>> your question exactly, but might be usefull):
>>
>> label foo and n. CA, "foo"
>>
>> Hope this helps,
>> Folmer
>>
>> 2013/5/21 Jordan Willis
>>
>>     Hello,
>>
>>     This should be straightforward,
>>
>>     Is it possible to label selections by their name?
>>
>>     If I have a selection named "foo" and I say label foo, "foo", it
>>     of course labels all the atoms. Is it possible to get one label
>>     for the entire selection without using pseudoatoms?
>>
>>     Jordan
-- 
Thomas Holder
PyMOL Developer
Schrödinger Contractor