pymol-users Mailing List for PyMOL Molecular Graphics System

>Hello All,

>Since I have long been such a big Mac stereo 3D proponent, it is
>especially important that I go on the record with an updated
>perspective.

>Based on all of the accumulated evidence to date, a verdict can now be
>rendered:  we have lost the case.  For stereo 3D visualization,
>Open-source Linux has beaten out Proprietary Mac OS X.


Warren,

According to Jordan Hubbard (on the X-11 users list) Apple is quite
willing to pay someone to work on this:

>Is there really no one out there who either is or even just knows
>someone capable of hacking on X11 servers at this level?   Apple is
>more than willing to try and address this entire area of suboptimal
>performance/functionality, but we have so many projects going at once
>right now that we just don't have the personnel resources and having
>money to throw at the problem hardly helps if you can't find anyone to
>(productively!) throw it at!

Rich

Marius,
 
Hmm...are you perhaps looking at the output before the file is closed and/or
flushed? You should issue ndx.flush() or ndx.close() before attempting to
use the output file.
 
Cheres,
Warren
 
  _____  

From: pym...@li...
[mailto:pym...@li...] On Behalf Of Marius
Retegan
Sent: Friday, June 27, 2008 9:01 AM
To: pymol-users
Subject: Re: [PyMOL] writing selection to a external file


Hi,
It seems that I run into a little problem. When I try to write a large
selection I get only a partial list of ID. If for example I print ID after
the iterate command, all the list is printed into pymol window. Do you have
any idea why?
I run Pymol 1.1pre5 under Fedora 8.



On Fri, Jun 27, 2008 at 1:36 PM, Tsjerk Wassenaar <ts...@gm...> wrote:


Hi,

This should've gone to the list... (isn't there an option "send
replies to list rather than to poster" to the mailing list?)

Tsjerk


On Fri, Jun 27, 2008 at 1:34 PM, Tsjerk Wassenaar <ts...@gm...> wrote:
> Hi Marius,
>
> You want iterate.
> You do have to make sure though that the numbering of your atoms in
> the structure file is correct. Than you can do:
>
> ndx=open("index.ndx","w")
> ndx.write("[ MyIndex ]\n")
> iterate selection, ndx.write("%d\n" % ID)
> ndx.close()
>
> I did make the assumption that you wanted the atom id's rather than
> the residue id's, since the latter are of no use to Gromacs.
>
> Hope it helps,
>
> Tsjerk
>
> On Fri, Jun 27, 2008 at 1:17 PM, Marius Retegan
> <mar...@gm...> wrote:
>> Hi All,
>> I'm using pymol to select (by residue) all the atoms around 10 angstroms
>> from a certain atom. Now I would like to write the residue id's of my
>> selection to an external file, so that I can integrated in the ndx file
from
>> Gromacs. Do you have any idea how I could do that?
>>
>> Thanks,
>>
>> Marius Retegan
>>
>> -------------------------------------------------------------------------
>> Check out the new SourceForge.net Marketplace.
>> It's the best place to buy or sell services for
>> just about anything Open Source.
>> http://sourceforge.net/services/buy/index.php
>> _______________________________________________
>> PyMOL-users mailing list
>> PyM...@li...
>> https://lists.sourceforge.net/lists/listinfo/pymol-users
>>
>>
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> Junior UD (post-doc)
> Biomolecular NMR, Bijvoet Center
> Utrecht University
> Padualaan 8
> 3584 CH Utrecht
> The Netherlands
> P: +31-30-2539931
> F: +31-30-2537623
>



--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

-------------------------------------------------------------------------
Check out the new SourceForge.net Marketplace.
It's the best place to buy or sell services for
just about anything Open Source.
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_______________________________________________
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Youzhong,

If you're still having trouble getting what you want with Michael's APBS
Plugin, here's how I might display two such maps using PyMOL commands
directly:

load pdbset1.pqr
load pdbset_1.dx

load pdbset3.pqr
load pdbset_3.dx

ramp_new ramp1, pdbset_1, [ -3, 0, 3]
ramp_new ramp3, pdbset_3, [ -3, 0, 3]

show surface

set surface_ramp_above_mode

set surface_color, ramp1, pdbset1
set surface_color, ramp3, pdbset3

Note that the surface_ramp_above_mode setting colors surfaces based on the
potential that would be felt by an atom in contact with the surface, as
opposed to the potential at the molecular surface itself (which is less
meaningful, since no atom could ever feel such a potential).
 
Cheers,
Warren

--
DeLano Scientific LLC
Subscriber Support Services
mailto:su...@de...


-----Original Message-----
From: pym...@li...
[mailto:pym...@li...] On Behalf Of Youzhong Guo
Sent: Thursday, June 26, 2008 7:28 PM
To: pym...@li...
Subject: [PyMOL] How to display two or multiple eleectrostatic
mapssimultaneously with PyMol?

Dear All,

I have difficulty to display two electrostatic maps with PyMol at the same
time .

I can correctly display one map with pdbset1.pqr and pdbset_1.dx as in slide
No.1.
I can also correctly display one map with pdbset3.pqr and pdbset_3.dx as in
slide No.2.
However, when I tried to load all of those four files with PyMol, what I can
get is as in slide No. 3 or No.4. As you can see in slide No.3 or No.4 the
map is not correct as expected.

Please download my files from the following link and see if you can
simultaneously display two maps as shown in slide  No.1 and No.2 with PyMol.

https://webspace.utexas.edu/yg387/Electron_static_potential.zip

Thanks in advance,


Youzhong

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Robert Campbell wrote:
> Hi,
>
> On Fri, 27 Jun 2008 13:25:02 -0400, Michael Lerner <mgl...@gm...>
> wrote:
>
>   
>> This is probably a fairly basic question, but I'm stumped. I want to
>> visualize electron densities along with my PDB file. So, say I'm interested
>> in 2DJX. I go to the PDB and download 2DJX.pdb and 2djx-sf.cif. PyMOL
>> doesn't seem to read the CIF file (?), so I downloaded and installed the
>> PDB's tool sf-convert (http://sw-tools.pdb.org/apps/SF-CONVERT/index.html).
>> I tried
>>
>> sf-convert -i CIF -o Xplor -sf 2djx-sf.cif
>>
>> but got some errors about the input format.
>>
>> sf-convert -i mmCIF -o Xplor -sf 2djx-sf.cif
>>
>> seemed to work (it produced a .Xplor file with what looks like data to me).
>> However, PyMOL gives me errors when I try to load the resulting .xplor file.
>>     
>
> The "sf" file that you have is not electron density but structure factors.
> You need to calculate electron density from the data in that file and phases,
> which you would have to calculate from the structure.  Fortunately someone
> else is already doing that for you.  Try the Electron Density Server
> (http://eds.bmc.uu.se/eds/).
>
> Simply enter the PDB code and you'll find ... oh dear ... that 2djx is not
> entered yet. :(
>
> I see that it is a fairly new structure (released yesterday) and EDS is
> updated weekly.  So either wait a week or so, or find a crystallographer to
> run the coordinates and structure factors through a single refmac cycle to
> calculate a map for you.
>
> 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
>
> -------------------------------------------------------------------------
> Check out the new SourceForge.net Marketplace.
> It's the best place to buy or sell services for
> just about anything Open Source.
> http://sourceforge.net/services/buy/index.php
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>   
Instructions for creating and displaying CCP4 maps in pymol can be found 
at http://www.pymolwiki.org/index.php/Display_CCP4_Maps. However, 
displaying a model with maps in pymol is perhaps not the most 
straightforward way to inspect models and maps. Even here, you will have 
to use the fft utility in CCP4 to generate the maps. (You will probably 
want to display a simple map.) To generate a CCP4 map, you will have to 
convert your mmCIF file to an appropriate MTZ file using another CCP4 
utility. It might be more straightforward to read in the PDB file and 
the appropriate MTZ file into Coot instead of pymol.

Cheers,


-- 
------------------------------------------------------------------------
Roger S. Rowlett
Professor
Colgate University Presidential Scholar
Department of Chemistry
Colgate University
13 Oak Drive
Hamilton, NY 13346

tel: (315)-228-7245
ofc: (315)-228-7395
fax: (315)-228-7935
email: rro...@ma...

Hi,

On Fri, 27 Jun 2008 13:25:02 -0400, Michael Lerner <mgl...@gm...>
wrote:

> This is probably a fairly basic question, but I'm stumped. I want to
> visualize electron densities along with my PDB file. So, say I'm interested
> in 2DJX. I go to the PDB and download 2DJX.pdb and 2djx-sf.cif. PyMOL
> doesn't seem to read the CIF file (?), so I downloaded and installed the
> PDB's tool sf-convert (http://sw-tools.pdb.org/apps/SF-CONVERT/index.html).
> I tried
> 
> sf-convert -i CIF -o Xplor -sf 2djx-sf.cif
> 
> but got some errors about the input format.
> 
> sf-convert -i mmCIF -o Xplor -sf 2djx-sf.cif
> 
> seemed to work (it produced a .Xplor file with what looks like data to me).
> However, PyMOL gives me errors when I try to load the resulting .xplor file.

The "sf" file that you have is not electron density but structure factors.
You need to calculate electron density from the data in that file and phases,
which you would have to calculate from the structure.  Fortunately someone
else is already doing that for you.  Try the Electron Density Server
(http://eds.bmc.uu.se/eds/).

Simply enter the PDB code and you'll find ... oh dear ... that 2djx is not
entered yet. :(

I see that it is a fairly new structure (released yesterday) and EDS is
updated weekly.  So either wait a week or so, or find a crystallographer to
run the coordinates and structure factors through a single refmac cycle to
calculate a map for you.

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

Hi,

This is probably a fairly basic question, but I'm stumped. I want to
visualize electron densities along with my PDB file. So, say I'm interested
in 2DJX. I go to the PDB and download 2DJX.pdb and 2djx-sf.cif. PyMOL
doesn't seem to read the CIF file (?), so I downloaded and installed the
PDB's tool sf-convert (http://sw-tools.pdb.org/apps/SF-CONVERT/index.html).
I tried

sf-convert -i CIF -o Xplor -sf 2djx-sf.cif

but got some errors about the input format.

sf-convert -i mmCIF -o Xplor -sf 2djx-sf.cif

seemed to work (it produced a .Xplor file with what looks like data to me).
However, PyMOL gives me errors when I try to load the resulting .xplor file.

This may not be directly related to PyMOL, but I'm hoping it's a common
enough task that someone can point me in the right direction.

Thanks,

-michael

-- 
Michael Lerner, Ph.D.
IRTA Postdoctoral Fellow
Laboratory of Computational Biology NIH/NHLBI
5635 Fishers Lane, Room T909
Rockville, MD 20852
http://www.umich.edu/~mlerner

Hi,

The current version of the APBS Plugin (http://www.umich.edu/~mlerner/PyMOL)
has two visualization panes. You can use them to control two separate
molecule/map combinations.

Please let me know if you need more assistance,

-Michael

On Thu, Jun 26, 2008 at 10:28 PM, Youzhong Guo <you...@gm...>
wrote:

> Dear All,
>
> I have difficulty to display two electrostatic maps with PyMol at the
> same time .
>
> I can correctly display one map with pdbset1.pqr and pdbset_1.dx as in
> slide No.1.
> I can also correctly display one map with pdbset3.pqr and pdbset_3.dx
> as in slide No.2.
> However, when I tried to load all of those four files with PyMol, what
> I can get is as in slide No. 3 or No.4. As you can see in slide No.3
> or No.4 the map is not correct as expected.
>
> Please download my files from the following link and see if you can
> simultaneously display two maps as shown in slide  No.1 and No.2 with
> PyMol.
>
> https://webspace.utexas.edu/yg387/Electron_static_potential.zip
>
> Thanks in advance,
>
>
> Youzhong
>
> -------------------------------------------------------------------------
> Check out the new SourceForge.net Marketplace.
> It's the best place to buy or sell services for
> just about anything Open Source.
> http://sourceforge.net/services/buy/index.php
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>



-- 
Michael Lerner, Ph.D.
IRTA Postdoctoral Fellow
Laboratory of Computational Biology NIH/NHLBI
5635 Fishers Lane, Room T909
Rockville, MD 20852
http://www.umich.edu/~mlerner

Hi,
It seems that I run into a little problem. When I try to write a large
selection I get only a partial list of ID. If for example I print ID after
the iterate command, all the list is printed into pymol window. Do you have
any idea why?
I run Pymol 1.1pre5 under Fedora 8.


On Fri, Jun 27, 2008 at 1:36 PM, Tsjerk Wassenaar <ts...@gm...> wrote:

> Hi,
>
> This should've gone to the list... (isn't there an option "send
> replies to list rather than to poster" to the mailing list?)
>
> Tsjerk
>
> On Fri, Jun 27, 2008 at 1:34 PM, Tsjerk Wassenaar <ts...@gm...>
> wrote:
> > Hi Marius,
> >
> > You want iterate.
> > You do have to make sure though that the numbering of your atoms in
> > the structure file is correct. Than you can do:
> >
> > ndx=open("index.ndx","w")
> > ndx.write("[ MyIndex ]\n")
> > iterate selection, ndx.write("%d\n" % ID)
> > ndx.close()
> >
> > I did make the assumption that you wanted the atom id's rather than
> > the residue id's, since the latter are of no use to Gromacs.
> >
> > Hope it helps,
> >
> > Tsjerk
> >
> > On Fri, Jun 27, 2008 at 1:17 PM, Marius Retegan
> > <mar...@gm...> wrote:
> >> Hi All,
> >> I'm using pymol to select (by residue) all the atoms around 10 angstroms
> >> from a certain atom. Now I would like to write the residue id's of my
> >> selection to an external file, so that I can integrated in the ndx file
> from
> >> Gromacs. Do you have any idea how I could do that?
> >>
> >> Thanks,
> >>
> >> Marius Retegan
> >>
> >>
> -------------------------------------------------------------------------
> >> Check out the new SourceForge.net Marketplace.
> >> It's the best place to buy or sell services for
> >> just about anything Open Source.
> >> http://sourceforge.net/services/buy/index.php
> >> _______________________________________________
> >> PyMOL-users mailing list
> >> PyM...@li...
> >> https://lists.sourceforge.net/lists/listinfo/pymol-users
> >>
> >>
> >
> >
> >
> > --
> > Tsjerk A. Wassenaar, Ph.D.
> > Junior UD (post-doc)
> > Biomolecular NMR, Bijvoet Center
> > Utrecht University
> > Padualaan 8
> > 3584 CH Utrecht
> > The Netherlands
> > P: +31-30-2539931
> > F: +31-30-2537623
> >
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> Junior UD (post-doc)
> Biomolecular NMR, Bijvoet Center
> Utrecht University
> Padualaan 8
> 3584 CH Utrecht
> The Netherlands
> P: +31-30-2539931
> F: +31-30-2537623
>
> -------------------------------------------------------------------------
> Check out the new SourceForge.net Marketplace.
> It's the best place to buy or sell services for
> just about anything Open Source.
> http://sourceforge.net/services/buy/index.php
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>

Tsjerk Wassenaar schrieb:
> Hi,
>
> This should've gone to the list... (isn't there an option "send
> replies to list rather than to poster" to the mailing list?)
>
> Tsjerk
>
>   
Depends on the list, but there is a nifty addon for thunderbird

http://alumnit.ca/wiki/index.php?page=ReplyToListThunderbirdExtension

Justin



-- 
Justin Lecher
Institute for  Neuroscience and Biophysics
INB 2 - Molecular Biophysics II
Research centre Juelich GmbH,
52425 Juelich,Germany
phone: +49 2461 61 5385

Hi,

This should've gone to the list... (isn't there an option "send
replies to list rather than to poster" to the mailing list?)

Tsjerk

On Fri, Jun 27, 2008 at 1:34 PM, Tsjerk Wassenaar <ts...@gm...> wrote:
> Hi Marius,
>
> You want iterate.
> You do have to make sure though that the numbering of your atoms in
> the structure file is correct. Than you can do:
>
> ndx=open("index.ndx","w")
> ndx.write("[ MyIndex ]\n")
> iterate selection, ndx.write("%d\n" % ID)
> ndx.close()
>
> I did make the assumption that you wanted the atom id's rather than
> the residue id's, since the latter are of no use to Gromacs.
>
> Hope it helps,
>
> Tsjerk
>
> On Fri, Jun 27, 2008 at 1:17 PM, Marius Retegan
> <mar...@gm...> wrote:
>> Hi All,
>> I'm using pymol to select (by residue) all the atoms around 10 angstroms
>> from a certain atom. Now I would like to write the residue id's of my
>> selection to an external file, so that I can integrated in the ndx file from
>> Gromacs. Do you have any idea how I could do that?
>>
>> Thanks,
>>
>> Marius Retegan
>>
>> -------------------------------------------------------------------------
>> Check out the new SourceForge.net Marketplace.
>> It's the best place to buy or sell services for
>> just about anything Open Source.
>> http://sourceforge.net/services/buy/index.php
>> _______________________________________________
>> PyMOL-users mailing list
>> PyM...@li...
>> https://lists.sourceforge.net/lists/listinfo/pymol-users
>>
>>
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> Junior UD (post-doc)
> Biomolecular NMR, Bijvoet Center
> Utrecht University
> Padualaan 8
> 3584 CH Utrecht
> The Netherlands
> P: +31-30-2539931
> F: +31-30-2537623
>



-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

Hi All,
I'm using pymol to select (by residue) all the atoms around 10 angstroms
from a certain atom. Now I would like to write the residue id's of my
selection to an external file, so that I can integrated in the ndx file from
Gromacs. Do you have any idea how I could do that?

Thanks,

Marius Retegan

Dear All,

I have difficulty to display two electrostatic maps with PyMol at the
same time .

I can correctly display one map with pdbset1.pqr and pdbset_1.dx as in
slide No.1.
I can also correctly display one map with pdbset3.pqr and pdbset_3.dx
as in slide No.2.
However, when I tried to load all of those four files with PyMol, what
I can get is as in slide No. 3 or No.4. As you can see in slide No.3
or No.4 the map is not correct as expected.

Please download my files from the following link and see if you can
simultaneously display two maps as shown in slide  No.1 and No.2 with
PyMol.

https://webspace.utexas.edu/yg387/Electron_static_potential.zip

Thanks in advance,


Youzhong

Hello All,

Since I have long been such a big Mac stereo 3D proponent, it is
especially important that I go on the record with an updated
perspective.  

Based on all of the accumulated evidence to date, a verdict can now be
rendered:  we have lost the case.  For stereo 3D visualization,
Open-source Linux has beaten out Proprietary Mac OS X. 
 
Given that Leopard stereo 3D still isn't entirely functional after three
OS updates, and that Apple doesn't permit its customers to run old (yet
fully-functional) operating systems on new hardware, if you purchase a
Mac Pro today, then you are going to have to run Linux natively (through
Boot Camp) in order to get your work done in stereo 3D.

Though it is hard not to love Apple hardware, there are less expensive
options for people who must run native Linux in order to do their jobs.
So together now, everyone:  

"Linux rules!  Long live community-driven open source solutions!" 

In point of fact, however, Linux-based stereo 3D remains dependent on
proprietary graphics drivers tied to the underlying hardware.  There is
no 100% open-source option for stereo 3D visualization.  Therefore, the
scientific visualization community has no choice but to rely upon a
proprietary solution to a significant extent, irrespective of who
provides it.  

Given my own past efforts, I am more sorry than anyone else that things
haven't worked out for stereo 3D with the company formerly known as
"Apple Computer, Inc."  Fortunately, however, nVidia has maintained
uninterrupted Linux stereo 3D support on higher-end Quadro cards.  I am
not sure what the situation is with respect to AMD/ATI, but it appears
that they are still supporting Linux stereo 3D as well.

Though I remain an ardent fan of relying upon the new "Apple, Inc." to
meet needs which clearly overlap those of mainstream consumer markets
(e.g. the need for sleek, fast, Intel-based laptops), given the
company's increasing emphasis on consumer devices, music and the like,
we simply cannot rely upon them for niche business, scientific, or
professional computing solutions unless or until consumers find matched
uses for such solutions as well.  

For example: imagine future adoption of stereo 3D in movies,
videoconferencing, or games.  That it what I believe it would take in
this case.

By the way, instead of Linux, you could also just run Windows XP.  In
contrast to Apple, Microsoft stops short of forcing its customers to run
Vista on newly minted PC hardware.  Whereas consumers don't typically
need to run older operating systems on current hardware, businesses and
professionals often do.  It all makes perfect sense when you think about
it...

Cheers,
Warren


> -----Original Message-----
> From: CCP4 bulletin board [mailto:CC...@JI...] On Behalf Of
Ben
> Eisenbraun
> Sent: Thursday, June 26, 2008 2:27 PM
> To: CC...@JI...
> Subject: Re: [ccp4bb] Reminder - still no 3D stereo under OS X 10.5
> 
> A follow up note:
> 
> I was at Apple's WWDC a couple weeks ago, and during one of the lunch
> time sessions for scientists, several people brought up the fact that
> stereo 3d was still broken on Leopard, and asked for it to be fixed.
> 
> The Apple engineer present hemmed and hawed a bit, and finally said
that
> fixing it would not be easy and that Apple was not sure that this was
a
> technology that they wanted to pursue.
> 
> As another note, Jordan Hubbard, who the "Director of Engineering of
> UNIX Technologies" at Apple has said that they don't have the internal
> resources to fix this in a timely manner.
> 
> http://lists.apple.com/archives/x11-users/2008/Apr/msg00130.html
> 
> Even if/when Apple fixes stereo on Leopard, I don't think I'll be
> recommending OS X for stereo applications.
> 
> -ben
> 
> --
> Ben Eisenbraun
> Structural Biology Grid                           Harvard Medical
School
> http://sbgrid.org
http://hms.harvard.edu
> 
> 

> But one more question, how is the new picture on the pymol homepage made?
The one in the
> middle? I love the light settings!

Me too :)


fetch 1ow9,async=0
zoom all, 3, state=1
set_color oxygen, [1.0,0.4,0.4]
set_color nitrogen, [0.5,0.5,1.0]
remove solvent
as spheres
util.cbaw
bg white
set light_count,10
set spec_count,1
set shininess, 10
set specular, 0.25
set ambient,0
set direct,0
set reflect,1.5
set ray_shadow_decay_factor, 0.1
set ray_shadow_deday_range, 2
unset depth_cue
viewport 400,400

Then press "ray".

Cheers,
Warren

--
DeLano Scientific LLC
Subscriber Support Services
mailto:su...@de...

Justin Lecher schrieb:
> Hi all,
> I am using the latest svn version of Pymol with python 2.5.2. Now I get
> following traceback when clicking the set grid button of the apbs plugin:
>
> Traceback (most recent call last):
>   File "/usr/lib/python2.5/site-packages/pmg_tk/__init__.py", line 35,
> in run
>     PMGApp(pymol_instance,skin).run(poll)
>   File "/usr/lib/python2.5/site-packages/pmg_tk/PMGApp.py", line 170, 
> in run
>     self.root.mainloop()
>   File "/usr/lib/python2.5/lib-tk/Tkinter.py", line 1023, in mainloop
>     self.tk.mainloop(n)
>   File "/usr/lib/python2.5/site-packages/Pmw/Pmw_1_2/lib/PmwBase.py",
> line 1751, in __call__
>     _reporterror(self.func, args)
>   File "/usr/lib/python2.5/site-packages/Pmw/Pmw_1_2/lib/PmwBase.py",
> line 1777, in _reporterror
>     msg = exc_type + ' Exception in Tk callback\n'
> TypeError: unsupported operand type(s) for +: 'type' and 'str'
>
>
> I am not that familiar with python, so that I couldn't figure out where
> it comes from.
>
> Thanks for help,
> jusitn
>
My fault, once again a mis formated pdb output from modeller!


But one more question, how is the new picture on the pymol homepage
made? The one in the middle? I love the light settings!

Thanks justin



-- 
Justin Lecher
Institute for  Neuroscience and Biophysics
INB 2 - Molecular Biophysics II
Research centre Juelich GmbH,
52425 Juelich,Germany
phone: +49 2461 61 5385

Hi all,
I am using the latest svn version of Pymol with python 2.5.2. Now I get
following traceback when clicking the set grid button of the apbs plugin:

Traceback (most recent call last):
   File "/usr/lib/python2.5/site-packages/pmg_tk/__init__.py", line 35,
in run
     PMGApp(pymol_instance,skin).run(poll)
   File "/usr/lib/python2.5/site-packages/pmg_tk/PMGApp.py", line 170, 
in run
     self.root.mainloop()
   File "/usr/lib/python2.5/lib-tk/Tkinter.py", line 1023, in mainloop
     self.tk.mainloop(n)
   File "/usr/lib/python2.5/site-packages/Pmw/Pmw_1_2/lib/PmwBase.py",
line 1751, in __call__
     _reporterror(self.func, args)
   File "/usr/lib/python2.5/site-packages/Pmw/Pmw_1_2/lib/PmwBase.py",
line 1777, in _reporterror
     msg = exc_type + ' Exception in Tk callback\n'
TypeError: unsupported operand type(s) for +: 'type' and 'str'


I am not that familiar with python, so that I couldn't figure out where
it comes from.

Thanks for help,
jusitn



-- 
Justin Lecher
Institute for  Neuroscience and Biophysics
INB 2 - Molecular Biophysics II
Research centre Juelich GmbH,
52425 Juelich,Germany
phone: +49 2461 61 5385

Last week I endorsed the Planar displays a promising alternative to CRTs.
Martin Montgomery (MRC-DUNN) was kind enough to provide some insightful
feedback on both Planar and Omnia displays, so I have included his comments
below (with permission) along with a link to an image showing the two
displays juxtaposed:

http://pymol.sf.net/pmimag/dual_lcd_stereo.jpg

It sounds like Omnia may have an edge on Planar in terms of comfort.
Additional experiences and feedback are welcome!

--
From: Martin Montgomery

We've had these displays in use for over two years now (and a dual projector
3D system in our seminar room).  We originally bought a MIMO screen from
Omnia in Spain (on the right in the photo).  This uses two samsung 20" LCDs
and the images are really sharp.  Looking at the screen in 3D mode for long
periods of time is now very easy on the eye compared to shutter glasses.  

At the time, Planar only had a smaller screen available so we went with the
Omnia.  However, earlier this year we bought one of the new widescreen
Planar screens to see if they were any better than the Omnia(on the left in
the pic - ignore the SGIs they are now expensive paperweights!).
Performance is much the same as the Omnia and the widescreen format is
helpful when using Coot as you can have the menu box at the side.  There are
however, some drawbacks to the Planar chassis.  The bottom screen is too
close to the desk and the glass mirror is not long enough so you end up
looking at the screen at a downward angle compared to the Omnia.  As it is
higher off the desk, you look straight at the screen so its more
comfortable.  

We got both screens from Inition in London (www.inition.co.uk).  Omnia now
do 22, 24 and 42" screens and it may be that these have the screen closer to
the desk to from the look of the pic on the Inition website.  We have yet to
try one.  One thing to be aware of is that the polarisation is not in the
same orientation in the Planar and Omnia so we need different glasses for
each.  Once you've used one of these, there's no going back to a CRT!

Junjun,

What version are you using?

Your script should work out of the box with the very latest PyMOL builds and
open-source code.

Prior to release 1.1, movies and scenes didn't work together so well because
of timing issues (use of wall clock versus frame/movie clock).  Those issues
are finally behind us.

The only change I would suggest would be to allow at least 90 frames (3
seconds) between scenes so that the camera interpolation has time to
complete.

Cheers,
Warren

--
DeLano Scientific LLC
Subscriber Support Services
mailto:su...@de...


-----Original Message-----
From: pym...@li...
[mailto:pym...@li...] On Behalf Of liu junjun
Sent: Monday, June 23, 2008 9:55 PM
To: pym...@li...
Subject: [PyMOL] question on making movie between two scenes with
differentpoint of view

Hello everybody,

I'm trying to make a movie for chaning the point of view on a structure. I
let PyMol read in matrix then define it as a scene. After the movie was set
up, I can watch the movie playing well on the PyMol window. However, if I
try to save the PNG sequence, I get few discontinuous picutures and a lot of
identical pictures. Can anybody please give me some suggestions? Thanks in
advance!

Please see the following script that I wrote for making the movie.

==== script for make movie ====
# read in point of view for two scene
@pml/view-ts3ab.pml
scene int3b , store
@pml/view-ts4.pml
scene int3b2 , store

# set up a movie
mset 1 x100
mdo 1: scene int3b
mdo 50: scene int3b2
mplay

# save the PNG sequences
set ray_trace_frames = 1
set cache_frame = 0
mpng png/int3b

===========

All the best!

Junjun

-------------------------------------------------------------------------
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It's the best place to buy or sell services for just about anything Open
Source.
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_______________________________________________
PyMOL-users mailing list
PyM...@li...
https://lists.sourceforge.net/lists/listinfo/pymol-users

Hello everybody,

I'm trying to make a movie for chaning the point of view on a
structure. I let PyMol read in matrix then define it as a scene. After
the movie was set up, I can watch the movie playing well on the PyMol
window. However, if I try to save the PNG sequence, I get few
discontinuous picutures and a lot of identical pictures. Can anybody
please give me some suggestions? Thanks in advance!

Please see the following script that I wrote for making the movie.

==== script for make movie ====
# read in point of view for two scene
@pml/view-ts3ab.pml
scene int3b , store
@pml/view-ts4.pml
scene int3b2 , store

# set up a movie
mset 1 x100
mdo 1: scene int3b
mdo 50: scene int3b2
mplay

# save the PNG sequences
set ray_trace_frames = 1
set cache_frame = 0
mpng png/int3b

===========

All the best!

Junjun

Ankit,

This has been detailed on the PyMOLWiki.  All you need is (1) a structure and 
(2) a text file with one number for each residue.  To make it more accurate, 
you can do one number per atom, but then the script(s) will need to be 
changed a little.

So, check out

	http://www.pymolwiki.org/index.php/Color#Reassigning_B-Factors_and_Coloring

and the section following it, called "Expanding to Surface" and you should be 
set.  Let me know if this isn't clear enough.

-- Jason


> Hi
>
> I want my chemical shift perturbation data to be mapped to the stucture. I
> am trying different things such as trying to get it to b-factor like
> position but haven't been successful. Is there any way I can get the data
> to be shown in pdb with various colors representing low/high perturbation
> in chemical shifts?
>
> Ankit


-- 

Jason Vertrees, PhD
Dartmouth: jv...@cs... (new)
UTMB: jav...@ut... (old)

http://www.best.utmb.edu/
http://www.pymolwiki.org/

Fengyuan,
 
Although we cannot answer specific questions about an unsupported interface,
your question about "self_cmd" is relevant to the overall project since we
are intending to support multiple PyMOL instances within a single Python
interpreter via: 
 
from pymol2 import PyMOL
 
instance1 = PyMOL()
instance2 = PyMOL()
 
Thus, the old way of messaging the PyMOL API:
 
from pymol import cmd
 
will not work correctly if there two or more active instances.  Instead,
each instance has its own "cmd" module and programming interface:
 
instance1.cmd
 
instance2.cmd
 
For example:
 
instance1.cmd.load("pdb1.pdb")
 
instance2.cmd.load("pdb2.pdb")
 
As for "self_cmd", all Python-based code called from the C layer must
therefore be given a handle pointing at the instance from which it was
called so that it can do useful work. This is the role of the self_cmd
argument, and you'll see similar constructs in both the Python-based wizards
and the Tcl/Tk GUIs.
 
Cheers,
Warren
 
--
DeLano Scientific LLC
Subscriber Support Services
mailto:su...@de...

  _____  

From: DeLano Scientific [mailto:de...@de...] 
Sent: Monday, June 23, 2008 9:31 AM
To: 'NeO'; 'su...@de...'; 'pym...@li...'
Subject: RE: [PyMOL] Question about PyMOL development


Fengyuan,
 
Unfortunately, the PyMOL's internal gui pop-up menu system was not designed
as nor intended to be a programmers interface and is subject to change at
any time.  Any code which relies upon its behavior may therefore break with
future versions of the software.  
 
 
Cheers,
Warren
--
DeLano Scientific LLC
Subscriber Support Services
mailto:su...@de...

  _____  

From: pym...@li...
[mailto:pym...@li...] On Behalf Of NeO
Sent: Sunday, June 22, 2008 7:46 AM
To: su...@de...; pym...@li...
Subject: Re: [PyMOL] Question about PyMOL development


Hi Warren,

I've read 'Executive.c' under '/trunk/pymol/layer3', it seems that you've
pre-defined all the cases that button actions and popup menu changes in
function ' ExecutiveClick ', I can understand only part of it. Now, I'm
wondering that if I want to implement my thought ( - left-click the C-alpha
atom in the structure, there will be a PopUp window coming out with
self-defined information in the Viewer window), I have to modify the source
code in C-layer and compile the whole source? Am I right? Or, is there any
trick to do this in Python-layer? 

Fengyuan


On Sun, Jun 22, 2008 at 1:59 PM, NeO <bob...@gm...> wrote:


Dear Warren,

How are you?


I'm writing a wizard, in which I want to implement the function that when I
left-click the C-alpha atom, there will be a PopUp window coming out with my
defined information in the Viewer window. I can do it using
'tkMessageBox.showinfo', but I want to make it beautiful.

I know that when you left-double click or right-click the protein structure,
the popup menu show up. I read the source code of 'menu.py', I'm not sure in
the function, the parameter 'self_cmd', what's it for? where the menu
functions are called? If I figure it out, I think I can code it in my
wizard.

Hope you can help me :)

Best Wishes

Fengyuan

Fengyuan,
 
Unfortunately, the PyMOL's internal gui pop-up menu system was not designed
as nor intended to be a programmers interface and is subject to change at
any time.  Any code which relies upon its behavior may therefore break with
future versions of the software.  
 
 
Cheers,
Warren
--
DeLano Scientific LLC
Subscriber Support Services
mailto:su...@de...

  _____  

From: pym...@li...
[mailto:pym...@li...] On Behalf Of NeO
Sent: Sunday, June 22, 2008 7:46 AM
To: su...@de...; pym...@li...
Subject: Re: [PyMOL] Question about PyMOL development


Hi Warren,

I've read 'Executive.c' under '/trunk/pymol/layer3', it seems that you've
pre-defined all the cases that button actions and popup menu changes in
function ' ExecutiveClick ', I can understand only part of it. Now, I'm
wondering that if I want to implement my thought ( - left-click the C-alpha
atom in the structure, there will be a PopUp window coming out with
self-defined information in the Viewer window), I have to modify the source
code in C-layer and compile the whole source? Am I right? Or, is there any
trick to do this in Python-layer? 

Fengyuan


On Sun, Jun 22, 2008 at 1:59 PM, NeO <bob...@gm...> wrote:


Dear Warren,

How are you?


I'm writing a wizard, in which I want to implement the function that when I
left-click the C-alpha atom, there will be a PopUp window coming out with my
defined information in the Viewer window. I can do it using
'tkMessageBox.showinfo', but I want to make it beautiful.

I know that when you left-double click or right-click the protein structure,
the popup menu show up. I read the source code of 'menu.py', I'm not sure in
the function, the parameter 'self_cmd', what's it for? where the menu
functions are called? If I figure it out, I think I can code it in my
wizard.

Hope you can help me :)

Best Wishes

Fengyuan

First, load a PDB file with values encoded in the B-factor column. Then
issue a command like the following:
 
spectrum b
 
specturm b, minimum=10, maximum=50
 
spectrum b, minimum=10, maximum=50, palette=blue_red
 
Predefined palettes include:
 
  blue_green            green_white_magenta   red_cyan            
  blue_magenta          green_white_red       red_green           
  blue_red              green_white_yellow    red_white_blue      
  blue_white_green      green_yellow          red_white_cyan      
  blue_white_magenta    green_yellow_red      red_white_green     
  blue_white_red        magenta_blue          red_white_yellow    
  blue_white_yellow     magenta_cyan          red_yellow          
  blue_yellow           magenta_green         red_yellow_green    
  cbmr                  magenta_white_blue    rmbc                
  cyan_magenta          magenta_white_cyan    yellow_blue         
  cyan_red              magenta_white_green   yellow_cyan         
  cyan_white_magenta    magenta_white_yellow  yellow_cyan_white   
  cyan_white_red        magenta_yellow        yellow_green        
  cyan_white_yellow     rainbow               yellow_magenta      
  cyan_yellow           rainbow2              yellow_red          
  gcbmry                rainbow2_rev          yellow_white_blue   
  green_blue            rainbow_cycle         yellow_white_green  
  green_magenta         rainbow_cycle_rev     yellow_white_magenta
  green_red             rainbow_rev           yellow_white_red    
  green_white_blue      red_blue              yrmbcg     
 
Cheers,
Warren
--
DeLano Scientific LLC
Subscriber Support Services
mailto:su...@de...
 

  _____  

From: pym...@li...
[mailto:pym...@li...] On Behalf Of Chavas Leo
Sent: Sunday, June 22, 2008 1:55 AM
To: Ankit Gupta
Cc: pym...@li...
Subject: Re: [PyMOL] NMR Chemical shift perturbation data to
surfacerepresentation


Dear Ankit -- 

On 20 Jun 2008, at 18:38, Ankit Gupta wrote:

I want my chemical shift perturbation data to be mapped to the stucture. I
am trying different things such as trying to get it to b-factor like
position but haven't been successful. Is there any way I can get the data to
be shown in pdb with various colors representing low/high perturbation in
chemical shifts?


I'm feeling that doing the ADP thing is the best solution. ConSurf is using
this column to display the conservation of amino acids, and it's working
very well! I don't know why it shouldn't with the chemical shift. You just
have to be careful that you don't have a negative value, although I'm not
sure PyMol cannot deal with those. Just normalize the all values and change
the ADP column of your pdb might do the trick. Just my opinion though.

HTH. Kind regards.

-- Leo --
------------------------------------------------------------
Chavas Leonard, Ph.D.
Research Associate
------------------------------------------------------------
Faculty of Life Sciences
The University of Manchester
The Michael Smith Building
Oxford Road
Manchester Lancashire
M13 9PT
------------------------------------------------------------
Tel: +44(0)161-275-1586
e-mail: Leo...@ma...
http://personalpages.manchester.ac.uk/staff/leonard.chavas/

Hi Warren,

I've read 'Executive.c' under '/trunk/pymol/layer3', it seems that you've
pre-defined all the cases that button actions and popup menu changes in
function ' ExecutiveClick ', I can understand only part of it. Now, I'm
wondering that if I want to implement my thought ( - left-click the C-alpha
atom in the structure, there will be a PopUp window coming out with
self-defined information in the Viewer window), I have to modify the source
code in C-layer and compile the whole source? Am I right? Or, is there any
trick to do this in Python-layer?

Fengyuan

On Sun, Jun 22, 2008 at 1:59 PM, NeO <bob...@gm...> wrote:

> Dear Warren,
>
> How are you?
>
> I'm writing a wizard, in which I want to implement the function that when I
> left-click the C-alpha atom, there will be a PopUp window coming out with my
> defined information in the Viewer window. I can do it using
> 'tkMessageBox.showinfo', but I want to make it beautiful.
>
> I know that when you left-double click or right-click the protein
> structure, the popup menu show up. I read the source code of 'menu.py', I'm
> not sure in the function, the parameter 'self_cmd', what's it for? where the
> menu functions are called? If I figure it out, I think I can code it in my
> wizard.
>
> Hope you can help me :)
>
> Best Wishes
>
> Fengyuan
>

Dear Warren,

How are you?

I'm writing a wizard, in which I want to implement the function that when I
left-click the C-alpha atom, there will be a PopUp window coming out with my
defined information in the Viewer window. I can do it using
'tkMessageBox.showinfo', but I want to make it beautiful.

I know that when you left-double click or right-click the protein structure,
the popup menu show up. I read the source code of 'menu.py', I'm not sure in
the function, the parameter 'self_cmd', what's it for? where the menu
functions are called? If I figure it out, I think I can code it in my
wizard.

Hope you can help me :)

Best Wishes

Fengyuan