pymol-users Mailing List for PyMOL Molecular Graphics System

As a newbie to pymol here a simple? question that I have tried to solve for
some time now (but to no avail):

Is there a way of selecting only those atoms of a protein that are part of
the surface (contact or solvent accessible s.)?

Reason I am asking is: if you've got a big (really big!) protein and you
want to explore cavities within this protein it might be nice to get rid of
the "inner"/non-surface atoms and thus have a higher performance when moving
around, rotating the protein/selection etc.

Any idea?

Thanks,
WDL

-- 
NEU +++ DSL Komplett von GMX +++ http://www.gmx.net/de/go/dsl
GMX DSL-Netzanschluss + Tarif zum supergünstigen Komplett-Preis!

On Tue, 30 Nov 2004, Tru Huynh wrote:

> On Tue, Nov 30, 2004 at 09:02:40PM +0800, Liu Shiyong wrote:
> >  
> >  yes, I reinstall tck+tk
> >  
> no, I wrote tkinter ->  tkinter-2.3.4-11.i386.rpm for FC3
> it is another package.
> 
> (please dont top-post)
> 
> Tru
> 

sorry.  :(

On Tue, Nov 30, 2004 at 09:02:40PM +0800, Liu Shiyong wrote:
>  
>  yes, I reinstall tck+tk
>  
no, I wrote tkinter ->  tkinter-2.3.4-11.i386.rpm for FC3
it is another package.

(please dont top-post)

Tru

 
 yes, I reinstall tck+tk
 
 pymol-0.97-2.fc2.mok.i386.rpm

 http://apt.bioxray.dk/fedora/2/i386/html/index_xray.html
 
 Building pymol sourcecode is very bad experiment. I will never taste it 
if it is still difficulty as now. :(



On Tue, 30 Nov 2004, Tru Huynh wrote:

> On Sun, Nov 28, 2004 at 06:08:08PM +0800, Liu Shiyong wrote:
> > Hi,
> ...
> >  Here is the error msg...
> > 
> ...
> > ImportError: No module named _tkinter
> 
> install the "tkinter" package ;)
> 
> Tru
> 

On Sun, Nov 28, 2004 at 06:08:08PM +0800, Liu Shiyong wrote:
> Hi,
...
>  Here is the error msg...
> 
...
> ImportError: No module named _tkinter

install the "tkinter" package ;)

Tru

hi, 
We have .pdbs of complexes containing receptor and ligands. Can u suggest any 
trick to color them with different shades, while using them as a single object. 
Any modifications to the file etc.  
 
Thanks 
Nishant 

Hi,

I'm trying to get a cartoon model of a pdb file to display a few selected
sidechains as sticks, I can see them in OpenGL, but when raytraycing the
sticks disappear. Using Pymol 0.96 under Windows XP. Ta for any help or
pointers

Peter

-- 
Dr Peter Teriete
Laboratory of Molecular Biophysics
Department of Biochemistry
University of Oxford
South Parks Rd.
Oxford
OX1 3QU
 
Tel: +44 1865 275742
Fax: +44 1865 275182

It is indeed a Octane with IRIX64 6.5.

Date: Thu, 25 Nov 2004 09:50:51 -0800 (PST)
From: Nat Echols <ec...@uc...>
To: pym...@li...
Subject: Re: [PyMOL] blinking pictures on sgi4DIRIX646

> Hi, I have pymol 0.97 installed on a sgi workstation. However it keeps
> the old picture when I move the molecule, which seems like a long time
> delay. I wonder if people have similar experience.

What kind of SGI?  Anything less powerful than an Octane is going to be
pretty useless for PyMOL.  O still runs well on them, but a $500 PC 
with a
$50 NVidia card will be superior for most tasks.  (Unfortunately, most 
PIs
are reluctant to replace a machine they payed $40,000 for back in '99.)

Hi,
 I download the sourcecode:   
 ext-0_95-src.tgz  pymol-0_98beta18-src.tar.gz

 compile source code according to INSTALL  on my fedora coreIII

 Now, compile done completely, but When I run pymol.com, the Tk windows
can not appear!!
  
 I can only see pymol window...


 Here is the error msg...

 Hit ESC anytime to toggle between text and graphics.

 OpenGL-based graphics engine:
  GL_VENDOR: Mesa project: www.mesa3d.org
  GL_RENDERER: Mesa GLX Indirect
  GL_VERSION: 1.2 (1.5 Mesa 6.1)
Traceback (most recent call last):
  File "/usr/local/pymol/pymol-0.98/modules/pymol/__init__.py", line
192, in exec_str    exec s in globals(),globals()
  File "<string>", line 1, in ?
  File "/usr/local/pymol/pymol-0.98/modules/pymol/__init__.py", line
311, in launch_gui
    __import__(invocation.options.gui)
  File "/usr/local/pymol/pymol-0.98/modules/pmg_tk/__init__.py", line
22, in ?
    from PMGApp import *
  File "/usr/local/pymol/pymol-0.98/modules/pmg_tk/PMGApp.py", line 15,
in ?
    from Tkinter import *
  File "/usr/local/pymol/ext-0_95/lib/python2.3/lib-tk/Tkinter.py", line
38, in ?
    import _tkinter # If this fails your Python may not be configured
for Tk
ImportError: No module named _tkinter


-- 
Shiyong Liu                    ++86 (0)6275 7520
Wellcome to MDL             sy...@md...
http://mdl.ipc.pku.edu.cn/~syliu

> Hi, I have pymol 0.97 installed on a sgi workstation. However it keeps
> the old picture when I move the molecule, which seems like a long time
> delay. I wonder if people have similar experience.

What kind of SGI?  Anything less powerful than an Octane is going to be
pretty useless for PyMOL.  O still runs well on them, but a $500 PC with a
$50 NVidia card will be superior for most tasks.  (Unfortunately, most PIs
are reluctant to replace a machine they payed $40,000 for back in '99.)

Hi,

 I download the following version.
 And setup it.
=20
 My os is fedora core3 .

http://delsci.com/beta/
PyMOL 0.98beta05=20

Linux: pymol-0_98beta05-bin-linux-x86.tgz ~10 MB

But, when I run pymol, error occurs

How can I run it successfully?




-------------------------------------------------------------------------=
--------------
 OpenGL-based graphics engine:
  GL_VENDOR: Mesa project: www.mesa3d.org
  GL_RENDERER: Mesa GLX Indirect
  GL_VERSION: 1.2 (1.5 Mesa 6.1)
Exception in thread Thread-1:
Traceback (most recent call last):
  File "/usr/local/pymol/ext/lib/python2.2/threading.py", line 408, in
__bootstrap
    self.run()
  File "/usr/local/pymol/ext/lib/python2.2/threading.py", line 396, in
run
    apply(self.__target, self.__args, self.__kwargs)
  File "/usr/local/pymol/modules/pmg_tk/__init__.py", line 33, in run
    PMGApp(balloon_state=3D'both').run()
  File "/usr/local/pymol/modules/pmg_tk/AbstractApp.py", line 44, in
__init__
    self.root =3D Tk()
  File "/usr/local/pymol/ext/lib/python2.2/lib-tk/Tkinter.py", line
1495, in __init__
    self.tk =3D _tkinter.create(screenName, baseName, className)
TclError: Can't find a usable init.tcl in the following directories:
    /home/local/warren/ext/lib/tcl8.4 /.4 /.4 /.4 /y /y /.y ///.4



This probably means that Tcl wasn't installed properly.


 PyMOL: abrupt program termination.

=3D----------------------------------------------------------------------=
------------


=D4=DA 2004-11-24=C8=FD=B5=C4 20:41 -0800=A3=ACpymol-users-request@lists.=
sourceforge.net=D0=B4=B5=C0=A3=BA

> Send PyMOL-users mailing list submissions to
> 	pym...@li...
>=20
> To subscribe or unsubscribe via the World Wide Web, visit
> 	https://lists.sourceforge.net/lists/listinfo/pymol-users
> or, via email, send a message with subject or body 'help' to
> 	pym...@li...
>=20
> You can reach the person managing the list at
> 	pym...@li...
>=20
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of PyMOL-users digest..."
>=20
>=20
> Today's Topics:
>=20
>    1. Perspective Rendering (at last!) (Warren DeLano)
>    2. blinking pictures on sgi4DIRIX646 (Yunfeng Hu)
>=20
> --__--__--
>=20
> Message: 1
> From: "Warren DeLano" <wa...@de...>
> To: <pym...@li...>
> Date: Wed, 24 Nov 2004 11:55:48 -0800
> Subject: [PyMOL] Perspective Rendering (at last!)
>=20
> PyMOL Users,
>=20
> Hooray -- PyMOL's ray tracer can finally do perspective rendering!  Why=
 is
> this such a good thing? =20
>=20
> Because (1) ray-traced images are now always "what you see is what you =
get"
> (WYSIWYG) versus OpenGL, (2) you can make rendered movies where molecul=
es
> move around still look right, and (3) it will soon become possible to
> generate rendered stereo pairs with 'perfect' visual geometry (no more =
+/- 3
> degree nonsense)...
>=20
> However, there is a price to pay:  Even though I've beat on the code wi=
th
> Apple's CHUD performance tool, perspective rendering is still 2-5X slow=
er
> than orthoscopic rendering.  That's because there are all kinds of
> mathematical simplifications one can make in orthoscopic scenes (where =
all
> the rays are parallel) that just don't apply to perspective scenes (whe=
re
> all the rays aren't parallel).  Regardless, even with perspective turne=
d on,
> PyMOL's renderer is as fast as PovRay for most basic molecular scenes.
>=20
> Updated beta builds for Windows & Mac at:  http://delsci.com/beta
> http://delsci.com/macbeta
>=20
> NOTE: perspective rendering is now the default in order to exactly matc=
h
> OpenGL geometry.  This means that default rendering will seem noticably
> slower.  If you want faster performance, then turn perspective off usin=
g
> "set orthoscopic" before rendering.
>=20
> Cheers,
> Warren
>=20
> --
> Warren L. DeLano, Ph.D.                    =20
> Principal Scientist
>=20
> . DeLano Scientific LLC =20
> . 400 Oyster Point Blvd., Suite 213          =20
> . South San Francisco, CA 94080   =20
> . Biz:(650)-872-0942  Tech:(650)-872-0834    =20
> . Fax:(650)-872-0273  Cell:(650)-346-1154
> . mailto:wa...@de...     =20
>=20
>=20
>=20
>=20
> --__--__--
>=20
> Message: 2
> To: pym...@li...
> From: Yunfeng Hu <yu...@sc...>
> Date: Wed, 24 Nov 2004 15:59:42 -0800
> Subject: [PyMOL] blinking pictures on sgi4DIRIX646
>=20
> Hi, I have pymol 0.97 installed on a sgi workstation. However it keeps=20
> the old picture when I move the molecule, which seems like a long time=20
> delay. I wonder if people have similar experience.
>=20
> Eric
>=20
>=20
>=20
>=20
> --__--__--
>=20
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
> End of PyMOL-users Digest

--=20
Shiyong Liu                    ++86 (0)6275 7520
Wellcome to MDL             sy...@md...
http://mdl.ipc.pku.edu.cn/~syliu

Hi,
 =20
Did someone compile pymol successfully on core3 ? =20
My uname -a is
Linux protein 2.6.8-1.541 #1 Wed Sep 1 18:01:20 EDT 2004 i686 athlon
i386 GNU/Linux .

I just tried to install pymol in my fedora core3 test3 OS.=20




Other Unix

     1. Download the source: pymol-0_97-src.tgz (alternate).
     2. Either configure PyMOL to use your existing external
        dependencies, or download and compile from sources:
        ext-0_95-src.tgz (alternate) includes:
              * Python-2.3.3
              * Numeric-22.0
              * Pmw-1.2
              * glut-3.7.6
              * tcl-8.4.6
              * tk-8.4.6
              * libpng-1.2.5
              * zlib-1.2.1
     3. Compile pymol (see INSTALL file for details).


________________________________________________________________________



=D4=DA 2004-11-23=B6=FE=B5=C4 20:45 -0800=A3=ACpymol-users-request@lists.=
sourceforge.net=D0=B4=B5=C0=A3=BA

> Send PyMOL-users mailing list submissions to
> 	pym...@li...
>=20
> To subscribe or unsubscribe via the World Wide Web, visit
> 	https://lists.sourceforge.net/lists/listinfo/pymol-users
> or, via email, send a message with subject or body 'help' to
> 	pym...@li...
>=20
> You can reach the person managing the list at
> 	pym...@li...
>=20
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of PyMOL-users digest..."
>=20
>=20
> Today's Topics:
>=20
>    1. Re: List participation commentary (Kristian Rother)
>    2. 0.98 beta 18 Selecting bug (Jules Jacobsen)
>    3. PyMol not displaying molecules (Greg Landrum)
>    4. Re: PyMol not displaying molecules (Greg Landrum)
>=20
> --__--__--
>=20
> Message: 1
> From: Kristian Rother <kri...@ch...>
> Organization: Charite Berlin
> To: pym...@li...
> Date: Tue, 23 Nov 2004 07:58:58 +0000
> Subject: [PyMOL] Re: List participation commentary
>=20
> On Monday 22 November 2004 18:49, Cameron Mura wrote:
> > >Ultimately the mailing list serves as a form of living manual to the
> > > program, so it would be nice to preserve as many of these insights =
as
> > > possible!
>=20
> Well, i have written up and sorted a number of answers to common proble=
ms o=3D
> n=3D20
> my homepage. However, it's far away from being a wiki. Neither it is co=
mple=3D
> te=3D20
> in any way.
>=20
> http://www.rubor.de/bioinf/pymol_tips.html
>=20
> Yours,
>=20
>    Kristian Rother
>    Humboldt Universit=3DE4t Berlin
>=20
>=20
> --__--__--
>=20
> Message: 2
> Date: Tue, 23 Nov 2004 11:26:43 +0000
> From: Jules Jacobsen <jo...@he...>
> To: pym...@li...
> Subject: [PyMOL] 0.98 beta 18 Selecting bug
>=20
> Oops! sorry, I just realized that the .pse was quite large. My apologie=
s.
>=20
> The pdbs used were 1hju, 1hjs and 1hjq. The following script will=20
> produce the same pse:
>=20
> select Binding, (resi 86,300)
> label Binding and elem o, (resn+'-'+resi)
> zoom Binding
>=20
>=20
> Jules
>=20
> -------- Original Message --------
> Subject: 0.98 beta 18 Selecting
> Date: Tue, 23 Nov 2004 11:05:01 +0000
> From: Jules Jacobsen <jo...@he...>
> To: pym...@li...
>=20
> Hi all,
>=20
> Has anyone else had the problem of not being able to select several
> identical residue types in aligned structures? eg in the .pse included,
> if you single left-click on Trp-86 (the left one of the 'Binding'
> selection) and try to select them all in the same manner, PyMOL won't
> add any more residues to the selection if it has the same resn/resi. It
> will select them if you use a shift-left-click. It will however, happil=
y
> remove them from the selection with a single left-click.
>=20
> I'm guessing this is a PyMOL rather than platform specific bug? (I'm
> running on WinXP)
>=20
> Cheers,
>=20
> Jules
>=20
>=20
>=20
>=20
> --__--__--
>=20
> Message: 3
> Date: Tue, 23 Nov 2004 17:11:54 -0800
> To: pym...@li...
> From: Greg Landrum <gre...@ea...>
> Subject: [PyMOL] PyMol not displaying molecules
>=20
>=20
> I've encountered a problem where PyMol will no longer display molecules=
=20
> using normal rendering on my machine.  (Symptoms: I load a molecule and=
 see=20
> nothing, but if I raytrace the image, the result looks fine).  I've=20
> verified that this happens in pymol versions 0.97 and 0.98beta18.
>=20
> System details:
> OS: Win2K
> Graphics Card: Radeon 7000 series
> Graphics Driver: the most recent ATI driver suite (6.14.10.6483).
>=20
> I'm not 100% certain, but I am pretty sure that the problem dates to my=
=20
> update of the graphics driver.  Any suggestions as to how I might work=20
> around this problem?
>=20
> Here's PyMol's startup output, in case that's useful:
>=20
>   PyMOL(TM) Molecular Graphics System, Version 0.98beta18.
>   Copyright (C) 2004 by DeLano Scientific LLC.
>   All Rights Reserved.
>=20
>      Created by Warren L. DeLano, Ph.D.
>=20
>      Other Major Authors and Contributors:
>=20
>         Ralf W. Grosse-Kunstleve, Ph.D.
>=20
>      PyMOL is user-supported open-source software.  Although most versi=
ons
>      are freely available, PyMOL is not in the public domain.
>=20
>      If PyMOL is helpful in your work or study, then please volunteer
>      support for our ongoing campaign to create open and affordable sof=
tware
>      for molecular research.
>=20
>      Updates and other information can be found at "http://www.pymol.or=
g".
>=20
>      Please cite PyMOL in publications and presentations:
>=20
>         Warren L. DeLano "The PyMOL Molecular Graphics System."
>         DeLano Scientific LLC, San Carlos, CA, USA. http://www.pymol.or=
g
>=20
>      Enter "help" for a list of commands.
>      Enter "help <command-name>" for information on a specific command.
>=20
>   Hit ESC anytime to toggle between text and graphics.
>=20
>   OpenGL-based graphics engine:
>    GL_VENDOR: ATI Technologies Inc.
>    GL_RENDERER: RADEON 7000 DDR x86/SSE2
>    GL_VERSION: 1.3.4650 Win2000 Release
>=20
> Thanks in advance for any help,
> -greg
>=20
> ----
> greg Landrum (gre...@ea...)
> Software Carpenter/Computational Chemist
>=20
>=20
>=20
> --__--__--
>=20
> Message: 4
> Date: Tue, 23 Nov 2004 20:08:33 -0800
> To: pym...@li...
> From: Greg Landrum <gre...@ea...>
> Subject: Re: [PyMOL] PyMol not displaying molecules
>=20
> At 05:11 PM 11/23/2004, I wrote:
>=20
> >I'm not 100% certain, but I am pretty sure that the problem dates to m=
y=20
> >update of the graphics driver.  Any suggestions as to how I might work=
=20
> >around this problem?
>=20
> For what it's worth, when I go back to an older version of the ATI driv=
er=20
> (6.14.10.6343, dated 4/28/2003), everything works fine.
>=20
> -greg
>=20
> ----
> greg Landrum (gre...@ea...)
> Software Carpenter/Computational Chemist
>=20
>=20
>=20
>=20
> --__--__--
>=20
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
> End of PyMOL-users Digest

--=20
Shiyong Liu                    ++86 (0)6275 7520
Wellcome to MDL             sy...@md...
http://mdl.ipc.pku.edu.cn/~syliu

Hi, I have pymol 0.97 installed on a sgi workstation. However it keeps 
the old picture when I move the molecule, which seems like a long time 
delay. I wonder if people have similar experience.

Eric

PyMOL Users,

Hooray -- PyMOL's ray tracer can finally do perspective rendering!  Why is
this such a good thing?  

Because (1) ray-traced images are now always "what you see is what you get"
(WYSIWYG) versus OpenGL, (2) you can make rendered movies where molecules
move around still look right, and (3) it will soon become possible to
generate rendered stereo pairs with 'perfect' visual geometry (no more +/- 3
degree nonsense)...

However, there is a price to pay:  Even though I've beat on the code with
Apple's CHUD performance tool, perspective rendering is still 2-5X slower
than orthoscopic rendering.  That's because there are all kinds of
mathematical simplifications one can make in orthoscopic scenes (where all
the rays are parallel) that just don't apply to perspective scenes (where
all the rays aren't parallel).  Regardless, even with perspective turned on,
PyMOL's renderer is as fast as PovRay for most basic molecular scenes.

Updated beta builds for Windows & Mac at:  http://delsci.com/beta
http://delsci.com/macbeta

NOTE: perspective rendering is now the default in order to exactly match
OpenGL geometry.  This means that default rendering will seem noticably
slower.  If you want faster performance, then turn perspective off using
"set orthoscopic" before rendering.

Cheers,
Warren

--
Warren L. DeLano, Ph.D.                     
Principal Scientist

. DeLano Scientific LLC  
. 400 Oyster Point Blvd., Suite 213           
. South San Francisco, CA 94080    
. Biz:(650)-872-0942  Tech:(650)-872-0834     
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:wa...@de...      

At 05:11 PM 11/23/2004, I wrote:

>I'm not 100% certain, but I am pretty sure that the problem dates to my 
>update of the graphics driver.  Any suggestions as to how I might work 
>around this problem?

For what it's worth, when I go back to an older version of the ATI driver 
(6.14.10.6343, dated 4/28/2003), everything works fine.

-greg

----
greg Landrum (gre...@ea...)
Software Carpenter/Computational Chemist

I've encountered a problem where PyMol will no longer display molecules 
using normal rendering on my machine.  (Symptoms: I load a molecule and see 
nothing, but if I raytrace the image, the result looks fine).  I've 
verified that this happens in pymol versions 0.97 and 0.98beta18.

System details:
OS: Win2K
Graphics Card: Radeon 7000 series
Graphics Driver: the most recent ATI driver suite (6.14.10.6483).

I'm not 100% certain, but I am pretty sure that the problem dates to my 
update of the graphics driver.  Any suggestions as to how I might work 
around this problem?

Here's PyMol's startup output, in case that's useful:

  PyMOL(TM) Molecular Graphics System, Version 0.98beta18.
  Copyright (C) 2004 by DeLano Scientific LLC.
  All Rights Reserved.

     Created by Warren L. DeLano, Ph.D.

     Other Major Authors and Contributors:

        Ralf W. Grosse-Kunstleve, Ph.D.

     PyMOL is user-supported open-source software.  Although most versions
     are freely available, PyMOL is not in the public domain.

     If PyMOL is helpful in your work or study, then please volunteer
     support for our ongoing campaign to create open and affordable software
     for molecular research.

     Updates and other information can be found at "http://www.pymol.org".

     Please cite PyMOL in publications and presentations:

        Warren L. DeLano "The PyMOL Molecular Graphics System."
        DeLano Scientific LLC, San Carlos, CA, USA. http://www.pymol.org

     Enter "help" for a list of commands.
     Enter "help <command-name>" for information on a specific command.

  Hit ESC anytime to toggle between text and graphics.

  OpenGL-based graphics engine:
   GL_VENDOR: ATI Technologies Inc.
   GL_RENDERER: RADEON 7000 DDR x86/SSE2
   GL_VERSION: 1.3.4650 Win2000 Release

Thanks in advance for any help,
-greg

----
greg Landrum (gre...@ea...)
Software Carpenter/Computational Chemist

Oops! sorry, I just realized that the .pse was quite large. My apologies.

The pdbs used were 1hju, 1hjs and 1hjq. The following script will 
produce the same pse:

select Binding, (resi 86,300)
label Binding and elem o, (resn+'-'+resi)
zoom Binding


Jules

-------- Original Message --------
Subject: 0.98 beta 18 Selecting
Date: Tue, 23 Nov 2004 11:05:01 +0000
From: Jules Jacobsen <jo...@he...>
To: pym...@li...

Hi all,

Has anyone else had the problem of not being able to select several
identical residue types in aligned structures? eg in the .pse included,
if you single left-click on Trp-86 (the left one of the 'Binding'
selection) and try to select them all in the same manner, PyMOL won't
add any more residues to the selection if it has the same resn/resi. It
will select them if you use a shift-left-click. It will however, happily
remove them from the selection with a single left-click.

I'm guessing this is a PyMOL rather than platform specific bug? (I'm
running on WinXP)

Cheers,

Jules

On Monday 22 November 2004 18:49, Cameron Mura wrote:
> >Ultimately the mailing list serves as a form of living manual to the
> > program, so it would be nice to preserve as many of these insights as
> > possible!

Well, i have written up and sorted a number of answers to common problems o=
n=20
my homepage. However, it's far away from being a wiki. Neither it is comple=
te=20
in any way.

http://www.rubor.de/bioinf/pymol_tips.html

Yours,

   Kristian Rother
   Humboldt Universit=E4t Berlin

I definitely second Seth's praise for the animation feature.  It may =
seem a little "hokey" at first, but in presentations it really helps to =
keep the viewers in register with the presenter... My only niggle with =
it is that it actually moves too fast (on my machine) - any way of =
throttling it, at least on beefy graphics cards (sort of like the fps =
setting for movies)??

-Tom


-----Original Message-----
From: pym...@li...
[mailto:pym...@li...]On Behalf Of Seth Harris
Sent: Monday, November 22, 2004 4:27 PM
To: pym...@li...
Subject: [PyMOL] linux and multi-button mouse

<very long mouse tail clipped>


>Last things were just mouse interface feedback for Warren,=20
>and to make those short...
>
>2) Animation is slick, Dr. DeLano! Particularly helps in=20
>sharing structures as people currently get disoriented=20
>when I recenter if they aren't "driving".  Don't feel=20
>strongly if it's on or off by default, though, since I=20
>tend to set things up how I like them using start up=20
>scripts (e.g. auto_zoom off like Tom was mentioning)
>
>-seth
>

Yo,
I just wrote a really long email to the list.  So long 
that my web mail secretly logged me out during the time 
that I was writing it.  The upshot of this is that 1) I am 
angry and 2) you are all spared the rambling version and 
hopefully get the more succinct version summarized here:

I have RedHat Linux Enterprise 3 or somesuch.  I got a 
wireless multi-button mouse and RedHat's auto configure 
thing (kudzu) managed to get it working after a fashion. 
 Middle click (i.e. clicking the scroll wheel), however, 
was very sluggish and I couldn't get it reliably work more 
than a dismal 1 in 10 tries.  Is this a problem for you? 
 Then read on...(although maybe it's only me as I haven't 
heard a peep about it)...

I figured why not map one of the currently non-functioning 
side buttons so that it behaves like the middle button. 
 Changed XF86Config file to treat the mouse as a 7-button 
mouse (see below).  The ZAxisMapping stuff is for the 
scroll wheel.

Identifier "Mouse1"
Driver "mouse"
Option "Protocol" "ExplorerPS/2"
Option "Device" "/dev/psaux"
Option "Emulate3Buttons" "no"
### To enable scrolling on a ps/2 or usb scroll
Option "ZAxisMapping" "6 7"

This resulted in all buttons being active, if not doing 
quite what I wanted yet (can run "xev" to check for mouse 
events).  That is, middle click was still on the scroll 
wheel, and the scroll wheel itself was showing unusual 
behavior in various applications.

Then found out about xmodmap which allows you to remap 
things.  The on-the-fly version goes something like:
xmodmap -e "pointer 1 6 3 7 2 4 5"
Since that worked for me I put the
pointer 1 6 3 7 2 4 5
line in my ~/.Xmodmap file.

Naturally the normal ordering of the pointer is 1 2 3 4 5 
6 7, corresponding I think to left, middle, right, side1, 
side2 buttons and scroll wheel up or down.  So by swapping 
position 2 to send function 6, I deactivate the middle 
scroll wheel button to do something else (whatever 6 is), 
and then position 5 (one of the side buttons) now sends 
function 2 (a middle click).  There was some other issue 
with the scroll wheel which necessitated shuffling around 
the 4 and 5 part, as well, but much to my amazement I now 
have a side button that is nice and responsive as a middle 
click, the scroll wheel still works both in pymol and 
other apps like web browsers, and serendipitously, the 
other side button is a double middle click so I can center 
with a single click...although this glory will be brief as 
it sounds like Warren is about to introduce that in the 
new changes (looking forward to it!)

I thought this might have some bearing on Charlie's 
question about mapping zoom functionality to scroll wheel 
instead of clipping planes, but this method will probably 
affect the mouse behaviour in all applications so maybe 
that's not a viable solution for him.  There is also 
imwheel which apparently allows you to map mouse clicks to 
other events/keystrokes in an application-dependent manner 
but I haven't tried it.

Wow, this is pretty long anyway.  Trust me, the other was 
longer.  Heck, maybe it even got sent even though I see no 
sign of it in which case you get double dosage...ouch!

By the way, this was with microsoft wireless desktop pro 
mouse (similar or same as explorer mouse?).  ImPS/2 is 
another XF86Config protocol you could try if this isn't 
working...

Last things were just mouse interface feedback for Warren, 
and to make those short...

1) Warren...I really like the mouse interface, basically 
one of the best I've ever used, the upcoming improvements 
seem just that...improvements.
2) Animation is slick, Dr. DeLano! Particularly helps in 
sharing structures as people currently get disoriented 
when I recenter if they aren't "driving".  Don't feel 
strongly if it's on or off by default, though, since I 
tend to set things up how I like them using start up 
scripts (e.g. auto_zoom off like Tom was mentioning)

-seth

Peter -

I can't remember if you sent this to the whole list or not (I only have=20
one sent to me, but if you send it to both places, I get two coppies, and=
=20
I often delete one of those), so I appologize in advance if you only sent=
=20
it to me.

On Mon, 22 Nov 2004, Peter Haebel wrote:

> On Monday 22 November 2004 20:29, you wrote:
>> Hi,
>>
>> I've heard this from a few people, and the answer seems to be that the n=
ew
>> version of APBS doesn't like chain information in the PyMOL-generated PQ=
R
>> files.  I'll release a new version of the plugin that fixes this soon, b=
ut
>> in the meantime, the easy solution is to remove the chain information fr=
om
>> the PDB file before you start the APBS calculation.
>
> how does apbs handle oligomeric proteins if it does not support chain ids=
? i
> think pymol is not happy, if you have residues with identical chain (or n=
o
> chain) and identical resi.

  - apbs just cares about points in space with radii and charge.  in fact,
some of the test cases that come with apbs actually have duplicate residue
ids.
  - i think apbs probably supports chain ids pretty well; i think there's
just a mismatch in file formats between pymol-generated pqr files and the
latest apbs.
  - i think (this one i haven't tried, but i'm pretty sure) that if you
load the protein up in pymol and then remove the chain ids, pymol will be
just fine.

>>   - PyMOL couldn't assign charges/radii to some of your atoms.  Do you h=
ave
>> a non-standard protein residue?  If not, it may be that you have a
>> terminal residue that PyMOL/champ doesn't understand.  Can you look at t=
he
>> PQR file to see which residues ended up with radii and charges of 0?
>>
>
> i have simply attached the original pdb file after refinement with CNS an=
d the
> converted pqr file.
>
> there seem to be two problems with
>
> a) C-terminus OT1 and OT2
> b) Ser, Thr, Try OH-groups
>
> this is by the way not the original pdb file 1ini, which i only used to=
=20
verify
> whether or not original pdb files work.

i think the OH groups are fine.  those have non-zero radii, so i think
it's just that the standard set of parameters don't put a charge on the
hydrogen there.  the terminal THRs, though, are trouble.  i think this is
a question for warren:

can champ handle terminal THRs?

(i'm really busy right now, so i don't quite have time to check .. if you
don't get an answer from warren soon, though, i'll double-check).

the first two and last two residues of the chain look like this in the pqr=
=20
file:

ATOM      1  N   LEU A   6      26.067  12.507  58.949   0.101   1.824
ATOM      2  CA  LEU A   6      25.986  11.536  57.819   0.010   1.908
ATOM      3  C   LEU A   6      25.209  10.280  58.196   0.612   1.908
ATOM      4  O   LEU A   6      24.704   9.579  57.322  -0.571   1.661
ATOM      5  CB  LEU A   6      27.394  11.138  57.356  -0.024   1.908
ATOM      6  CG  LEU A   6      28.271  12.223  56.726   0.342   1.908
ATOM      7  CD1 LEU A   6      29.621  11.630  56.341  -0.411   1.908
ATOM      8  CD2 LEU A   6      27.578  12.796  55.501  -0.410   1.908
ATOM      9 HD23 LEU A   6      27.308  11.986  54.823   0.098   1.487
ATOM     10  H3  LEU A   6      26.642  12.122  59.684   0.215   0.600
ATOM     11  HA  LEU A   6      25.454  12.034  57.009   0.105   1.100
ATOM     12  HB2 LEU A   6      27.282  10.342  56.620   0.026   1.487
ATOM     13  HG  LEU A   6      28.430  13.025  57.446  -0.038   1.487
ATOM     14 HD13 LEU A   6      29.914  12.001  55.359   0.098   1.487
ATOM     15 HD22 LEU A   6      28.250  13.487  54.993   0.098   1.487
ATOM     16  H2  LEU A   6      25.140  12.687  59.306   0.215   0.600
ATOM     17  HB3 LEU A   6      27.916  10.861  58.272   0.026   1.487
ATOM     18 HD12 LEU A   6      29.546  10.543  56.312   0.098   1.487
ATOM     19 HD21 LEU A   6      26.677  13.327  55.809   0.098   1.487
ATOM     20  H1  LEU A   6      26.475  13.371  58.621   0.215   0.600
ATOM     21 HD11 LEU A   6      30.369  11.923  57.078   0.098   1.487
ATOM     22  N   ASP A   7      25.123   9.988  59.492  -0.516   1.824
ATOM     23  CA  ASP A   7      24.402   8.804  59.946   0.038   1.908
ATOM     24  C   ASP A   7      22.955   8.814  59.477   0.537   1.908
ATOM     25  O   ASP A   7      22.238   9.804  59.631  -0.582   1.661
ATOM     26  CB  ASP A   7      24.450   8.684  61.470  -0.030   1.908
ATOM     27  CG  ASP A   7      25.795   8.193  61.972   0.799   1.908
ATOM     28  OD1 ASP A   7      26.303   7.191  61.420  -0.801   1.661
ATOM     29  OD2 ASP A   7      26.339   8.801  62.917  -0.801   1.661
ATOM     30  HB2 ASP A   7      23.679   7.983  61.791  -0.012   1.487
ATOM     31  H   ASP A   7      25.563  10.594  60.170   0.294   0.600
ATOM     32  HA  ASP A   7      24.899   7.940  59.506   0.088   1.387
ATOM     33  HB3 ASP A   7      24.284   9.678  61.886  -0.012   1.487
ATOM   3218  N   LEU A 227      17.723 -10.762  41.310  -0.416   1.824
ATOM   3219  CA  LEU A 227      18.730 -10.979  42.344  -0.052   1.908
ATOM   3220  C   LEU A 227      19.890 -11.839  41.842   0.597   1.908
ATOM   3221  O   LEU A 227      21.057 -11.531  42.098  -0.568   1.661
ATOM   3222  CB  LEU A 227      18.088 -11.633  43.573  -0.110   1.908
ATOM   3223  CG  LEU A 227      17.174 -10.734  44.413   0.353   1.908
ATOM   3224  CD1 LEU A 227      16.527 -11.535  45.530  -0.412   1.908
ATOM   3225  CD2 LEU A 227      17.993  -9.584  44.989  -0.412   1.908
ATOM   3226 HD23 LEU A 227      18.234  -9.795  46.031   0.100   1.487
ATOM   3227  H   LEU A 227      16.782 -11.097  41.457   0.272   0.600
ATOM   3228  HA  LEU A 227      19.136 -10.005  42.617   0.092   1.387
ATOM   3229  HB2 LEU A 227      18.890 -11.990  44.219   0.046   1.487
ATOM   3230  HG  LEU A 227      16.382 -10.332  43.781  -0.036   1.487
ATOM   3231 HD13 LEU A 227      16.466 -10.922  46.429   0.100   1.487
ATOM   3232 HD22 LEU A 227      17.417  -8.661  44.928   0.100   1.487
ATOM   3233  HB3 LEU A 227      17.445 -12.422  43.183   0.046   1.487
ATOM   3234 HD12 LEU A 227      17.125 -12.423  45.734   0.100   1.487
ATOM   3235 HD21 LEU A 227      18.915  -9.474  44.419   0.100   1.487
ATOM   3236 HD11 LEU A 227      15.524 -11.835  45.227   0.100   1.487
ATOM   3237  N   THR A 228      19.569 -12.911  41.124   0.000   0.000
ATOM   3238  C   THR A 228      20.590 -13.807  40.593   0.000   0.000
ATOM   3239  C   THR A 228      21.444 -13.108  39.535   0.000   0.000
ATOM   3240  C   THR A 228      19.948 -15.058  39.957   0.000   0.000
ATOM   3241  C   THR A 228      21.031 -16.038  39.496   0.000   0.000
ATOM   3242  O   THR A 228      19.102 -15.703  40.918   0.000   0.000
ATOM   3243  O   THR A 228      20.959 -12.123  38.939   0.000   0.000
ATOM   3244  O   THR A 228      22.581 -13.566  39.299   0.000   0.000
ATOM   3245  H   THR A 228      22.852 -13.310  38.414   0.000   0.000
ATOM   3246  H   THR A 228      18.596 -13.109  40.942   0.000   0.000
ATOM   3247  H   THR A 228      21.221 -14.102  41.431   0.000   0.000
ATOM   3248  H   THR A 228      22.133 -12.425  39.039   0.000   0.000
ATOM   3249  H   THR A 228      19.359 -14.749  39.093   0.000   0.000
ATOM   3250  H   THR A 228      21.259 -15.860  38.445   0.000   0.000
ATOM   3251  H   THR A 228      18.974 -15.123  41.673   0.000   0.000
ATOM   3252  H   THR A 228      20.771 -12.360  38.028   0.000   0.000
ATOM   3253  H   THR A 228      20.675 -17.060  39.623   0.000   0.000
ATOM   3254  H   THR A 228      21.931 -15.891  40.093   0.000   0.000
TER    3255      THR A 228

-michael


>> thanks,
>>
>> -michael
>>
>> --
>> This isn't a democracy;|                        _  |Michael Lerner
>>   it's a cheer-ocracy.  | ASCII ribbon campaign ( ) |   Michigan
>> -Torrence,  Bring It On|  - against HTML email  X  |  Biophysics
>>
>>                         |                       / \ | mlerner@umich
>>
>> On Mon, 22 Nov 2004, Peter Haebel wrote:
>>> Hi Michael,
>>>
>>> i have just updated to the latest version of apbs-0.3.2 and pymol-0.97
>>> under debian linux and get the following error messages (see below) + a
>>> completely positively charged protein surface...
>>>
>>> using a pqr-file generated at 'http://nbcr.sdsc.edu/pdb2pqr/index.html'
>>> of the same protein works, so there seems to be a problem with the
>>> build-in generation of pqr-files.
>>>
>>> i tried 3 different proteins from the PDB with and w/o ligand and water
>>> atoms.
>>>
>>> any idea what's going wrong?
>>>
>>> cheers,
>>>
>>> Peter
>>>
>>> -----------------------------------------------------------------------=
--
>>> -----
>>>
>>> PDB code 1ini
>>> all waters and ligand atoms removed by hand
>>>
>>> ...
>>> radiobutton said to generate it Use PyMOL generated PQR and PyMOL
>>> generated Hydrogens and termini so i am returning pymol-generated.pqr
>>> radiobutton said to generate it Use PyMOL generated PQR and PyMOL
>>> generated Hydrogens and termini so i am returning pymol-generated.pqr
>>> WARNING: 5 atoms did not have formal charges assigned
>>> WARNING: 10 atoms did not have properties assigned
>>> ...
>>>
>>> This executable compiled on Nov 22 2004 at 15:59:46
>>>
>>> Parsing input file pymol-generated.in...
>>> parsePBE:  Warning -- parsed deprecated "bcfl 1" statement
>>> parsePBE:  Please use "bcfl sdh" instead.
>>> NOsh:  Warning -- parsed deprecated statment "chgm 1".
>>> NOsh:  Please use "chgm spl2" instead!
>>> parsePBE:  Warning -- parsed deprecated "srfm 1" statement.
>>> parsePBE:  Please use "srfm smol" instead.
>>> parsePBE:  Warning -- parsed deprecated "calcenergy 0" statement.
>>> parsePBE:  Please use "calcenergy no" instead.
>>> parsePBE:  Warning -- parsed deprecated "calcforce 0" statement.
>>> parsePBE:  Please use "calcforce no" instead.
>>> Parsed input file.
>>> Got PQR paths for 1 molecules
>>> Reading PQR-format atom data from pymol-generated.pqr.
>>> Valist_readPDB:  Unable to parse resSeq token (A) as int!
>>> Valist_readPDB:  Error while parsing residue name!
>>> Valist_readPQR:  Error parsing ATOM field!
>>> Error while reading molecule from pymol-generated.pqr
>>> Error reading molecules!
>>> ObjectMapLoadDXFile: Loading from 'pymol-generated.dx'.
>>> DXStrToMap: Dimensions: 129 129 97
>>> DXStrToMap: Origin   14.554  -48.010   -7.484
>>> DXStrToMap: Grid    0.579    0.523    0.664
>>> DXStrToMap: 1614177 data points.
>>> ObjectMap: Map Read.  Range =3D 3352.843994 to 12333.959961
>>>
>>> ___________________________________________
>>>
>>> Peter Haebel
>>>
>>> Philipps-Universit=E4t Marburg
>>> Institut f=FCr Pharmazeutische Chemie
>>> Marbacher Weg 6
>>> D-35032 Marburg
>>>
>>> phone: +49-6421-28-25072
>>> fax: +49-6421-28-28994
>>>
>>> email: pet...@st...
>>> http://www.agklebe.de
>>>
>>> NAD3-Workshop 2005 - Divide&Conquer
>>> http://www.agklebe.de/workshop2005
>
> --=20
> ___________________________________________
>
> Dr. Peter Haebel
>
> Philipps-Universit=E4t Marburg
> Institut f=FCr Pharmazeutische Chemie
> Marbacher Weg 6
> D-35032 Marburg
>
> phone: +49-6421-28-25072
> fax: +49-6421-28-28994
>
> email: pet...@st...
> http://www.agklebe.de
>
> NAD3-Workshop 2005 - Divide&Conquer
> http://www.agklebe.de/workshop2005
>

Is it possible to make this an option by means of a switch?

i.e. set mouse_toggle=0 (or 1)

Or manually configure each click-and-release?

I see how it could be useful, however I often double click the left 
mouse button randomly when ... thinking ... and in this beta release I 
accidentally invoke selection toggle (multiple times).  On the flip 
side, this might be good way for me to pick random atoms.

Thanks,
Doug


On Nov 19, 2004, at 12:53 PM, Warren DeLano wrote:
>
>  - If you left-click-and-release, you get selection toggle behavior.
>  - If you middle-click-and-release you get centering behavior.
>  - If you right-click-and-release you get a context-sensitive pop-up 
> menu.
>
> Also, if you right click on an active selection, the pop-up menu is now
> selection-oriented menu rather than being the standard atom-click menu.
>
> Is this better?  Let me know...I very much think so. 
>  

Hi,

I've heard this from a few people, and the answer seems to be that the new=
=20
version of APBS doesn't like chain information in the PyMOL-generated PQR=
=20
files.  I'll release a new version of the plugin that fixes this soon, but=
=20
in the meantime, the easy solution is to remove the chain information from=
=20
the PDB file before you start the APBS calculation.

There are a couple of other errors in your run:

  - APBS is complaining that I'm using an old style of input file.  I'll=20
fix that in the next version of my plugin, but the old style still works,=
=20
so it's not really causing trouble.

  - PyMOL couldn't assign charges/radii to some of your atoms.  Do you have=
=20
a non-standard protein residue?  If not, it may be that you have a=20
terminal residue that PyMOL/champ doesn't understand.  Can you look at the=
=20
PQR file to see which residues ended up with radii and charges of 0?

thanks,

-michael

--
This isn't a democracy;|                        _  |Michael Lerner
  it's a cheer-ocracy.  | ASCII ribbon campaign ( ) |   Michigan
-Torrence,  Bring It On|  - against HTML email  X  |  Biophysics
                        |                       / \ | mlerner@umich

On Mon, 22 Nov 2004, Peter Haebel wrote:

> Hi Michael,
>
> i have just updated to the latest version of apbs-0.3.2 and pymol-0.97 un=
der
> debian linux and get the following error messages (see below) + a complet=
ely
> positively charged protein surface...
>
> using a pqr-file generated at 'http://nbcr.sdsc.edu/pdb2pqr/index.html' o=
f the
> same protein works, so there seems to be a problem with the build-in
> generation of pqr-files.
>
> i tried 3 different proteins from the PDB with and w/o ligand and water a=
toms.
>
> any idea what's going wrong?
>
> cheers,
>
> Peter
>
> -------------------------------------------------------------------------=
-----
>
> PDB code 1ini
> all waters and ligand atoms removed by hand
>
> ...
> radiobutton said to generate it Use PyMOL generated PQR and PyMOL generat=
ed
> Hydrogens and termini so i am returning pymol-generated.pqr
> radiobutton said to generate it Use PyMOL generated PQR and PyMOL generat=
ed
> Hydrogens and termini so i am returning pymol-generated.pqr
> WARNING: 5 atoms did not have formal charges assigned
> WARNING: 10 atoms did not have properties assigned
> ...
>
> This executable compiled on Nov 22 2004 at 15:59:46
>
> Parsing input file pymol-generated.in...
> parsePBE:  Warning -- parsed deprecated "bcfl 1" statement
> parsePBE:  Please use "bcfl sdh" instead.
> NOsh:  Warning -- parsed deprecated statment "chgm 1".
> NOsh:  Please use "chgm spl2" instead!
> parsePBE:  Warning -- parsed deprecated "srfm 1" statement.
> parsePBE:  Please use "srfm smol" instead.
> parsePBE:  Warning -- parsed deprecated "calcenergy 0" statement.
> parsePBE:  Please use "calcenergy no" instead.
> parsePBE:  Warning -- parsed deprecated "calcforce 0" statement.
> parsePBE:  Please use "calcforce no" instead.
> Parsed input file.
> Got PQR paths for 1 molecules
> Reading PQR-format atom data from pymol-generated.pqr.
> Valist_readPDB:  Unable to parse resSeq token (A) as int!
> Valist_readPDB:  Error while parsing residue name!
> Valist_readPQR:  Error parsing ATOM field!
> Error while reading molecule from pymol-generated.pqr
> Error reading molecules!
> ObjectMapLoadDXFile: Loading from 'pymol-generated.dx'.
> DXStrToMap: Dimensions: 129 129 97
> DXStrToMap: Origin   14.554  -48.010   -7.484
> DXStrToMap: Grid    0.579    0.523    0.664
> DXStrToMap: 1614177 data points.
> ObjectMap: Map Read.  Range =3D 3352.843994 to 12333.959961
>
> ___________________________________________
>
> Peter Haebel
>
> Philipps-Universit=E4t Marburg
> Institut f=FCr Pharmazeutische Chemie
> Marbacher Weg 6
> D-35032 Marburg
>
> phone: +49-6421-28-25072
> fax: +49-6421-28-28994
>
> email: pet...@st...
> http://www.agklebe.de
>
> NAD3-Workshop 2005 - Divide&Conquer
> http://www.agklebe.de/workshop2005
>
>
>

Hi Michael,

i have just updated to the latest version of apbs-0.3.2 and pymol-0.97 unde=
r=20
debian linux and get the following error messages (see below) + a completel=
y=20
positively charged protein surface...

using a pqr-file generated at 'http://nbcr.sdsc.edu/pdb2pqr/index.html' of =
the=20
same protein works, so there seems to be a problem with the build-in=20
generation of pqr-files.

i tried 3 different proteins from the PDB with and w/o ligand and water ato=
ms.

any idea what's going wrong?=20

cheers,

Peter

=2D------------------------------------------------------------------------=
=2D----

PDB code 1ini
all waters and ligand atoms removed by hand

=2E..
radiobutton said to generate it Use PyMOL generated PQR and PyMOL generated=
=20
Hydrogens and termini so i am returning pymol-generated.pqr
radiobutton said to generate it Use PyMOL generated PQR and PyMOL generated=
=20
Hydrogens and termini so i am returning pymol-generated.pqr
 WARNING: 5 atoms did not have formal charges assigned
 WARNING: 10 atoms did not have properties assigned
=2E..

This executable compiled on Nov 22 2004 at 15:59:46

Parsing input file pymol-generated.in...
parsePBE:  Warning -- parsed deprecated "bcfl 1" statement
parsePBE:  Please use "bcfl sdh" instead.
NOsh:  Warning -- parsed deprecated statment "chgm 1".
NOsh:  Please use "chgm spl2" instead!
parsePBE:  Warning -- parsed deprecated "srfm 1" statement.
parsePBE:  Please use "srfm smol" instead.
parsePBE:  Warning -- parsed deprecated "calcenergy 0" statement.
parsePBE:  Please use "calcenergy no" instead.
parsePBE:  Warning -- parsed deprecated "calcforce 0" statement.
parsePBE:  Please use "calcforce no" instead.
Parsed input file.
Got PQR paths for 1 molecules
Reading PQR-format atom data from pymol-generated.pqr.
Valist_readPDB:  Unable to parse resSeq token (A) as int!
Valist_readPDB:  Error while parsing residue name!
Valist_readPQR:  Error parsing ATOM field!
Error while reading molecule from pymol-generated.pqr
Error reading molecules!
 ObjectMapLoadDXFile: Loading from 'pymol-generated.dx'.
 DXStrToMap: Dimensions: 129 129 97
 DXStrToMap: Origin   14.554  -48.010   -7.484
 DXStrToMap: Grid    0.579    0.523    0.664
 DXStrToMap: 1614177 data points.
 ObjectMap: Map Read.  Range =3D 3352.843994 to 12333.959961

 ___________________________________________

Peter Haebel

Philipps-Universit=E4t Marburg
Institut f=FCr Pharmazeutische Chemie
Marbacher Weg 6
D-35032 Marburg

phone: +49-6421-28-25072
fax: +49-6421-28-28994

email: pet...@st...
http://www.agklebe.de

NAD3-Workshop 2005 - Divide&Conquer
http://www.agklebe.de/workshop2005

>
>
>Ultimately the mailing list serves as a form of living manual to the program, so it would be
>nice to preserve as many of these insights as possible!
>
Thomas' above sentence reminds me -- has anyone thought about a PyMOL 
wiki? :-)
Given that one of the points of pymol is to provide a user-friendly and 
intuitive interface(!), I don't think this is something that's 
overwhelmingly necessary... but it may help illuminate pymol's dustier 
corners, serve as a central repository of obscure/specialized snippets 
of code and pymol macros, etc...
Cam.


=== pym...@li... wrote (on 11/19/2004 08:17 
PM): ===

>Today's Topics:
>
>   4. List participation commentary...... (Thomas Stout)
>   7. Re: List participation commentary...... (Filipe Maia)
>  
>
> ------------------------------------------------------------------------
>
> Subject:
> [PyMOL] List participation commentary......
> From:
> Thomas Stout <tho...@ya...>
> Date:
> Wed, 17 Nov 2004 10:48:49 -0800 (PST)
> To:
> pym...@li...
>
>
>Hi All --
>
>Recently I've noticed a growing number of questions
>being posed to the PyMOL mailing list that never seem
>to get responses.  I infer from this that one or both
>of two things are happening: either 1) list members
>that know the answers to these questions are not
>responding to the questions, or 2) the responses are
>happening off-list.......either way I would like to
>appeal to everyone to use the list fully.  There are
>many "lurkers" (myself included) that would very much
>like to see and learn from the answers to many of
>these questions.  Other mailing lists (eg, CCP4) have
>adopted an additional SOP where the original poser of
>a question ultimately follows-up with a summary of the
>responses - this seems like a good idea to me for this
>list as well.  Ultimately the mailing list serves as a
>form of living manual to the program, so it would be
>nice to preserve as many of these insights as
>possible!
>
>Many thanks,
>Tom Stout (thomasstout - yahoo / com)
>
>PS - And, yes, I am guilty of some of this myself!  I
>promise to follow my own request.....
>  
>
> ------------------------------------------------------------------------
>
> Subject:
> Re: [PyMOL] List participation commentary......
> From:
> "Filipe Maia" <fm...@gm...>
> Date:
> Fri, 19 Nov 2004 18:11:00 +0100
> To:
> pym...@li...
>
>
> On Wed, 17 Nov 2004 10:48:49 -0800 (PST), Thomas Stout  
> <tho...@ya...> wrote:
>
>> Hi All --
>>
>> Recently I've noticed a growing number of questions
>> being posed to the PyMOL mailing list that never seem
>> to get responses.  I infer from this that one or both
>> of two things are happening: either 1) list members
>> that know the answers to these questions are not
>> responding to the questions, or 2) the responses are
>> happening off-list.......either way I would like to
>> appeal to everyone to use the list fully.  There are
>> many "lurkers" (myself included) that would very much
>> like to see and learn from the answers to many of
>> these questions.  Other mailing lists (eg, CCP4) have
>> adopted an additional SOP where the original poser of
>> a question ultimately follows-up with a summary of the
>> responses - this seems like a good idea to me for this
>> list as well.  Ultimately the mailing list serves as a
>> form of living manual to the program, so it would be
>> nice to preserve as many of these insights as
>> possible!
>
>
> I agree entirely. It would also be nice if the default reply
> was to the list and not only to the individual that asked the question.
>