Re: [PyMOL] wild card

2004-02-19 Thread Laurence Pearl
Beware of sweeping statements -  I work with nucleic acids (mostly  
bound to proteins) and I am continually irritated by the use of * in  
nucleic acid names, and I think I qualify as anyone.


Now that the ASCII code has settled down somewhat,  '  could take  
it's rightful place in PDB files, liberating  *  to its otherwise  
universal role as wild-card.


Laurence Pearl


On Wednesday, February 18, 2004, at 05:25  pm, Eric Zollars wrote:

Anyone who works with nucleic acids will certainly prefer the current  
situation.  From the PDB format guidelines:


* The asterisk (*) is used in place of the prime character (') for  
naming atoms of the sugar group. The prime was avoided historically  
because of non-uniformity of its external representation.


Eric



David A. Horita wrote:

Warren,
Personally, I'd much rather have wild-card selections in atom names  
and have to deal individually with the ill-conceived PDB files than  
the other way around.

Regards,
David Horita

-Original Message-
From: pymol-users-ad...@lists.sourceforge.net  
[mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Warren  
DeLano

Sent: Wednesday, February 18, 2004 10:56 AM
To: 'John Berrisford'; pymol-users@lists.sourceforge.net
Subject: RE: [PyMOL] selecting multiple atoms ie oxygen


John,

   color red, 5paa and elem o

The problem with using asterices as wildcards in atom names is that  
some ill-conceived PDB files actually use them in atom names.


However, PyMOL does support the use of a terminal wildcard in some  
cases, such as with the delete command...


create obj01, none
create obj02, none
delete obj*

And with residue names

color red, as*
color blue, gl*
color pink, hi*

Cheers,
Warren




-Original Message-
From: pymol-users-ad...@lists.sourceforge.net
[mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of
John Berrisford
Sent: Wednesday, February 18, 2004 3:42 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] selecting multiple atoms ie oxygen

I wish to select multiple oxygens (labelled O1, O2 etc..
within my pdb file) and colour them red for example. Is there
any easy way of doing this other than typing out a list of
all the oxygens I wish to select?

eg. color red, (5paa and (name o1+o1a+o2+o3+o4+o5+o1p+o2p+o3p))

I know in molscript its posible to use a o* label to select
all oxygens, is such a switch possible in pymol. It doesn't
work, or I am using the wrong syntax if its possible.

Any thoughts would be appreciated.

John


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--

  Laurence H. Pearl

  Section of Structural Biology, Institute of Cancer Research
  Chester Beatty Laboratories,  237 Fulham Road, London SW3 6JB, UK

  Phone +44-207-970 6045 : Secretary +44-207-970 6046
  FAX   +44-207-970 6051 : E-Mail laurence.pe...@icr.ac.uk
 
--

   Live Simply and do Serious Things ..  - Dorothy Crowfoot Hodgkin
 
--





[PyMOL] Povray

2004-02-19 Thread Tsjerk Wassenaar

Hi Guys,

I seem to have some trouble rendering with povray. The render starts and 
finishes fine, and the image is created, but Pymol crashes with a 
segmentation fault as soon as the rendering is done. The image is not 
loaded to the viewer. I'm using povray 3.5 with Pymol 0.93 on a laptop 
(Intel Centrino) with SuSe 9.0. I have changed povray_exe in povray.py 
in modules to povray.


Any hints?

Than to Warren probably, it would be great if Pymol would be able to 
write a povray object (include file) from a given selection. That would 
combine the strong points of pymol where it comes to showing the thing 
as you want it, with those of Povray, where it comes to lighting, 
positioning, colouring, textures and so on. Since Pymol is already 
capable of producing povray input it wouldn't be very hard I would guess?


Greetings,

Tsjerk

--
~
-- :)
-- :)   Tsjerk A. Wassenaar, M.Sc.
-- :)   Molecular Dynamics Group
-- :)   Dept. of Biophysical Chemistry
-- :)   University of Groningen
-- :)   Nijenborgh 4
-- :)   9747 AG Groningen
-- :)   The Netherlands
-- :)
~
-- :)
-- :)   Hi! I'm a .signature virus!
-- :)   Copy me into your ~/.signature to help me spread!
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Re: [PyMOL] Ray Tracing Bug in Pymol 0.93 on SuSE Linux 8.2

2004-02-19 Thread Robert Campbell
Michael,

* Michael Banck mba...@gmx.net [2004-02-19 12:24] wrote:
 On Thu, Feb 19, 2004 at 08:22:14AM +0100, Thomas Siegmund wrote:
  For me PyMol on SuSE 8.2 crashed always when raytracing a line element. 
 
 That seems to be identical to Debian Bug #229080
 (http://bugs.debian.org/229080)
 
  The stock  compiler on SuSE 8.2 is gcc 3.3 20030226 (prerelease). I
  got the same crash with  gcc 3.3.1, but not with gcc 2.95. I have not
  tried it on SUSE 9 yet, installing and using gcc 2.95 (for PyMol only)
  solved the problem for me. See PyMol bugreport 806361.
 
 Thanks for the information, I will see whether that helps on Debian,
 too.

Just as another data point. I use the CVS version of PyMOL (currently
version 0.94) under Debian testing (using gcc-3.3.3 20040125). I haven't
seen any crashes.  (In case it makes a difference: Athlon XP+ 2500 and
Radeon 9500 Pro graphics).

Cheers,
Rob
-- 
Robert L. Campbell, Ph.D. r...@post.queensu.ca
Senior Research Associatephone: 613-533-6821
Dept. of Biochemistry, Queen's University, fax: 613-533-2497
Kingston, ON K7L 3N6  Canada   http://adelie.biochem.queensu.ca/~rlc
PGP Fingerprint: 9B49 3D3F A489 05DC B35C  8E33 F238 A8F5 F635 C0E2



Re: [PyMOL] Povray

2004-02-19 Thread Robert Campbell
* Tsjerk Wassenaar t.a.wassen...@chem.rug.nl [2004-02-19 04:30] wrote:
 
 Hi Guys,
 
 I seem to have some trouble rendering with povray. The render starts and 
 finishes fine, and the image is created, but Pymol crashes with a 
 segmentation fault as soon as the rendering is done. The image is not 
 loaded to the viewer. I'm using povray 3.5 with Pymol 0.93 on a laptop 
 (Intel Centrino) with SuSe 9.0. I have changed povray_exe in povray.py 
 in modules to povray.

I never use the povray rendering directly from within PyMOL.  I find the
PyMOL ray-tracer is great for most things and if it isn't sufficient, I
want to be able to edit the povray input as you suggest below.

 Any hints?

Yes!

 Than to Warren probably, it would be great if Pymol would be able to 
 write a povray object (include file) from a given selection. That would 
 combine the strong points of pymol where it comes to showing the thing 
 as you want it, with those of Povray, where it comes to lighting, 
 positioning, colouring, textures and so on. Since Pymol is already 
 capable of producing povray input it wouldn't be very hard I would guess?

It can do this. I use a simple little script that I call make_pov.py:

##
# make_pov.py
from pymol import cmd

def make_pov(file):
  (header,data) = cmd.get_povray()
  povfile=open(file,'w')
  povfile.write(header)
  povfile.write(data)
  povfile.close()
##

Load the file with 'run make_pov.py' and then within pymol do:

make_pov('povray.input')

Then outside PyMOL feed this file to povray with whatever command-line
options you need. You do need to look at the size of the image reported
by the make_pov.  It looks something like:

  PyMOLmake_pov('povray.input')
   RayRenderPOV: w 1100 h 900 f   63.349 b  102.310
   RayRenderPOV: vol  -17.316   17.316  -14.168
   RayRenderPOV: vol   14.168   63.349  102.310
   RayRenderPovRay: processed 714 graphics primitives.
   Ray: total time: 0.03 sec. = 123885.9 frames/hour. (0.03 sec. accum.)

You'll need to use the same width and height (or the same ratio) to
make your povray output have the correct width to height ratio, e.g.:

  povray +Ipovray.input +W550 +H450

Cheers,
Rob
-- 
Robert L. Campbell, Ph.D. r...@post.queensu.ca
Senior Research Associatephone: 613-533-6821
Dept. of Biochemistry, Queen's University, fax: 613-533-2497
Kingston, ON K7L 3N6  Canada   http://adelie.biochem.queensu.ca/~rlc
PGP Fingerprint: 9B49 3D3F A489 05DC B35C  8E33 F238 A8F5 F635 C0E2



[PyMOL] using the build function

2004-02-19 Thread Moriarty, Daniel
Hello everyone,

I'm trying to build some model proteins for a diagram showing a protein 
unfolding over several steps.  I'm using the build function in the 0.95beta10 
release.  The main problem is that I can't control the angle of the protein 
chain, so the chain just goes off in one direction only, unless proline is 
placed in the middle of a helix at which point it goes off at a new angle.   
This makes me think that it can be specified, but I just don't know how to do 
it.


Any help would be appreciated,

Dan




RE: [PyMOL] using the build function

2004-02-19 Thread Warren DeLano
Dan,

I think it's fair to say that PyMOL's currently molecular building
capabilities are at the stage of a technology
demonstration/proof-of-concept, but very little effort has yet been expended
toward making them useful for real work.  

Part of that is because we don't yet have a general back-end
modeling engine inside of PyMOL (molecular sculpting is a pure GIGO kind
of thing).  That is still an important long-term goal.

But the other reason is that I don't really have a clear idea in my
mind for how such a builder should operate.  What I would like to get from
you and all other interested PyMOL users are wish-lists for how PyMOL's
molecular builder should work (better).  No hurry though -- feedback over
the next month or two should be fine, and anyone attending MUG or CUP is
welcome to give me an ear-full next week.

Basically, a major goal is to evolve PyMOL into a builder that can
be useful across the board for biology and drug discovery:  for proteins,
small molecules, nucleic acids, carbohydrates, solvent, and so on.  As a
general tool, it should be capable of supporting crystallography-oriented
building, manual homology modeling, and hypothetical hand modeling of
small molecules, as well as simple illustrative tasks such as the one you're
working on.  Of course, specialty tools like O, Quanta, Modeller, and
MacroModel will always be superior in their respective niches, but I hope
PyMOL can become eventually become good enough for simple common molecular
building tasks...

Questions to consider:

What are the best builders out there today that we should learn
from? 
What are the key functions PyMOL must absolutely have to be a
builder?
What other extra attractive feature should PyMOL seek to emulate?
How can we make the best use of what is already in PyMOL, unique or
otherwise?
What are the biggest holes in the current versions?

Things that are already on the radar:

Rotamer-libraries.
A 1-D sequence viewer with alignment and editing capabilities.
An integrated builder tutorial.
Finding an existing force-field provider to work with...
Back and forth 2D to 3D for small molecules.

Dan,  

It sounds like a feature you would like is that ability to aim the
chain being built towards a certain direction.

In the meantime, to accomplish your task, build the chain first,
then turn on Auto-Sculpting in the Sculpting menu, put the mouse into
editing mode, then control-left-click-and-drag to move the chain where you
want it to go.  Ctrl-middle-click to pick one (or more -- in the latests
betas) joints...and then shift-left-or-middle click-and-drag, or
control-left-click-and-drag to move the resulting fragments.  If your chain
is small, increase the number of Cycles per Update to accelerate
convergence.

Cheers,
Warren



 -Original Message-
 From: pymol-users-ad...@lists.sourceforge.net 
 [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of 
 Moriarty, Daniel
 Sent: Thursday, February 19, 2004 9:47 AM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] using the build function
 
 Hello everyone,
 
 I'm trying to build some model proteins for a diagram showing 
 a protein unfolding over several steps.  I'm using the build 
 function in the 0.95beta10 release.  The main problem is that 
 I can't control the angle of the protein chain, so the chain 
 just goes off in one direction only, unless proline is placed 
 in the middle of a helix at which point it goes off at a new 
 angle.   This makes me think that it can be specified, but I 
 just don't know how to do it.
 
 
 Any help would be appreciated,
 
 Dan
 
 
 
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[PyMOL] drawing hydrogen bonds or dashes

2004-02-19 Thread John Berrisford
I have searched the manual and forum and cannot find how to draw a hydrogen bond
between two specific atoms. 

I wish to do the equivalent to the following molscript command
line position res-atom A97 OE1 to position res-atom M200 MN;

which draws a line between two atoms A97 OE1 and Mn200. So not a hydrogen bond
but a specific line.

Is this possible in pymol?

I have read posts on changing the thickness of a dash and the number of dashes
in a line. But none on how to draw the line.

Can anyone help me, i'm a new user by the way!

thanks

John




[PyMOL] cartoons

2004-02-19 Thread ALEX DAJKOVIC
dear all, 
i am new to pymol and i have a question about cartoons. 
i saw the demo of cartoon ribbons and really liked it, but i haven't
been able to get my protein displayed that way.  when i give the command
cartoon automatic all i get is a simple line that apparently traces
the backbone of my protein chain.  cartoon loop does the same thing. 
with cartoon tube i get a thicker line.  how do i set the parameters
so that i get nice helices and sheets like the ones showed in the demo?
thanks, 
alex




[PyMOL] Making the selection indicators bigger

2004-02-19 Thread Matthew Zimmerman

Hello --

So I've installed PyMOL onto a new system, and I'm having trouble with 
the little pink indicators that pop up when you make a selection. On 
this machine they appear to about a single pixel wide, which on a 
1280x1024 resolution screen makes them practically invisible! I've tried 
poking about in the options a little but I don't know what to change... 
Any guidance?


--
  Matt

  Matthew Zimmerman
  Interdisciplinary Biophysics, University of Virginia
  http://www.people.virginia.edu/~mdz4c/
  
 Lab: 4-223 Jordan Hall, 1300 Jefferson Park Avenue,
  Charlottesville, VA 22908  (434)924-2948
Home: 2655-C Barracks Road
  Charlottesville, VA 22901  (434)244-7989




Re: [PyMOL] Ray Tracing Bug in Pymol 0.93 on SuSE Linux 8.2

2004-02-19 Thread Morri Feldman
Hi Michael,

I downloaded pymol-0_93-bin-linux-libc6-i386.tgz to my Debian machine.
When I run this copy rather than the .deb version I am able to ray trace
lines without a crash.

Best,
Morri

 On Thu, 19 Feb 2004, Michael Banck wrote:

 On Thu, Feb 19, 2004 at 08:22:14AM +0100, Thomas Siegmund wrote:
  For me PyMol on SuSE 8.2 crashed always when raytracing a line element.

 That seems to be identical to Debian Bug #229080
 (http://bugs.debian.org/229080)

  The stock  compiler on SuSE 8.2 is gcc 3.3 20030226 (prerelease). I
  got the same crash with  gcc 3.3.1, but not with gcc 2.95. I have not
  tried it on SUSE 9 yet, installing and using gcc 2.95 (for PyMol only)
  solved the problem for me. See PyMol bugreport 806361.

 Thanks for the information, I will see whether that helps on Debian,
 too.


 Michael


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RE: [PyMOL] Making the selection indicators bigger

2004-02-19 Thread Warren DeLano
Matt,

Try:

set selection_width, 6
set selection_width, 7
  set selection_width, 8

Cheers,
Warren
 

 -Original Message-
 From: pymol-users-ad...@lists.sourceforge.net 
 [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of 
 Matthew Zimmerman
 Sent: Thursday, February 19, 2004 2:46 PM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] Making the selection indicators bigger
 
 Hello --
 
 So I've installed PyMOL onto a new system, and I'm having 
 trouble with the little pink indicators that pop up when you 
 make a selection. On this machine they appear to about a 
 single pixel wide, which on a
 1280x1024 resolution screen makes them practically invisible! 
 I've tried poking about in the options a little but I don't 
 know what to change... 
 Any guidance?
 
 -- 
Matt
 
Matthew Zimmerman
Interdisciplinary Biophysics, University of Virginia
http://www.people.virginia.edu/~mdz4c/

   Lab: 4-223 Jordan Hall, 1300 Jefferson Park Avenue,
Charlottesville, VA 22908  (434)924-2948
 Home: 2655-C Barracks Road
Charlottesville, VA 22901  (434)244-7989
 
 
 
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RE: [PyMOL] Ray Tracing Bug in Pymol 0.93 on SuSE Linux 8.2

2004-02-19 Thread Warren DeLano
Morri has a good point:  

The standalone pymol-0_xx-bin-linux-libc6-i386.tgz binary builds
should be capable of running on virtually any current x86-based Linux
system: RH, SUSE, Debian, Fedora, or whatever.

So, if you're having trouble with compilation or use of
distribution-specific packages on Linux and simply want to use PyMOL as a
standalone tool, then downloading those binaries is an easy way to get
going.  Installation is trivial and you don't need root privileges.

1) tar zxvf pymol-(version)-bin-linux-libc6-i386.tgz
2) cd pymol
3) ./setup.sh
4) ./pymol.com 

Cheers,
Warren

FYI: those builds are built using GCC 2.96 under RedHat 6.2 for maximum
compatibility -- they're not the fastest PyMOL binaries in the world, but
they do run without a hassle.
 
 -Original Message-
 From: pymol-users-ad...@lists.sourceforge.net 
 [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of 
 Morri Feldman
 Sent: Thursday, February 19, 2004 3:18 PM
 To: Michael Banck
 Cc: pymol users
 Subject: Re: [PyMOL] Ray Tracing Bug in Pymol 0.93 on SuSE Linux 8.2
 
 Hi Michael,
 
 I downloaded pymol-0_93-bin-linux-libc6-i386.tgz to my Debian machine.
 When I run this copy rather than the .deb version I am able 
 to ray trace lines without a crash.
 
 Best,
 Morri
 
  On Thu, 19 Feb 2004, Michael Banck wrote:
 
  On Thu, Feb 19, 2004 at 08:22:14AM +0100, Thomas Siegmund wrote:
   For me PyMol on SuSE 8.2 crashed always when raytracing a 
 line element.
 
  That seems to be identical to Debian Bug #229080
  (http://bugs.debian.org/229080)
 
   The stock  compiler on SuSE 8.2 is gcc 3.3 20030226 
 (prerelease). I 
   got the same crash with  gcc 3.3.1, but not with gcc 2.95. I have 
   not tried it on SUSE 9 yet, installing and using gcc 2.95 
 (for PyMol 
   only) solved the problem for me. See PyMol bugreport 806361.
 
  Thanks for the information, I will see whether that helps 
 on Debian, 
  too.
 
 
  Michael
 
 
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RE: [PyMOL] molecular surface colored by hydrophobicity

2004-02-19 Thread Warren DeLano
Rongjin,

PyMOL can certainly color surfaces by atom color and other properties.

   show surface
   color green, elem c
   color violet, elem n+o 

But Grasp's hydrophobicity function may be doing something more
sophisticated then that...

Cheers,
Warren


 -Original Message-
 From: pymol-users-ad...@lists.sourceforge.net 
 [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of 
 gu...@umbi.umd.edu
 Sent: Wednesday, February 18, 2004 7:12 PM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] molecular surface colored by hydrophobicity
 
 Dear all,
 I am preparing a figure of a molecualr surface, colored by 
 the hydrophobicity of surface residues. Can pymol do this job? 
 How about showing atom C* in a color, and N* and O* in another color?
 
 In fact I have tried GRASP but failed in coloring the 
 surface. I used r=hyd, but could not color the surface of 
 those redisues. This is an old version of grasp (1.0?). I am 
 not familiar with this program. If anybody can tell me the 
 correct way of doing it in grasp, it will also be greatly appreciated.
 
 Rongjin Guan
 
 
 
 
 
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[PyMOL] cartoons

2004-02-19 Thread Scott Classen

Alex
try typing:

dss


this will assign secondary structure to your PDB and then the cartoon 
will show you the sheets and helices you desire.

Scott


On Feb 19, 2004, at 1:44 PM, ALEX DAJKOVIC wrote:


dear all,
i am new to pymol and i have a question about cartoons.
i saw the demo of cartoon ribbons and really liked it, but i haven't
been able to get my protein displayed that way.  when i give the 
command

cartoon automatic all i get is a simple line that apparently traces
the backbone of my protein chain.  cartoon loop does the same thing.
with cartoon tube i get a thicker line.  how do i set the parameters
so that i get nice helices and sheets like the ones showed in the demo?
thanks,
alex



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  Scott Classen, Ph.D.
  ACS Postdoctoral Fellow
  Department of Molecular  Cell Biology
  University of California, Berkeley
  237 Hildebrand Hall #3206
  Berkeley, CA 94720-3206
  LAB 510.643.9491
  FAX 510.643.9290