pymol-users — Collaborative support and tips for PyMOL users

[PyMOL] Re: Screen problem - G3 Powerbook - external display [Mac OS X 10.2.1]

[Kersey B. <kb...@js...>]

Hi all,

I posted a few days ago about a screen problem I was having.  In short 
form it was that the color map was getting screwed up when trying to 
drive an external monitor (though that was not specified in the 
original note), even with mirroring, even with all possible 
combinations of color profile settings, and even at relatively low 
resolutions.
I am doing this on a 400 MHz G3 Powerbook, which has 8 (non-upgradable) 
MB of VRAM.
I have seen a couple of flaky behaviors before which probably relate to 
this limitation in hardware, though for all but a couple of things, 
including PyMOL, driving an external display generally works fine.
None the less, this problem potentially restricts my ability to use 
PyMOL interactively in presentations.

Warren came up with a fix that seems to be working!
Thus, instead of writing back to him alone with thanks for his time, I 
thought I would post this
fix for others who may encounter the same problem, and save him having 
to answer this query in the future (or at least reduce that load).

And I quote ...
>
> I have an idea: try disabling display caching
>
> set cache_display=0

I added this to a script and all seems to be well.  I will let you know 
if that changes.

Thanks again

Cheers,
Kersey

________________________________________________________
Kersey Black							Joint Science Program
Professor of Chemistry					Claremont Colleges

[PyMOL] reading mol2 files with pymol

[Luca F. <l.a...@so...>]

Dear Pymolers,       

I've read on pymol-users mail list
(http://sourceforge.net/mailarchive/message.php?msg_id=1804599) that it
is now possible for pymol to read directly mol2 files. This would be
really handy for me, since I'd like to use pymol to directly read GOLD
output without having to convert them.
I've browsed the CVS repository: 
- is the file I'm looking for the one called mol.py?
(http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/pymol/pymol/modules/chempy/mol.py)
- or is the one called importing.py?
(http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/pymol/pymol/modules/pymol/importing.py)?
if neither of them is, could any of you please point me to the right
one?
many thanks, 

	luca

-- 
Universities are places of knowledge.  The freshman each bring a little
in with them, and the seniors take none away, so knowledge accumulates.

[PyMOL] RE: Low-cost movie construction (OSX)

[Andy C. <afc...@li...>]

Making movies in MacOS X:

Not to forget QuickTime Pro which can do the same from numbered .png files

OR

GraphicConverter
the best graphics conversion program for the Mac in the entire universe
from http://www.lemkesoft.com $30-35 (you can try before you buy). Converts
just about any image format to just about any image format. Search on
http://www.versiontracker.com for end user comments. One of the highest
rated bits of software for the Mac. Makes movies too.

My only connection is that I have paid my registration fee and have been a
user for years and years.


-- 
.-Dr-Andy-Calder----------.
| Materials Modelling Group\
| Materials Science & Eng.  \
| University of Liverpool   /
| UK .---------------------'

Re: [PyMOL] pymol movies (again, sorry) and windows

[<kri...@be...>]

> In 
> powerpoint you can create what is called a hyperlink to pymol, and then 
> you can just load in your macro (pml script) and your movie starts 
> playing embedded in powerpoint.  


This is great news! 

(I've already wondered if we need something to embed Word and Powerpoint *into* PyMOL.)

Kristian

--
berlin.de - meine stadt im netz. Jetzt eigene eMail-adresse @berlin.de sichern!
http://webmail.berlin.de

Re: [PyMOL] Low-cost movie construction (Windows)

[Tsjerk W. <t.a...@ch...>]

Hi there,

For making movies there are also lots of free tools available. For 
instance, AVI's can be made under windows with MakeAVI:

https://sourceforge.net/projects/makeavi/

Very easy to use, fast, and free.

Cheers,

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!
-- :)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

[PyMOL] Re: CCL:scripting pymol

[Warren L. D. <wa...@su...>]

Luca,

   For future reference, please direct technical PyMOL questions like
this to the PyMOL mailing list. (See MailLists on http://www.pymol.org)

Over the past couple of years, we've built up an active community of
nearly 300 PyMOL users who are there to learn and to help each other get
the most out of this free/open-source molecular viewer.  Please join in!

The answer to your question is:

Launch PyMOL with a "-p" command-line argument.  PyMOL will then listen
for commands on standard input.  Using a Perl pipe, you can then control
PyMOL interactively and send commands as required in order to load new
structures, change the view, color, and so on.

The only trick with Perl is that you need to turn autoflush on so
that commands get passed along right away.

use FileHandle;
open(FILE,"|pymol -p");
FILE->autoflush(1);
print FILE "load \$PYMOL_PATH/test/dat/pept.pdb\n";
while(1) {
    sleep 0.2;
    print FILE "turn x,5\n";
}

Please excuse my non-OOP-0Perl4-vintage example...I've been a Python
addict for some time now.

If you want PyMOL to be just a minimal molecular display window, then
consider  launching PyMOL as:

pymol -qpxif 0

This will make PyMOL open a single window with no visible GUI, text, or
controls.

Cheers,
Warren

On Mon, 28 Oct 2002, Luca Fenu wrote:

> Dear all,
>
> I need to scan and make a choice about a list of molecules. does anyone
> knows how to send command to pymol through a perl or shell script? I've
> read pymol's manual, and it's possible to pass pymol some scripts, from
> its internal shell. but I don't know how to pass commands to it from
> another program. starting the process in foreground and feeding the
> command from the stdout of perl to the stdin of pymol doesn't work. I
> think pymol use another filehandle for aquiring commands. how can I
> avoid to restar a new pymol for every molecule?
> any suggestion? many thanks
>
> 	luca
>
>
>

RE: [PyMOL] PyMol Manual

[DeLano, W. <wa...@su...>]

Gordon,

    I fully agree with your assessment that PyMOL is currently unable to =
reach its potential due to a number of factors, including poor =
documentation.=20

    Nevertheless, I do have a defined plan for eliminating these =
deficits.  It involves securing funding to hire people under contract to =
document, support, and develop PyMOL on an ongoing basis.  While I am =
grateful for the continued assistance of PyMOL users on numerous minor =
tasks, it is not reasonable to expect anyone to prepare a complete =
"well-written" manual or to perform other major tasks without some form =
of compensation.  Also, PyMOL is still immature enough in certain areas =
that a full manual really can't be constructed until the 1.0 features =
are settled upon (soon hopefully!).

    Understanding this situation, several large pharmaceutical companies =
and many smaller entities have lent support to PyMOL development through =
donations and license purchases.  At present the flux is low, but we are =
getting to a point where some real headway can be made.  The forthcoming =
"Incentive PyMOL (iPyMOL)" add-on will hopefully increase the flux by =
providing a specific reward to those who fund the PyMOL development =
effort. =20

    I know it may sound like PyMOL/iPyMOL is becoming commercial =
gray-ware, but that's not it at all.  I haven't devoted thousands of =
hours to this project just to see it end up as yet another expensive, =
lousy, inflexible, and closed-source commercial tool.  PyMOL will remain =
a vital open-source project, and iPyMOL will exist solely to accelerate =
PyMOL's growth and guarantee its long-term health.  Nurturing PyMOL and =
similar efforts to fruition on such terms is central to my career vision =
-- it's what I stand for in this industry.

    I believe that well-supported, well-documented, and well-maintained =
open-source software will be a superior research product to what is =
currently offered by the major scientific software vendors.  My hope is =
that scientists in industry and academia will eventually come to =
appreciate this, and then choose to make creation of such software =
economically viable through funding of balanced approaches such as the =
one I am taking with PyMOL.

    Free software is great once it exists, but there are far too few =
developers in this field to expect the kinds of dramatic successes =
achieved by the Linux, GNU, and BSD communities.  If =
open-source/free-software is going to have a large impact on molecular =
modeling, it will need direct support from users, universities, =
governments, and for-profit companies.  If really good open-source tools =
were available and able to meet the needs of research, would you be =
willing to pay reasonable amounts of money for their development, =
maintenance, and support?  I hope so.

    Thus, pharmaceutical companies like EMD/Lexigen/Merck can choose to =
continue to spend millions of dollars on traditional closed-source =
packages with no hope of a reprieve, or they can choose to funnel a =
small fraction of that money into efforts like PyMOL.  Over the long =
term, open-source packages offer vendor-independence, =
cost-effectiveness, flexibility, opportunities for innovation, and =
support for broad sharing of information and technology.  These are all =
key ingredients in scientific progress, both within a single =
organization and across the industry. =20

    Realistically, it will take a year or more before PyMOL can fulfill =
the potential you described.  How soon this happens will depend in part =
on whether people like yourself are content to merely gripe about the =
status quo, or whether you are prepared to commit resources towards =
improving it.

Cheers,

Warren L. DeLano, Ph.D.
PyMOL Creator &
Founder, DeLano Scientific

-----Original Message-----
From: gwe...@le... [mailto:gwe...@le...]
Sent: Monday, October 28, 2002 10:33 AM
To: pym...@li...
Subject: [PyMOL] PyMol Manual



Fellow PyMol Users=20

Although I like using PyMol, I would like to submit a gripe about the =
severe lack of a decent PyMol manual.=20

A deeper description of the program's features is required if people are =
seriously going to use PyMol for tricky things beyond simple =
visualization (simple visualization programs are ten-a-penny and PyMol =
could be so much more)=20

Particularly lacking are details of structural editing (mutation, bond =
rotation, cut-and-paste etc.), interfaces (if any exist) to routines for =
enegy minimization and a detailed description of the Python command line =
interface with examples of scripting and how to extend PyMol's =
capabilities.=20

By neglecting to adequately document what may be a really useful =
program, the PyMol user community might fail to attract the kind of user =
base and support that it deserves and that it needs to ensure its =
success.=20

A good, clear and well-thought out manual really helps to make a case =
for using a particular piece of software (and it might also lower the =
odds of PyMol having to join the gray legions of commercial "payware").=20

Gordon=20
EMD Lexigen Research Center=20

[PyMOL] pymol movies (again, sorry) and windows

[<wg...@ch...>]

Dear Stephen Miller:

Also, don't overlook the fact that pymol itself is a movie player.  In 
powerpoint you can create what is called a hyperlink to pymol, and then 
you can just load in your macro (pml script) and your movie starts 
playing embedded in powerpoint.  This is far better because you can 
move the molecule around while the movie plays, zoom in and out, etc.  
This gives a sense of immediacy in a presentation that is lost with an 
animated gif, or whatever movie player you might use.  The hyperlink 
feature works better in windows powerpoint than mac powerpoint, BTW.


William G. Scott

Associate Professor
Department of Chemistry and Biochemistry
and The Center for the Molecular Biology of RNA
Sinsheimer Laboratories
University of California at Santa Cruz
Santa Cruz, California 95064
USA

phone:  +1-831-459-5367 (office)
                +1-831-459-5292 (lab)
fax:         +1-831-4593139  (fax)

[PyMOL] making movies (animated gifs)

[<wg...@ch...>]

There is a program called gif-builder (Mac OS 9 and 10) that is free 
and uses a variety of input types to make an animated gif which then is 
platform-independent.  Sadly the link is broken 
http://www.macupdate.com/info.php/id/235  but if anyone needs it I can 
email you mine.

Also if you have quicktime pro (PC version also exists) it is very 
simple to string together pictures to make quicktime movies.

HTH


William G. Scott

Associate Professor
Department of Chemistry and Biochemistry
and The Center for the Molecular Biology of RNA
Sinsheimer Laboratories
University of California at Santa Cruz
Santa Cruz, California 95064
USA

phone:  +1-831-459-5367 (office)
                +1-831-459-5292 (lab)
fax:         +1-831-4593139  (fax)

Re: [PyMOL] PyMol Manual

[<gwe...@le...>]

Dear Byron

Yes, it's a nice Catch-22 isn't it ... write a PyMol manual so people like 
myself will be able to learn PyMol well enought to be able to write the 
PyMol manual!

Gordon





Byron Delabarre <by...@SL...>
10/28/2002 01:32 PM
Please respond to byron

 
        To:     gwe...@le...
        cc:     pym...@li...
        Subject:        Re: [PyMOL] PyMol Manual


So write one.

gwe...@le... wrote:
>
> Fellow PyMol Users
>
> Although I like using PyMol, I would like to submit a gripe about the
> severe lack of a decent PyMol manual.
>
> A deeper description of the program's features is required if people are
> seriously going to use PyMol for tricky things beyond simple
> visualization (simple visualization programs are ten-a-penny and PyMol
> could be so much more)
>
> Particularly lacking are details of structural editing (mutation, bond
> rotation, cut-and-paste etc.), interfaces (if any exist) to routines for
> enegy minimization and a detailed description of the Python command line
> interface with examples of scripting and how to extend PyMol's
> capabilities.
>
> By neglecting to adequately document what may be a really useful
> program, the PyMol user community might fail to attract the kind of user
> base and support that it deserves and that it needs to ensure its 
success.
>
> A good, clear and well-thought out manual really helps to make a case
> for using a particular piece of software (and it might also lower the
> odds of PyMol having to join the gray legions of commercial "payware").
>
> Gordon
> EMD Lexigen Research Center


--
Byron DeLaBarre
Stanford University / HHMI
Dept. of Molecular and Cellular Physiology
P250 MSLS Building//(L)650 736 1714 (C)650 468 5677

Re: [PyMOL] PyMol Manual

[Byron D. <by...@SL...>]

So write one.

gwe...@le... wrote:
> 
> Fellow PyMol Users
> 
> Although I like using PyMol, I would like to submit a gripe about the 
> severe lack of a decent PyMol manual.
> 
> A deeper description of the program's features is required if people are 
> seriously going to use PyMol for tricky things beyond simple 
> visualization (simple visualization programs are ten-a-penny and PyMol 
> could be so much more)
> 
> Particularly lacking are details of structural editing (mutation, bond 
> rotation, cut-and-paste etc.), interfaces (if any exist) to routines for 
> enegy minimization and a detailed description of the Python command line 
> interface with examples of scripting and how to extend PyMol's 
> capabilities.
> 
> By neglecting to adequately document what may be a really useful 
> program, the PyMol user community might fail to attract the kind of user 
> base and support that it deserves and that it needs to ensure its success.
> 
> A good, clear and well-thought out manual really helps to make a case 
> for using a particular piece of software (and it might also lower the 
> odds of PyMol having to join the gray legions of commercial "payware").
> 
> Gordon
> EMD Lexigen Research Center


-- 
Byron DeLaBarre
Stanford University / HHMI
Dept. of Molecular and Cellular Physiology
P250 MSLS Building//(L)650 736 1714 (C)650 468 5677

[PyMOL] PyMol Manual

[<gwe...@le...>]

Fellow PyMol Users

Although I like using PyMol, I would like to submit a gripe about the 
severe lack of a decent PyMol manual.

A deeper description of the program's features is required if people are 
seriously going to use PyMol for tricky things beyond simple visualization 
(simple visualization programs are ten-a-penny and PyMol could be so much 
more)

Particularly lacking are details of structural editing (mutation, bond 
rotation, cut-and-paste etc.), interfaces (if any exist) to routines for 
enegy minimization and a detailed description of the Python command line 
interface with examples of scripting and how to extend PyMol's 
capabilities.

By neglecting to adequately document what may be a really useful program, 
the PyMol user community might fail to attract the kind of user base and 
support that it deserves and that it needs to ensure its success.

A good, clear and well-thought out manual really helps to make a case for 
using a particular piece of software (and it might also lower the odds of 
PyMol having to join the gray legions of commercial "payware").

Gordon
EMD Lexigen Research Center

Re: [PyMOL] Low-cost movie construction (OSX)

[Luca J. <luc...@ma...>]

An even cheaper alternative to Premiere, if you are using Mac OSX, is a 
$20 shareware program called QuickMovie:

	http://www.chaoticsoftware.com/ProductPages/QuickMovie.html

I have recently tested it to generate a QuickTime movie from PyMOL PNG 
frames, and it worked just fine; it supports various formats and allows 
you to specify output dimensions, as well as frame rate.

Note that I am note associated in any way to the company who makes this 
software, just thought other Mac PyMOL users might find this information 
useful...

-Luca

--------------------------------------------------------
Luca Jovine, Ph.D.
Department of Molecular, Cell & Developmental Biology
Mount Sinai School of Medicine
Annenberg Building, Room 25-18
One Gustave L. Levy Place, New York, NY 10029-6574, USA
Voice: +1.212.241-8620  FAX: +1.509.356-2832
E-Mail: luc...@ma...
W3: http://www.mssm.edu/students/jovinl02
--------------------------------------------------------

[PyMOL] Isomesh level units?

[Kelley M. <mo...@ar...>]

Dear Pymolers,
 
I am trying to create a carved electron density around a ligand for a
publication figure and I have come up with a question: what is the
relationship between the level number in an isomesh command line versus a
sigma level for a display of the density map in an application such as
Xtalview. It does not appear that a value of 1.0 for level in Pymol yields a
similar level of density in a map representation as a 1.0 sigma value in
Xtalview. The relationship appears to be approximately 0.5 level in Pymol =
1.0 sigma in Xtalview.  Is there a defined set of units or conversions for
the Pymol level value?  Are these the units even comparable?  Thanks for
your assistance.

Kelley 

Dr. Kelley Moremen 
Associate Professor
Complex Carbohydrate Research Center
Department of Biochemistry and Molecular Biology
University of Georgia, Athens, GA 30602-7229
Office (706) 542-1705    Fax: (706) 542-1759
Email: mo...@ar...
(send email with large attachments to: mo...@bm...)
Website: http://bmbiris.bmb.uga.edu/moremen/lab/

[PyMOL] Low-cost movie construction (Windows)

[Stephen M. <SM...@ke...>]

Jasc, the guys that make Paint Shop Pro, have a product called Animation =
Shop 3 that can directly import a set of .png files and output movie =
files in several formats (including .avi, .gif). I've used this to =
create animations for use in Powerpoint presentations that are quite =
reasonable. The software only costs $39 and is bundled with the version =
of Paint Shop Pro 7 that is currently available. A significant savings =
over Adobe Premiere and it eliminates the step of having to convert file =
formats using ImageMagick (althoug Paint Shop Pro 7 can also batch =
convert between file formats).

Worth a look if you are interested in presenting your PyMol animations.

RE: [PyMOL] color by partial charge? (electrostatics)

[DeLano, W. <wa...@su...>]

Mark,

   Coloring by partial charge should work fine, provided that you supply =
partial charges to PyMOL...which isn't trivial.  You could either assign =
them using the 'alter' command after loading a PDB or SDF file, or you =
could convert your molecule into a Chemical Python "model" object, =
assign them via Python, and then load the model back into PyMOL.

   Coloring by electrostatic potential is something I am hoping to get =
into version 1.0...but PyMOL's current support for it is weak to =
non-existent.

Cheers,
Warren


> -----Original Message-----
> From: Mark Wall [mailto:mw...@di...]
> Sent: Thursday, October 24, 2002 12:25 PM
> To: pym...@li...
> Subject: [PyMOL] color by partial charge? (electrostatics)
>=20
>=20
> Hello,
>=20
>=20
> Background
>    I want to create a surface colored by electrostatic=20
> potential in PyMOL. =20
>    I can simulate this by coloring atoms by a formal charge which is=20
>    either 1, 0 or -1, ...
>=20
>    color white
>    color blue, (fc; > 0.5)
>    color red, (fc; < -0.5)
>    show surface
>=20
>    Of course this does not look like a surface colored by=20
> Poisson-Boltzmann=20
>    calculated potentials
>=20
> Questions
>    1. Can I color atoms by partial_charge? (this did not seem=20
> to work for
> me)
>    2. Is there a better way using only PyMOL to approximate=20
> P-B calculated
>        potentials?
>=20
>=20
> Thanks,
> Mark
>=20
>=20
>=20
> -------------------------------------------------------
> This sf.net email is sponsored by: Influence the future=20
> of Java(TM) technology. Join the Java Community=20
> Process(SM) (JCP(SM)) program now.=20
> http://ads.sourceforge.net/cgi-bin/redirect.pl?sunm0003en
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20

[PyMOL] amber support in CVS PyMOL

[Viktor H. <ho...@cs...>]

I was wondering if anyone got support for amber topology and
trajectory formats working in CVS pymol. Here is what I tried:

1. I tried to build PyMOL using "Approach 2" (i.e. standalone PyMOL
using Makefile) in RedHat7.3 (python1.5, gcc-2.96). The build 
finishes successfuly (i.e. no error just bunch of warnings) but when
I try to run 'pymol.com', the following error appears:

Traceback (innermost last):
  File "/usr/local/pymol/modules/pymol/__init__.py", line 92, in ?
    import pymol
  File "/usr/local/pymol/modules/pymol/__init__.py", line 220, in ?
    import cmd
  File "/usr/local/pymol/modules/pymol/cmd.py", line 752, in ?
    from importing import \
  File "/usr/local/pymol/modules/pymol/importing.py", line 26, in ?
    from pymol import m4x
  File "/usr/local/pymol/modules/pymol/m4x.py", line 17
    from chempy import cex as CEX
                            ^
SyntaxError: invalid syntax

2. I repeated the same build procedure but in RedHat8.0 (python2.2,
gcc-3.2) and, to my big surprise, it builds and runs! (I find it hard
to believe that a switch from python1.5 to python2.2 would be that 
easy, but I'd surely not complain as RH8.0 is my current working OS). 
In any case, I tried to load amber topology and trajectory:

load test.top
(this seems to succeed as the message appears:
ObjectMolecule: Assuming this is an Amber6 topology file.
Executive: object "test" created.)

load_traj test.trj
..and here is where I got stuck, the message is:
CmdLoadTraj-Error: must load object topology before loading trajectory!

Was someone successful to get this working?
Thanks very much,

-Viktor
-- 
===================================================================
Viktor Hornak
SUNY at Stony Brook      
Stony Brook, NY 11794-5115   E-mail: Vik...@su...   
===================================================================

[PyMOL] amber support in CVS PyMOL

[Viktor H. <vik...@su...>]

I was wondering if anyone got support for amber topology and
trajectory formats working in CVS pymol. Here is what I tried:

1. I tried to build PyMOL using "Approach 2" (i.e. standalone PyMOL
using Makefile) in RedHat7.3 (python1.5, gcc-2.96). The build 
finishes successfuly (i.e. no error just bunch of warnings) but when
I try to run 'pymol.com', the following error appears:

Traceback (innermost last):
  File "/usr/local/pymol/modules/pymol/__init__.py", line 92, in ?
    import pymol
  File "/usr/local/pymol/modules/pymol/__init__.py", line 220, in ?
    import cmd
  File "/usr/local/pymol/modules/pymol/cmd.py", line 752, in ?
    from importing import \
  File "/usr/local/pymol/modules/pymol/importing.py", line 26, in ?
    from pymol import m4x
  File "/usr/local/pymol/modules/pymol/m4x.py", line 17
    from chempy import cex as CEX
                            ^
SyntaxError: invalid syntax

2. I repeated the same build procedure but in RedHat8.0 (python2.2,
gcc-3.2) and, to my big surprise, it builds and runs! (I find it hard
to believe that a switch from python1.5 to python2.2 would be that 
easy, but I'd surely not complain as RH8.0 is my current working OS). 
In any case, I tried to load amber topology and trajectory:

load test.top
(this seems to succeed as the message appears:
ObjectMolecule: Assuming this is an Amber6 topology file.
Executive: object "test" created.)

load_traj test.trj
..and here is where I got stuck, the message is:
CmdLoadTraj-Error: must load object topology before loading trajectory!

Was someone successful to get this working?
Thanks very much,

-Viktor
-- 
===================================================================
Viktor Hornak
SUNY at Stony Brook      
Stony Brook, NY 11794-5115   E-mail: Vik...@su...   
===================================================================

[PyMOL] Screen problems Mac OS X 10.2.1

[Kersey B. <kb...@js...>]

Hi,

Just installed PyMOL 0.84beta -- looks great.  Hoping to use it instead 
of Molscript on the SGI.

However, the image on the screen is screwed up -- looks like it has the 
wrong color map,
mixed in with some bad dithering.  The background is dark green.
When I click to move the structure, or put it in motion with "Rock", it 
snaps to become clear and it is fine.
It is screwed up only when at rest.  Actually, when I release the 
mouse, there is a small lag with the imge
just the way it should be on the screen, and then it goes bad.

Sorry to bug this list with this one, but i have not found mention of 
this in the archives.

Any help would be great.

Thanks

PS -- running a G3 powerbook if it matters.

[PyMOL] color by partial charge? (electrostatics)

[Mark W. <mw...@di...>]

Hello,


Background
   I want to create a surface colored by electrostatic potential in PyMOL.  
   I can simulate this by coloring atoms by a formal charge which is 
   either 1, 0 or -1, ...

   color white
   color blue, (fc; > 0.5)
   color red, (fc; < -0.5)
   show surface

   Of course this does not look like a surface colored by Poisson-Boltzmann 
   calculated potentials

Questions
   1. Can I color atoms by partial_charge? (this did not seem to work for
me)
   2. Is there a better way using only PyMOL to approximate P-B calculated
       potentials?


Thanks,
Mark

RE: [PyMOL] complete surface of selection

[DeLano, W. <wa...@su...>]

Frank suggested a good approach.  You can also do the job within one =
object:

show surface, (resi 110,128,134,135,120,131,118,138,121,129,132,136)
flag ignore,(not (resi 110,128,134,135,120,131,118,138,121,129,132,136))
rebuild

Cheers,
Warren

-----Original Message-----
From: Vondelft, Frank=20

Hi Sri
=20
Really easy:  make a new object of the residues, then do the surface:

create mysel, (resi 110,128,134,135,120,131,118,138,121,129,132,136)
show surface, mysel


-----Original Message-----
From: Mad Max [mailto:mad...@ya...]
Sent: Thursday, October 24, 2002 10:04 AM
To: pym...@li...
Subject: [PyMOL] complete surface of selection


Hi,=20
    I am trying to render the surface of only selected residues but =
using=20
show surface, (resi 110,128,134,135,120,131,118,138,121,129,132,136) =
only shows components of the overall surface contributed by the external =
residues in my selection.
I want to depict the entire surface of individual residues even if they =
are internal. I was unable to figure out how to do it. Sorry if this is =
a trivial question.
Thanks
Sri.




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RE: [PyMOL] complete surface of selection

[Vondelft, F. <Fra...@sy...>]

Hi Sri
 
Really easy:  make a new object of the residues, then do the surface:

create mysel, (resi 110,128,134,135,120,131,118,138,121,129,132,136)
show surface, mysel
 
 
Cheers
phx.

-----Original Message-----
From: Mad Max [mailto:mad...@ya...]
Sent: Thursday, October 24, 2002 10:04 AM
To: pym...@li...
Subject: [PyMOL] complete surface of selection



Hi, 

    I am trying to render the surface of only selected residues but
using 

show surface, (resi 110,128,134,135,120,131,118,138,121,129,132,136)
only shows components of the overall surface contributed by the external
residues in my selection.

I want to depict the entire surface of individual residues even if they
are internal. I was unable to figure out how to do it. Sorry if this is
a trivial question.

Thanks

Sri.




  _____  

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your web site


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[PyMOL] complete surface of selection

[Mad M. <mad...@ya...>]

Hi, 

    I am trying to render the surface of only selected residues but using 

show surface, (resi 110,128,134,135,120,131,118,138,121,129,132,136) only shows components of the overall surface contributed by the external residues in my selection.

I want to depict the entire surface of individual residues even if they are internal. I was unable to figure out how to do it. Sorry if this is a trivial question.

Thanks

Sri.



---------------------------------
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Re: [PyMOL] pymol and povray

[Robert C. <rl...@k2...>]

* Schubert, Carsten <Car...@3d...> [2002-10-23 16:59] wrote:
> Don't know about MACs but this works on PCs and SGIs:
> -------------------------------------------------
> Exporting Povray scripts from PyMol
>  
> 
> The choice of the renderer is defined by the variable "ray_default_renderer". A
> value of 0 points to the internal renderer, a value of 1 creates a povray file
> called "tmp_pymol.pov" in the current directory.
> 
> To change the setting use:
> 
>         cmd.set('ray_default_renderer',1)
> 
> Alternatively use this script:
> 
>         util.ray_shadows('heavy')
>         (header,data) = cmd.get_povray()
>         file=open('povray.pov','w')
>         file.write(header)
>         file.write(data)
>         file.close()
> 
> 
I definitely prefer the second idea, because I like to tweek the
povray.pov file to get the best output.

Cheers,
Robert
-- 
Robert L. Campbell, Ph.D.               http://biophysics.med.jhmi.edu/rlc
rl...@k2...                                    phone: 410-614-6313
Research Specialist/X-ray Facility Manager
HHMI/Dept. of Biophysics & Biophysical Chem., The Johns Hopkins University
    PGP Fingerprint: 9B49 3D3F A489 05DC B35C  8E33 F238 A8F5 F635 C0E2

RE: [PyMOL] pymol and povray

[Schubert, C. <Car...@3d...>]

Don't know about MACs but this works on PCs and SGIs:
-------------------------------------------------
Exporting Povray scripts from PyMol
 

The choice of the renderer is defined by the variable
"ray_default_renderer". A value of 0 points to the internal renderer, a
value of 1 creates a povray file called "tmp_pymol.pov" in the current
directory.

To change the setting use:

	cmd.set('ray_default_renderer',1)

Alternatively use this script:

	util.ray_shadows('heavy')
	(header,data) = cmd.get_povray()
	file=open('povray.pov','w')
	file.write(header)
	file.write(data)
	file.close()


Thanks for the original contributors.


Happy PyMOLing

	Carsten


> -----Original Message-----
> From: Craig Smith [mailto:boi...@ma...]
> Sent: Wednesday, October 23, 2002 16:48
> To: pym...@li...
> Subject: [PyMOL] pymol and povray
> 
> 
> I have a apple G4 powerbook using OS10.2.  Is it possible to 
> write out 
> a pov-ray type script file that could be directly input into pov-ray?
> 
> 
> Craig L. Smith, Ph. D.
> Molecular Microbiology
> Washington University School of Medicine
> 660 South Euclid Box 8230
> Voice: (314) 362-9054
> Fax: (314) 362-1232
> e-mail: sm...@bo...
> 
> 
> 
> -------------------------------------------------------
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