pymol-users — Collaborative support and tips for PyMOL users

[PyMOL] Sphere Scale Preference

[Fergus B. <f.b...@au...>]

Dear Sir

How can I alter the sphere_scale to affect only specific named 
selections. At present, changing the scale alters all the loaded 
molecules at the same time.

Thankyou

Fergus Binnie
University of Auckland 

[PyMOL] selections

[Michael S. C. Ph.D. <co...@co...>]

Hi, I am new to pymol. I was wondering if someone could help me with 
selecting multiple noncontinuous residues with the same name. For example, 
I have tried the following:
select name1, a/79/ .....# to select a single residue,
select name2, a/79:85/ ......# to select a continuous string of residues,
How do I select a collection of noncontinuous of residues that can be given 
the same name (i.e. name3)

Thanks,

Michael

RE: [PyMOL] using external python interpreter to control pymol ??

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

NOTE: the following is unix-specific.

This is a common problem with PyMOL.  Right now it is impossible (in
practice) to use PyMOL as merely an imported module within an external
interpreter (i.e. without using "pymol.com" instead of "python" to
invoke the interpreter).  This will be fixed in a later version.

For example:

#!/bin/csh
python <<END
from pymol import cmd
cmd.cls()
END

...will fail.

For now, you need to use the pymol.com script to launch your Python
interpreter if you are going to use PyMOL.

Normal commands are interpreted first by PyMOL and then passed to Python
if PyMOL doesn't recognize the command.  You can skip PyMOL evaluation
with a preceeding /, which is almost equivalent to typing the same
command (without a preceeding slash) in a Python interpreter:

print "hello"
/print "hello"

However, you can run native Python script in external using the run
command:

run myscript.py

...which is almost equivalent to typing:

python myscript.py

...on the unix or windows command shell, or by issuing

execfile("myscript.py")=20

...from within an existing Python interpreter.

IMPORTANT CONCEPT:

The key difference between=20

python myscript.py    # on command line
pymol.com myscript.py # on commmand line
run myscript.py       # in PyMOL

is that default evaluation in PyMOL currently takes place in the "pymol"
module, not "__main__".  Right now there is no easy way to start a
process in the "__main__" module.  I will remedy this in the next public
release, and probably make __main__ the default namespace for the run
command (so long as that doesn't break anything).

You can however, force evaluation of your script to occur in its own
name-space:

run myscript.py,module

...or in a local namespace:

run myscript.py,local

--
mailto:wa...@su...
Warren L. DeLano, Ph.D.
Informatics Manager
Sunesis Pharmaceuticals, Inc.
341 Oyster Point Blvd.
S. San Francisco, CA 94080
(650)-266-3606  FAX:(650)-266-3501

> From: Ingo Dramburg [mailto:dra...@Ma...]
=20
> Hi,
>=20
> I want to include my own modules into PyMOL for visualization
> purposes.=20
> If I try to use the pymol.cmd module to control a running
> PyMOL process from an external python interpreter
> I always get a segmentation fault. (SuSE 7.2, Python 2.0)
> Everything else works fine.
>=20
> Example:
> >> from pymol import cmd
> >> cmd.cls()
> segmentaion fault
>=20
> Is it possible to do such things in general or is it possible
> to switch to a 'native' python mode in the PyMOL window to enter=20
> python commands directly :-).=20
>=20
> The next question is how can I pass selections from PyMOL to external=20
> scripts to do calculations that are not supported by PyMOL=20
> and later back to
> PyMOL for visualization.
>=20
> Thanks you for any help,
>=20
> Ingo.
> --=20
> ************************************************************
> Ingo Dramburg=20
>=20
> Institute of Pharmaceutical Chemistry
> Philipps-University Marburg
> Marbacher Weg 6, D 35032 Marburg, Germany
>=20
> Tel. + 49 6421 282 1313
> Fax  + 49 6421 282 8994
> e-mail dra...@ma...
> http://www.agklebe.de/
>=20
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20

[PyMOL] RE: VDW Radii i

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

Michael,

I've cc'd the list with my response.

   "Correct" VDW radii are only in version 0.78 and beyond -- they were
important for the sculpting feature.  Before, PyMOL was using a set that
was about 5% too large (they were originally taken from another popular
graphics program...). =20

Here are the values for key atoms in the current set.

C 1.7
N 1.55
O 1.52
H 1.2
S 1.80
Cl 1.75
Br 1.85
F 1.47
I 1.98
P 1.80

   After loading a molecule, you can use the alter command to provide
your own vdw radii.

   A solvent accessible dot surface (only) can be had with

set dot_mode=3D1
show dots

   Want more dots?  Set dot_density to 3.

   There's no equivalent yet for solid or mesh surfaces.

   Electrostics are in progress -- no public announcements yet.

Warren


--
mailto:wa...@su...
Warren L. DeLano, Ph.D.

> From: michaelw [mailto:mic...@we...]

> I need to confirm that PyMOL is using vanderWaals distances=20
> for generation of=20
> surfaces. Also, has anyone written surface charge or solvent=20
> accessible=20
> surface functions for PyMOL yet?
>=20
> PyMOL is excellent!
>=20
> CHEERS!
>=20
> Michael
>=20

[PyMOL] using external python interpreter to control pymol ??

[Ingo D. <dra...@Ma...>]

Hi,

I want to include my own modules into PyMOL for visualization
purposes. 
If I try to use the pymol.cmd module to control a running
PyMOL process from an external python interpreter
I always get a segmentation fault. (SuSE 7.2, Python 2.0)
Everything else works fine.

Example:
>> from pymol import cmd
>> cmd.cls()
segmentaion fault

Is it possible to do such things in general or is it possible
to switch to a 'native' python mode in the PyMOL window to enter 
python commands directly :-). 

The next question is how can I pass selections from PyMOL to external 
scripts to do calculations that are not supported by PyMOL and later back to
PyMOL for visualization.

Thanks you for any help,

Ingo.
-- 
************************************************************
Ingo Dramburg 

Institute of Pharmaceutical Chemistry
Philipps-University Marburg
Marbacher Weg 6, D 35032 Marburg, Germany

Tel. + 49 6421 282 1313
Fax  + 49 6421 282 8994
e-mail dra...@ma...
http://www.agklebe.de/

Re: [PyMOL] (no subject)

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

On Sun, 17 Feb 2002, Nat wrote:

> From an earlier reply...
> > The easiest way to use PyMOL as a module is to use PyMOL as your Python
> > interpreter.  It isn't trivial to launch PyMOL from within a running
> > Python interpreter, but it can be done under unix (only).  See pymol.com
> > and modules/launch_pymol.py for an example of how to do it.
> 
> Got this working.  Now, I'm trying to create movie frames from the
> command line; I've got two systems I've tried this on, one SuSE
> 7.something (compiled manually), the other RedHat 7.2 (rpms).  I'm
> wondering whether this is even possible.  I've modified pymol.com to
> launch my script instead; what it does is this:
> 

You shouldn't (need to) modify any of the launch
scripts.  Just use the "-c" option to get
PyMOL running in command-line only mode.
(see "help launching for all the command-line options")

pymol.com -c script.py
pymol.com -c script.pml

Cheers,
Warrren

[PyMOL] (no subject)

[Nat <nat...@ya...>]

From an earlier reply...
> The easiest way to use PyMOL as a module is to use PyMOL as your Python
> interpreter.  It isn't trivial to launch PyMOL from within a running
> Python interpreter, but it can be done under unix (only).  See pymol.com
> and modules/launch_pymol.py for an example of how to do it.

Got this working.  Now, I'm trying to create movie frames from the
command line; I've got two systems I've tried this on, one SuSE
7.something (compiled manually), the other RedHat 7.2 (rpms).  I'm
wondering whether this is even possible.  I've modified pymol.com to
launch my script instead; what it does is this:

----------------------------------------
import thread
import threading
import os
import sys
import time
import glob

modules_path = os.environ['PYMOL_PATH']+'/modules'

if modules_path not in sys.path:
   sys.path.append(modules_path)

import pymol
from pymol import cmd, util

pymol.invocation.parse_args(sys.argv)

mid = "635272-10321"
method = 1
frames = 10
os.chdir("/bh1/nat/movie/" + mid)
print "Set..."
cmd.set("auto_zoom", 0)
----------------------------------------

... and there's more, except it segfaults as soon as it hits cmd.set().
Same thing happens when I try using it from the command line.  Obviously
since I can get as far as pymol.invocation I'm doing something right, but
I can't actually use the cmd module.

What am I missing?  I'm not even sure I need the "pymol.invocation..."
part, but I know I can't call start_pymol().  Am I missing something, or
simply misunderstanding PyMOL's capabilities?  It's the perfect tool for
what I'm trying to accomplish (lots of high-quality movies), but I need
something non-graphical/non-interactive.  Everything else I've tried has
been less flexible and more obscure in varying degrees.

thanks,
Nat

[PyMOL] Video

[Marc S. <mar...@mp...>]

 > Message: 1
 > Subject: [PyMOL] RE: Pymol and Movie

 > Anyone know of a respectable freeware solution for making movies?

Bink&Smacker is good, if you like DivX! Don't know how that compares to 
the above mentioned codecs, but it should work quite well.

See http://www.radgametools.com/

-- 
Bye,  Marc Saric

Max-Planck-Institut fuer molekulare Physiologie
Otto-Hahn-Str.11  44227 Dortmund  phone:0231/133-2168

[PyMOL] SGi O2 Hardware Stereo?

[Kostrewa D. <dir...@ps...>]

Dear PyMol users,

neither PyMol 0.73 nor 0.78 appears to work with hardware stereo on our SGI
O2 machines, despite the correct recognition of the graphics card and
hardware stereo capability. I've set the frame buffer to 32x32 and hardware
window stereo works with another application. PyMol, when switched to
stereo, correctly changes the resolution to 1024x786_96s and lets the
emitter start working, but there is still only a mono picture in the viewer.
Warren has no O2 around (yet), so he can't do the necessary checks by
himself. Is there somebody successfully using PyMol with hardware stereo on
an SGI O2? If yes, could you please help to fix that problem? 

Best regards,

Dirk. 


*****************************************************
Dirk Kostrewa
Paul Scherrer Institut   e-mail: dir...@ps...
Life Sciences             phone: +41-56-310-4722
OSRA/007                    fax: +41-56-310-4556
CH-5232 Villigen PSI        WWW: http://sb.web.psi.ch
Switzerland
*****************************************************

RE: [PyMOL] RE: Pymol and Movie

[Abhinav K. <ak...@pl...>]

I tried the gifmerge which worked just fine.

Thanks
Abhinav


-----Original Message-----
From: Daan van Aalten [mailto:da...@da...] 
Sent: Wednesday, February 13, 2002 1:50 PM
To: DeLano, Warren
Cc: Abhinav Kumar; pym...@li...
Subject: Re: [PyMOL] RE: Pymol and Movie


Yes: use animated GIF!

Very simple to make and you can stick it into your webpages without any
horrible platform-specific plugins - it'll just start running straight
away. They also work in PowerPoint (if you really insist on using that
program).
You can make them with the ImageMagick package, with The Gimp and also
with a tiny C program called gifmerge which you can located through a
Google search. For some examples, see my homepage, under "Presentations".
Needless to say I'll be using PyMOL for all these in the future, rather
than molscript!

cheers

Daan


On Wed, 13 Feb 2002, DeLano, Warren wrote:

> If you can't get Premiere, the only options I know of are mpeg_encode
> (any unix) or mediaconvert (IRIX specific).  Unfortunately, both of
> these produce noticably inferior results when compared to AVI (Cinepak)
> or Quicktime (Sorenson).
> 
> Anyone know of a respectable freeware solution for making movies?
> 
> - Warren
> 
> > Hi,
> > 
> > I am a new user of Pymol and am very impressed with a few 
> > things that I have
> > been able to do. In particular I like the ease with which 
> > movies can be
> > made.
> > 
> > Since I am new, please help me understand and do a few things:
> > After the movie is made, a bunch of files (*.png) are created in the
> > directory. What will be the best/easiest way to import the movie in
> > Powerpoint/Web presentation? I do not have Adobe Premiere. 
> > 
> > I am using a Linux machine (red hat 7.1).
> > 
> > Thanks for the help.
> 
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
> 


############################################################################
##
 
Dr. Daan van Aalten                    Wellcome Trust RCD Fellow 
Wellcome Trust Biocentre, Dow Street   TEL: ++ 44 1382 344979 
Div. of Biol.Chem. & Mol.Microbiology  FAX: ++ 44 1382 345764 
School of Life Sciences                E-mail:
da...@da...
Univ. of Dundee, Dundee DD1 5EH, UK    WWW:
http://davapc1.bioch.dundee.ac.uk 

        O     C           O     C         Visit the PRODRG server to take 
        "     |           "     |         the stress out of your topologies!
  N--c--C--N--C--C--N--C--C--N--C--C--O   
     |           "     |           "      http://davapc1.bioch.dundee.ac.uk/
     C-C-O       O   C-C-C         O             programs/prodrg/prodrg.html
       "         
       O         

RE: [PyMOL] RE: Pymol and Movie

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

A great answer for intranets and PowerPoint presentations!  Thanks
Daan...

You can assemble these on the fly with ImageMagick, but I've found it
takes two passes. One to make the gif, and a second to adjust the frame
rate.  The whole movie assembly process can then be reduced to a single
PyMOL script.  Awesome!

But be warned: animated-GIFs are grossly inefficient for molecular
animations in internet web pages.  They very rapidly exceed a reasonable
size even when you cut down on the number of colors. =20

In contrast, JPEG's animated with client-side Javascript can give you at
least 5X the number of frames in the same space, but they're not
self-contained.

--
mailto:wa...@su...
Warren L. DeLano, Ph.D.

> From: Daan van Aalten [mailto:da...@da...]

> Yes: use animated GIF!
>=20
> Very simple to make and you can stick it into your webpages=20
> without any
> horrible platform-specific plugins - it'll just start running straight
> away. They also work in PowerPoint (if you really insist on using that
> program).
> You can make them with the ImageMagick package, with The Gimp and also
> with a tiny C program called gifmerge which you can located through a
> Google search. For some examples, see my homepage, under=20
> "Presentations".
> Needless to say I'll be using PyMOL for all these in the=20
> future, rather
> than molscript!
>=20
> cheers
>=20

RE: [PyMOL] secondary structure

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

> How does this affect movies involving conformation changes?  Secondary
> structure info from the first frame appears to carry over=20
> into the others-
> whereas in reality some helixes or sheets change to varying=20
> degrees.  This
> leads to warping in something like calmodulin.  Would I need to render
> frames separately and run 'alter'?

Secondary structure in PyMOL is currently an atomic not a coordinate
property.  This is probably a design flaw, which will need to be fixed
later on.  Same goes for occupancy and B-factors (anything else?).

Anyway, if you want it to change secondary structure during a
trajectory, the easiest thing to do is split the trajectory over two
objects with non-overlapping states (ie. use the 'state' option to
load), and then assign the secondary structure independently...

state    1 2 3 4 5 6 7 8 =20
object1  X X X X=20
object2          X X X X=20

> However, I'm finding that using PyMOL as a module is failing. I built
> from source and have everything installed in=20
> /usr/local/python, and when I
> try to do 'from pymol import cmd, util' I get this:
> Traceback (most recent call last):
>   File "./render.py", line 7, in ?
>     import pymol
>   File "/usr/local/pymol/modules/pymol/__init__.py", line 24, in ?
>     import _cmd
> ImportError: shared object not open

The easiest way to use PyMOL as a module is to use PyMOL as your Python
interpreter.  It isn't trivial to launch PyMOL from within a running
Python interpreter, but it can be done under unix (only).  See pymol.com
and modules/launch_pymol.py for an example of how to do it.

Re: [PyMOL] RE: Pymol and Movie

[Daan v. A. <da...@da...>]

Yes: use animated GIF!

Very simple to make and you can stick it into your webpages without any
horrible platform-specific plugins - it'll just start running straight
away. They also work in PowerPoint (if you really insist on using that
program).
You can make them with the ImageMagick package, with The Gimp and also
with a tiny C program called gifmerge which you can located through a
Google search. For some examples, see my homepage, under "Presentations".
Needless to say I'll be using PyMOL for all these in the future, rather
than molscript!

cheers

Daan


On Wed, 13 Feb 2002, DeLano, Warren wrote:

> If you can't get Premiere, the only options I know of are mpeg_encode
> (any unix) or mediaconvert (IRIX specific).  Unfortunately, both of
> these produce noticably inferior results when compared to AVI (Cinepak)
> or Quicktime (Sorenson).
> 
> Anyone know of a respectable freeware solution for making movies?
> 
> - Warren
> 
> > Hi,
> > 
> > I am a new user of Pymol and am very impressed with a few 
> > things that I have
> > been able to do. In particular I like the ease with which 
> > movies can be
> > made.
> > 
> > Since I am new, please help me understand and do a few things:
> > After the movie is made, a bunch of files (*.png) are created in the
> > directory. What will be the best/easiest way to import the movie in
> > Powerpoint/Web presentation? I do not have Adobe Premiere. 
> > 
> > I am using a Linux machine (red hat 7.1).
> > 
> > Thanks for the help.
> 
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
> 


##############################################################################
 
Dr. Daan van Aalten                    Wellcome Trust RCD Fellow 
Wellcome Trust Biocentre, Dow Street   TEL: ++ 44 1382 344979 
Div. of Biol.Chem. & Mol.Microbiology  FAX: ++ 44 1382 345764 
School of Life Sciences                E-mail: da...@da...
Univ. of Dundee, Dundee DD1 5EH, UK    WWW: http://davapc1.bioch.dundee.ac.uk 

        O     C           O     C         Visit the PRODRG server to take 
        "     |           "     |         the stress out of your topologies!
  N--c--C--N--C--C--N--C--C--N--C--C--O   
     |           "     |           "      http://davapc1.bioch.dundee.ac.uk/
     C-C-O       O   C-C-C         O             programs/prodrg/prodrg.html
       "         
       O         

[PyMOL] RE: Pymol and Movie

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

If you can't get Premiere, the only options I know of are mpeg_encode
(any unix) or mediaconvert (IRIX specific).  Unfortunately, both of
these produce noticably inferior results when compared to AVI (Cinepak)
or Quicktime (Sorenson).

Anyone know of a respectable freeware solution for making movies?

- Warren

> Hi,
>=20
> I am a new user of Pymol and am very impressed with a few=20
> things that I have
> been able to do. In particular I like the ease with which=20
> movies can be
> made.
>=20
> Since I am new, please help me understand and do a few things:
> After the movie is made, a bunch of files (*.png) are created in the
> directory. What will be the best/easiest way to import the movie in
> Powerpoint/Web presentation? I do not have Adobe Premiere.=20
>=20
> I am using a Linux machine (red hat 7.1).
>=20
> Thanks for the help.

[PyMOL] RE: question

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

QnkgZGVmYXVsdCwgY3VycmVudCB2ZXJzaW9ucyBvZiBQeU1PTCBleGNsdWRlcyBQREIgSEVUQVRN
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IGZpbGUgaW4gcXVlc3Rpb24uDQpCcnlhbg0K

Re: [PyMOL] secondary structure

[Nat <nat...@ya...>]

> You can bypass the requirement for having secondary structure in the PDB
> file by explicitly assigning secondary structure using the alter command.

Ah.  This is probably what I was looking for.

> PyMOL just stores one bit of secondary structure information per residue 
> (the "ss" property of the CA atom).  Just remember to set cartoon mode to
> "auto" after making changes in order to force an update of the graphical 
> cartoons.

How does this affect movies involving conformation changes?  Secondary
structure info from the first frame appears to carry over into the others-
whereas in reality some helixes or sheets change to varying degrees.  This
leads to warping in something like calmodulin.  Would I need to render
frames separately and run 'alter'?

> It should be pretty straighforward to write a Python script which
> assigns secondary structure based on any file format.  Of course, from a
> Python python script, the above commands would look like

Definitely a good idea, since I'm using a combination of Perl and Python
with many intermediate files right now, and the result is not pretty.  I'd
much rather do everything in Python (which, unfortunately, I'm much less
familiar with).

However, I'm finding that using PyMOL as a module is failing. I built
from source and have everything installed in /usr/local/python, and when I
try to do 'from pymol import cmd, util' I get this:
Traceback (most recent call last):
  File "./render.py", line 7, in ?
    import pymol
  File "/usr/local/pymol/modules/pymol/__init__.py", line 24, in ?
    import _cmd
ImportError: shared object not open

I do have /usr/local/python/modules in the shared library path
(/etc/ld.so.conf under SuSE 7).  I'm not quite sure what's going on... all
I really need to do is execute a .pml file and run a few system calls for
now, until I create something more rigorous.

thanks,
Nat

Re: [PyMOL] secondary structure

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

On Tue, 12 Feb 2002, Nat wrote:

> 
> Forgive my ignorance, but what would be the best way to add secondary
> structure data to a PDB file, or coerce it into some format that PyMOL can
> read?  I've been fiddling around with STRIDE and DSSP, but the outputs
> from these need to be parsed into the official PDB format for
> secondary structure annotation (which I assume from the manual that PyMol
> can use).  Is there some better (e.g. quicker) way to do this? I've found
> util.ss() works fine, but Warren has repeatedly said not to use it and
> these images will be presented.

You can bypass the requirement for having secondary structure in the PDB
file by explicitly assigning secondary structure using the alter command.

load tst.pdb
alter tst & */ca, ss='L'
alter tst & 5-30/ca, ss='H'
alter tst & 35-40/ca, ss='S'
alter tst & 42-47/ca, ss='S'
cartoon auto
show cartoon

> On a related note, if I do get a script to parse STRIDE data working,
> what's the minimum amount of annotation that PyMOL requires for a sheet?
> PDB seems to use a lot more data which I don't believe I can supply, like
> which sheets are parallel/antiparallel to eachother.

PyMOL just stores one bit of secondary structure information per residue 
(the "ss" property of the CA atom).  Just remember to set cartoon mode to
"auto" after making changes in order to force an update of the graphical 
cartoons.

It should be pretty straighforward to write a Python script which
assigns secondary structure based on any file format.  Of course, from a
Python python script, the above commands would look like

from pymol import cmd
cmd.load("tst.pdb")
cmd.alter("tst & */ca","ss='L'")
cmd.alter("tst & 5-30/ca","ss='H'")
cmd.alter("tst & 35-40/ca","ss='L'")
cmd.alter("tst & 42-37/ca","ss='L'")
cmd.cartoon("auto")
cmd.show("cartoon")

...and you'd replace those fixed strings with string expressions if you
were dynamically parsing a file.

It would be great if someone would volunteer to investigate how
different util.ss is compared to DSSP.  The reason I caution against
using it is that it doesn't conform to any published criterion and
hasn't been adequately tested or validated.   Like nearly every other
feature in PyMOL, it was cooked up on the fly to solve an immediate need,
without much in the way of rigorous follow-up.

Cheers,
Warren

[PyMOL] secondary structure

[Nat <nat...@ya...>]

Forgive my ignorance, but what would be the best way to add secondary
structure data to a PDB file, or coerce it into some format that PyMOL can
read?  I've been fiddling around with STRIDE and DSSP, but the outputs
from these need to be parsed into the official PDB format for
secondary structure annotation (which I assume from the manual that PyMol
can use).  Is there some better (e.g. quicker) way to do this? I've found
util.ss() works fine, but Warren has repeatedly said not to use it and
these images will be presented.

On a related note, if I do get a script to parse STRIDE data working,
what's the minimum amount of annotation that PyMOL requires for a sheet?
PDB seems to use a lot more data which I don't believe I can supply, like
which sheets are parallel/antiparallel to eachother.

thanks,
Nat Echols

[PyMOL] Labeling stretches

[Jacob C. <jc...@gl...>]

So here's yet another question, oh-so-soon after the first.

Is there a way to label long stretches of residues with a single
user-defined label? So far I've only been able to label *every* residue
along a stretch according to a some property. I could instead just
create 2 selections, one being the stretch and another being a single
residue in that stretch, then label the single residue. But I can't
quite figure out how to assign my own label to that amino acid.
If you can think of a more elegant solution than what I just
mentioned, what I'd really like to do is have a single bit of text
that I've defined rocking along with the molecule in a movie.

Thanks
Jacob

RE: [PyMOL] hydrogen bonds

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

> From: Daan van Aalten [mailto:da...@da...]

> Is there an option to change the following parameters for=20
> drawing hydrogen
> bonds:
> - thickness of the lines
> - number of dashes
> - label (on/off, and fontsize)

The settings you need to change are:

"dash_length" and "dash_gap", which control the length and spacing of
dashes

"dash_width" which controls the pixel thickness of dashes

"dash_radius" which controls the radius of dashes when ray-traced.

You can use "Edit All..." under the settings menu to inspect and adjust
these values.

In recent versions of PyMOL, labels can be shown or hidden with=20

hide lables,<distance-object-name>
show labels,<distance-object-name>

Unfortunately, font size is not adjustable because PyMOL currently only
has one uniform bitmap font.  You currently need to use something like
PowerPoint, Photoshop, or Illustrator to add nicer labels onto your
images.

Cheers,
Warren

--
mailto:wa...@su...
Warren L. DeLano, Ph.D.

=20

[PyMOL] hydrogen bonds

[Daan v. A. <da...@da...>]

Hi Warren

Is there an option to change the following parameters for drawing hydrogen
bonds:
- thickness of the lines
- number of dashes
- label (on/off, and fontsize)

cheers

Daan

##############################################################################
 
Dr. Daan van Aalten                    Wellcome Trust RCD Fellow 
Wellcome Trust Biocentre, Dow Street   TEL: ++ 44 1382 344979 
Div. of Biol.Chem. & Mol.Microbiology  FAX: ++ 44 1382 345764 
School of Life Sciences                E-mail: da...@da...
Univ. of Dundee, Dundee DD1 5EH, UK    WWW: http://davapc1.bioch.dundee.ac.uk 

        O     C           O     C         Visit the PRODRG server to take 
        "     |           "     |         the stress out of your topologies!
  N--c--C--N--C--C--N--C--C--N--C--C--O   
     |           "     |           "      http://davapc1.bioch.dundee.ac.uk/
     C-C-O       O   C-C-C         O             programs/prodrg/prodrg.html
       "         
       O         

Re: [PyMOL] Rocking on the y axis

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

On Sat, 9 Feb 2002, Jacob Corn wrote:

> First off, let me congratulate Dr. DeLano for creating such an
> amazingly useful program. The combination of GUI and command-line is
> great, making it easier to use than MolScript and more functional than
> DeepView. Not to mention the *very* polished graphics that it is
> capable of producing.

Can I quote you on that?  Seriously.  A web page containing genuine 
endorsements from well-respected scientists might help others get over 
the PyMOL activation barrier by encouraging them to learn the program.
 
If anyone else would like to submit a candid quote for the web site, then
please email me directly in order to avoid unnecessary list traffic.  
I'll put something up if 9or when) I get about a half-dozen responses.  
These quotes shouldn't be just praise -- honest identification of
strengths and weaknesses would do more to inform potential users.

Thanks for making my day!  Molscript and DeepView are awesome programs,
so it's very satisfying to hear someone other than *myself* suggesting
that PyMOL might be able to compete in their league.  

> For an upcoming talk we'd like to show some footage of our molecule of
> interest rocking along the y axis (thus swinging back and
> forth along some putative sites on the "top" of the protein).
> I'm assuming there's a way to do this, but I'm not sure exactly how to
> do so. I took a look at the mrock function in movie.py, and noticed that, while
> one passes it 5 arguments from the command line, there are actually 6
> variables in the function, the last one being "axis," explaining my
> inability to pass the function an argument for the axis of rotation.
> However, in my desperation, I've even gone so far as changing this last variable to
> axis='y' within movie.py itself, but the molecule continued to rock on
> the x axis. Any suggestions?

   I'm puzzled -- the current version of movie.rock rocks about the Y axis
by default, but that is easily changed as shown below.  Note the use of
a named argument in order to override the default value for the 6th
argument while skipping over the 4th and 5th arguments.  That flexibility
is part of the reason I love Python.

# first, just load something, define, and play the movie...

fragment phe
mset 1 x30
mplay

# x-axis
movie.rock 1,30,15,axis=x

# y-axis
movie.rock 1,30,15,axis=y

# z-axis
movie.rock 1,30,15,axis=z

#---

Jacob, are you using the current version 0.78?  If not, then perhaps
there was a problem with an older version which has been fixed.  

By the way, if you are using straight Python instead of the PyMOL command
language, then you need to add back the quotes and parentheses:

from pymol import movie
movie.rock(1,30,15,axis='y')

Cheers,
Warren

[PyMOL] Rocking on the y axis

[Jacob C. <jc...@gl...>]

Hi all,
First off, let me congratulate Dr. DeLano for creating such an
amazingly useful program. The combination of GUI and command-line is
great, making it easier to use than MolScript and more functional than
DeepView. Not to mention the *very* polished graphics that it is
capable of producing.

So now that I've dispensed with the praise, here's my question.
For an upcoming talk we'd like to show some footage of our molecule of
interest rocking along the y axis (thus swinging back and
forth along some putative sites on the "top" of the protein).
I'm assuming there's a way to do this, but I'm not sure exactly how to
do so. I took a look at the mrock function in movie.py, and noticed that, while
one passes it 5 arguments from the command line, there are actually 6
variables in the function, the last one being "axis," explaining my
inability to pass the function an argument for the axis of rotation.
However, in my desperation, I've even gone so far as changing this last variable to
axis='y' within movie.py itself, but the molecule continued to rock on
the x axis. Any suggestions?

Jacob Corn
Gladstone Institute of Neurological Disease
jc...@gl...

[PyMOL] Molecular Sculpting Video

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

Friends,

I've updated the animation on the PyMOL Web page to show a
demonstration of PyMOL 0.78's new building and molecular sculpting
features.  Please take a look when you get a chance...

http://pymol.sf.net

Cheers,
Warren L. DeLano, Ph.D.
DeLano Scientific

Re: [PyMOL] Some experiences with the new 0.78-rpms

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

Marc,
   
> The Redhat72-rpm can only be installed if used with the --force and 
> --nodeps switches (otherwise it complains about not having Python 2.1). 
> During installation, some error-messages come up, stating that user 
> "warren" is not available (should I give him an account on my machine 
> ;-) and root is used instead.

   Hmm. there must be some ownership issues on some of the files --
I'll fix that in a 3rd release.

> After that, pymol works fine though. The only disatvantage is the 
> somewhat too small font in the Tk-log-window.
 
This is a recurring issue with Tcl/Tk under Linux: different
machines give different sized fonts, and I don't know why.  To
increase the font size, open up pymol/modules/pmg_tk/PMGAPP.py and search
for "my_fw_font".  It is currently size 7 for linux -- it probably needs
to be 9 or 10 for your machine.  Perhaps someone know why this happens?  

> So in essence: The Redhat72-rpms work on SuSE 7.3 also.

Wonderful!

-Warren