pymol-users — Collaborative support and tips for PyMOL users

RE: [PyMOL] Pymol ignores SCALE records in PDB files

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

Keith,

	Thank you for bringing this issue to my attention.

	I can confirm that PyMOL doesn't currently read SCALE records. In order =
to generate correct crystal symmetry, it requires the input PDB =
coordinates to be  properly oriented and translated with respect to the =
crystal lattice origin and axes.  However, I think this is the default =
case with most of the standard refinement programs.  At the very least, =
PyMOL should print a warning if it finds a SCALE record!

	I'll see if we can't get SCALE handling in before the next release.

Cheers,
Warren


> -----Original Message-----
> From: Keith Refson [mailto:kr...@is...]
> Sent: Wednesday, November 27, 2002 7:02 AM
> To: pym...@li...
> Subject: [PyMOL] Pymol ignores SCALE records in PDB files
>=20
>=20
> Just to repeat the subject, it appears that pymol takes no account of
> the SCALE records in a PDB file.
>=20
> The built in assumptions of the orientation of the unit cell therefore
> gives an erroneous relationship between the unit cell and the atomic
> co-ordinates.  The attached file demonstrates the problem.
> "Show->Cell" puts the long dimension of the cell perpendicular to the
> line of the atoms, rather than collinear with them as it ought to be.
> More seriously then, "symexp" gives a completely wrong expansion.
>=20
> HEADER    UNKNOWN
> TITLE
> AUTHOR    GENERATED BY XX2PDB (Keith Refson, 1998)
> CRYST1    5.024    5.024    5.024  39.69  39.69  39.69 P 1
> SCALE1      0.338511  0.000000  0.072121        0.00000
> SCALE2     -0.169255  0.293159  0.072121        0.00000
> SCALE3     -0.169255 -0.293159  0.072121        0.00000
> HETATM    1  H00 NON A   1       0.000   0.000   6.933  1.00 =20
> 0.00           H
> HETATM    2  F00 NON A   1       0.000   0.000   5.792  1.00 =20
> 0.00           F
> HETATM    3  F00 NON A   1       0.000   0.000   8.073  1.00 =20
> 0.00           F
> HETATM    4 Na00 NON A   1       0.000   0.000   0.000  1.00 =20
> 0.00          Na
> TER       4      NON A   1
> END
>=20
> sincerely
>=20
> Keith Refson
> --=20
> Dr Keith Refson,=20
> Building R3
> Rutherford Appleton Laboratory
> Chilton
> Didcot
> Oxfordshire OX11 0QX
> T: 01235 778023		K.Refson@
> F: 01235 445720		@rl.ac.uk
>=20
>=20
>=20
> -------------------------------------------------------
> This SF.net email is sponsored by: Get the new Palm Tungsten T=20
> handheld. Power & Color in a compact size!=20
> http://ads.sourceforge.net/cgi-bin/redirect.pl?palm0002en
> _______________________________________________
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> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20

[PyMOL] Pymol ignores SCALE records in PDB files

[Keith R. <kr...@is...>]

Just to repeat the subject, it appears that pymol takes no account of
the SCALE records in a PDB file.

The built in assumptions of the orientation of the unit cell therefore
gives an erroneous relationship between the unit cell and the atomic
co-ordinates.  The attached file demonstrates the problem.
"Show->Cell" puts the long dimension of the cell perpendicular to the
line of the atoms, rather than collinear with them as it ought to be.
More seriously then, "symexp" gives a completely wrong expansion.

HEADER    UNKNOWN
TITLE
AUTHOR    GENERATED BY XX2PDB (Keith Refson, 1998)
CRYST1    5.024    5.024    5.024  39.69  39.69  39.69 P 1
SCALE1      0.338511  0.000000  0.072121        0.00000
SCALE2     -0.169255  0.293159  0.072121        0.00000
SCALE3     -0.169255 -0.293159  0.072121        0.00000
HETATM    1  H00 NON A   1       0.000   0.000   6.933  1.00  0.00           H
HETATM    2  F00 NON A   1       0.000   0.000   5.792  1.00  0.00           F
HETATM    3  F00 NON A   1       0.000   0.000   8.073  1.00  0.00           F
HETATM    4 Na00 NON A   1       0.000   0.000   0.000  1.00  0.00          Na
TER       4      NON A   1
END

sincerely

Keith Refson
-- 
Dr Keith Refson, 
Building R3
Rutherford Appleton Laboratory
Chilton
Didcot
Oxfordshire OX11 0QX
T: 01235 778023		K.Refson@
F: 01235 445720		@rl.ac.uk

[PyMOL] pymol and mmtk

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

Hi folks:

I just installed a python-based molecular modelling and dynamics 
program called mmtk and am trying to get it to play nicely with pymol.  
I can get it to use pymol as the default pdb displayer, but I can't 
figure out how to make them talk intelligently to one another.  For 
example, if I run a sample program from mmtk within pymol, everything 
works but then it opens up another pymol window within pymol, which is 
kind of annoying.

I've only used mmtk for about 37 seconds so I haven't managed to grok 
it completely, but if there is an obvious quick solution to this please 
let me know.

BTW if you want to install mmtk via fink on OS X I have an install 
script here:

http://chemistry.ucsc.edu/~wgscott/xtal/xtalfink_html.html


Thanks in advance.

Bill Scott



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] OT: BioMT

[Chris A. <chr...@br...>]

Hi Guys,

This is a slightly off topic question but I was wondering if you could help.

I have a crystal structure (1KAS) which is the monomer of a homodimer
related by a two fold symmetry axis. Basically I want to be able to look at
the dimeric structure but I haven't a clue how to use the BioMT matrix to
transform the structure. Is there a nice easy way of doing this?

Thanks in advance

Chris

Snippet from the PDB file...

REMARK 300 BIOMOLECULE
REMARK 300 THE BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 300 MOLECULE IS A DIMER.
REMARK 350
REMARK 350 GENERATING THE BIOMOLECULE
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW.  BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350
REMARK 350 APPLY THE FOLLOWING TO CHAINS: NULL
REMARK 350   BIOMT1   1 -0.500000  0.866050  0.000000        0.00000
REMARK 350   BIOMT2   1  0.866000  0.500000  0.000000        0.00000
REMARK 350   BIOMT3   1  0.000000  0.000000 -1.000000        0.00000
REMARK 525

[PyMOL] symexp in scripts

[Cynthia F. <cn...@it...>]

Warren,

I am able to create symmetry-related molecules by typing the symexp 
command into the PyMol window interactively, but including the 
identical command in my script (see below) does not work.  This is 
frustrating, as I need to create H-bonds to the symmetry molecules, 
and now must type all of these commands in by hand (or as a later 
script, I suppose).

Am I doing something wrong?  Or is this a bug you're aware of?

Another question related to symexp:  Is there a pattern to how PyMol 
names the object created by symexp?  The object created by:

symexp S=mainA,(resi 202),5

is S05000000.  Can I predict this? (currently the only way I guessed 
this name is by typing the command into the PyMol window and reading 
the output)  Can I rename this object name to something more useful 
to me?

Thanks for all your work. This is a great program.  I'm excited to 
hear that a more thorough manual is on the way--I'm looking forward 
to learning more about what we can do with PyMol!

-Cynthia (David Agard's lab, UCSF :) )

Script I'm using:

#  LOAD PDB AND MAP
#load /Users/cynthia/Desktop/sgi_files/wtalp_19c_2fofc_sm.xplor, 2fofc
#load /Users/cynlap/Desktop/sgi_files/from_iMac/wtalp_19c_pymol.ent, main
load /Users/cynthia/Desktop/sgi_files/wtalp_19c_pymolA.ent, mainA
load /Users/cynthia/Desktop/sgi_files/wtalp_19c_pymolB.ent, mainB

# ALTER SETTINGS FOR PUBLICATION QUALITY
set mesh_radius = 0.008
set antialias = 1
set stick_radius = 0.1
bg_color white
set depth_cue=1
set ray_trace_fog=1
set spec_power = 200 #to increase glossyness, see faq
set spec_refl=1.5 #to increase glossyness, see faq
set dash_radius=0.05

hide all

#  CREATE GROUPS
create interest, (resi 36,143,202)
show sticks, interest
create oxyhole, (resi 140:144)
show sticks, oxyhole

symexp S=mainA,(resi 202),5     #create symmetry-related molecules
show sticks, S05000000

create water, (resn HOH)
show nb_spheres, water
#hide (not (resi 202 expand 8))	  #only atoms w/in 8A of 202
#hide (!(byres ((mainA///202) around 8))) #not working: symexp not recognized

#  DISTANCE LINES (H-BONDS)
distance one=(143/OG),(mainA///202/O1)
distance two=(mainB///143/OG),(resi 36 and name NE2)
distance three=(resi 202 and name O1),(resi 141 and name N)
distance four=(mainA///202/O4),(resi 140 and name NE)
distance five=(mainB///202/O3),(resi 140 and name NE)
distance six=(mainB///202/O4),(S05000000///89/NH1)

color grey, one
color grey, two
color grey, three
color grey, four
color grey, five
color grey, six

set dash_radius=0.03   #see maillist search dash for more edit options

#  DRAW MAP
#isomesh msh_2fofc, 2fofc, 2, interest, carve=1
#color cyan, msh_2fofc

#  SET UP FOR DISPLAY
set_view (\
     -0.085494332,   -0.754236877,    0.651016355,\
      0.352779120,    0.588155329,    0.727744758,\
     -0.931792915,    0.291883081,    0.215793610,\
      0.000000000,    0.000000000,  -39.378192902,\
     13.142999649,   30.863000870,   14.019000053,\
     35.878196716,   43.628189087,    0.000000000 )

symexp S=mainA,(resi 202),5     #symexp not recognized here, either
show sticks, S05000000

-- 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cynthia N. Fuhrmann
Department of Biochemistry & Biophysics			cn...@it...
University of California, San Francisco			(415) 502-2930
513 Parnassus Ave., Box 0448 				(415) 476-1902 (fax)
San Francisco, CA  94143-0448 		       http://www.msg.ucsf.edu/agard
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

RE: [PyMOL] Re: PyMOL-users digest, Vol 1 #218 - 1 msg

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

Kelley,

	Unfortunately PyMOL doesn't have object-specific Z-clip.  (That is a =
cool idea though, perhaps in the future...)

	The closest thing to this you can accomplish is to selectively show or =
hide the surface on certain atoms in order to create a view which shows =
the full ligand and only part of the surface.  This would be a lot of =
work though, so I can't recommend it.

Sorry,
Warren


> -----Original Message-----
> From: Kelley Moremen [mailto:mo...@ar...]
> Sent: Monday, November 25, 2002 2:03 PM
> To: pym...@li...
> Subject: [PyMOL] Re: PyMOL-users digest, Vol 1 #218 - 1 msg
>=20
>=20
> Hi Carsten,
>=20
> I appreciate your reply and I would assume that it makes impressive
> graphics, but it sounds WAY beyond my meager abilities (I am=20
> struggling with
> the Mac OS X version of Pymol after all and haven't ventured=20
> into the realm
> of raster3D yet).  I assume that since there has been a=20
> resounding lack of
> response within the Pymol masses that it either can't be done=20
> or hasn't been
> done. Just in case somebody missed the prior posting I would=20
> like to be able
> to perform a selective Z-clipping in order to cross-section=20
> an active site
> pocket with a bound ligand. The challenge comes in trying to=20
> Z-clip the
> protein structure (shown as a "surface" display) while=20
> retaining the entire
> ligand (no Z-clip on the ligand). Prior attempts have either Z-clipped
> everything (create protein as an object, create ligand as an=20
> object, then
> Z-clip) or Z-clipped nothing (create protein as an object, execute the
> Z-clip, then create ligand as an object and display it).  Somehow the
> creation of the ligand as an object and displaying it=20
> over-rides the prior
> Z-clip and both objects are displayed in their entirety.
>=20
> Any suggestion within the Pymol world?
>=20
> Thanks,
>=20
> Kelley
>=20
>=20
>=20
> On 11/25/02 3:06 PM, "pym...@li..."
> <pym...@li...> wrote:
> > --__--__--
> >=20
> > Message: 1
> > From: "Schubert, Carsten" <Car...@3d...>
> > To: "'Kelley Moremen'" <mo...@ar...>,
> >  pym...@li...
> > Subject: RE: [PyMOL] Selective Z-clipping
> > Date: Mon, 25 Nov 2002 09:07:13 -0500
> >=20
> > Hi Kelley,
> >=20
> > I just worked out a procedure to do this with VMD/Raster3D=20
> (oops, this is
> > the PyMol list ...). Anyhow, it boils down to that you can=20
> apply selective
> > bounding or clipping planes in Raster3D. In the case of a=20
> clipped surface
> > you want to use a bounding plane, which slices through an object and
> > produces a sealed cut (bounding plane) or really play with=20
> the lights to get
> > rid of all the interior surfaces exposed by a non-sealing cut with a
> > clipping plane. I played around a little bit with Povray to=20
> achieve the same
> > effect. I figured out to use an intersection with CGOs but=20
> somehow I could
> > not get it to work with a surface definition. May be=20
> somebody else knows how
> > to do this. I'd be interested in it to.
> >=20
> > Here is what I did. Split your scene into their components=20
> and write out the
> > raster3d input files. Remove all headers from the r3d files=20
> and save one
> > header into a control script (master.r3d) If you use vmd=20
> (oops again...) you
> > have to get rid of the object 17 in the surface definition,=20
> otherwise you
> > will not be able change colors, transparency etc. Use=20
> remove_17.pl for this.
> > The animate_bounding.pl script allows you to move the=20
> bounding plane in a
> > given range to find the right orientation. The only way to=20
> do this is by
> > trial and error. A good starting point is a plane defined=20
> by the normal
> > vector 0,0,1 (x,y plane at origin of scene).
> >=20
> > good luck.
> >=20
> >=20
> > Carsten
>=20
>=20
> Dr. Kelley Moremen=20
> 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/
>=20
>=20
>=20
>=20
> -------------------------------------------------------
> This SF.net email is sponsored by: Get the new Palm Tungsten T=20
> handheld. Power & Color in a compact size!=20
> http://ads.sourceforge.net/cgi-bin/redirect.pl?palm0002en
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20

[PyMOL] Re: PyMOL-users digest, Vol 1 #218 - 1 msg

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

Hi Carsten,

I appreciate your reply and I would assume that it makes impressive
graphics, but it sounds WAY beyond my meager abilities (I am struggling with
the Mac OS X version of Pymol after all and haven't ventured into the realm
of raster3D yet).  I assume that since there has been a resounding lack of
response within the Pymol masses that it either can't be done or hasn't been
done. Just in case somebody missed the prior posting I would like to be able
to perform a selective Z-clipping in order to cross-section an active site
pocket with a bound ligand. The challenge comes in trying to Z-clip the
protein structure (shown as a "surface" display) while retaining the entire
ligand (no Z-clip on the ligand). Prior attempts have either Z-clipped
everything (create protein as an object, create ligand as an object, then
Z-clip) or Z-clipped nothing (create protein as an object, execute the
Z-clip, then create ligand as an object and display it).  Somehow the
creation of the ligand as an object and displaying it over-rides the prior
Z-clip and both objects are displayed in their entirety.

Any suggestion within the Pymol world?

Thanks,

Kelley



On 11/25/02 3:06 PM, "pym...@li..."
<pym...@li...> wrote:
> --__--__--
> 
> Message: 1
> From: "Schubert, Carsten" <Car...@3d...>
> To: "'Kelley Moremen'" <mo...@ar...>,
>  pym...@li...
> Subject: RE: [PyMOL] Selective Z-clipping
> Date: Mon, 25 Nov 2002 09:07:13 -0500
> 
> Hi Kelley,
> 
> I just worked out a procedure to do this with VMD/Raster3D (oops, this is
> the PyMol list ...). Anyhow, it boils down to that you can apply selective
> bounding or clipping planes in Raster3D. In the case of a clipped surface
> you want to use a bounding plane, which slices through an object and
> produces a sealed cut (bounding plane) or really play with the lights to get
> rid of all the interior surfaces exposed by a non-sealing cut with a
> clipping plane. I played around a little bit with Povray to achieve the same
> effect. I figured out to use an intersection with CGOs but somehow I could
> not get it to work with a surface definition. May be somebody else knows how
> to do this. I'd be interested in it to.
> 
> Here is what I did. Split your scene into their components and write out the
> raster3d input files. Remove all headers from the r3d files and save one
> header into a control script (master.r3d) If you use vmd (oops again...) you
> have to get rid of the object 17 in the surface definition, otherwise you
> will not be able change colors, transparency etc. Use remove_17.pl for this.
> The animate_bounding.pl script allows you to move the bounding plane in a
> given range to find the right orientation. The only way to do this is by
> trial and error. A good starting point is a plane defined by the normal
> vector 0,0,1 (x,y plane at origin of scene).
> 
> good luck.
> 
> 
> Carsten


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/

Re: [PyMOL] settings of ribbons and cartoons

[Jules J. <jo...@he...>]

Hi Kristl

The problem is that the secondary structure of your protein hasn't been
defined in the PDB file. This is why the cartoon looks ike a tube. What
you need to do is type util.ss into the command line and this will
calculate some sort of secondary structure for you although it's not
that accurate. Alternatively click on the little diamond next to your
protein name in the in the OpenGL window and then click on 'assign ss'.

As for your best bet on finding out how to do things this is probably it.

Jules

On Mon, 25 Nov 2002, Kristl Adams wrote:

>
> Where can I find a list of what I can set with regard to ribbons and
> cartoons.  Currently the cartoons command just shows a thin round tube and
> the ribbons command shows just a thin line.
>
> I'd ideally like to have cartoonishly round ribbons with some of the
> residues on them drawn in sticks.  I'm a new pymole user and am finding it
> frustrating  to work with because it isn't that well documented ... Am I
> just not looking in the correct places for documentation?  I have the pdf
> at http://pymol.scourceforge.net/userman.pdf, but it isn't specific
> enough.
>
> Please help the hopelessly confussed.
> Kristl
>
>
>
> -------------------------------------------------------
> This SF.net email is sponsored by: Get the new Palm Tungsten T
> handheld. Power & Color in a compact size!
> http://ads.sourceforge.net/cgi-bin/redirect.pl?palm0002en
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>

Re: [PyMOL] settings of ribbons and cartoons

[Kadmon <ka...@wa...>]

Have you set your sheet and helix part in your pdb? For my personal case,
things you experienced happened when this part wasn't built.
I guess that PyMOL cannot find the secondary structures as softwares like
Rasmol can.
Try to determine your secondary structures with DSSP for example and to
paste it in your pdb file before loading it in PyMOL, your cartoonish
rendering should be great :)

Cheers

Virgile ADAM

[PyMOL] settings of ribbons and cartoons

[Kristl A. <kr...@ph...>]

Where can I find a list of what I can set with regard to ribbons and
cartoons.  Currently the cartoons command just shows a thin round tube and
the ribbons command shows just a thin line.

I'd ideally like to have cartoonishly round ribbons with some of the
residues on them drawn in sticks.  I'm a new pymole user and am finding it
frustrating  to work with because it isn't that well documented ... Am I
just not looking in the correct places for documentation?  I have the pdf
at http://pymol.scourceforge.net/userman.pdf, but it isn't specific
enough.

Please help the hopelessly confussed.
Kristl

[PyMOL] selecting specific hetatm's

[<chu...@in...>]

Hello, while this is a simple question, I can't seem to find the answer
anywhere.

How do I select a specific hetatm:
The pdb file says:
HET    BCL  C   1      51
    
HET    BCL  C   2      66
    
HET    BCL  C   3      66
    
HET    BCL  C   4      66
    
HET    BPH  C   5      51
    
HET    BPH  C   6      65
    
HET    FE2  C   7       1
    
HET    U10  C   8      38
    
HET    U10  C   9      44
    
HET    LDA  C  10      16
    
HET    LDA  C  11      16
    
HET    LDA  C  12      16
    
HET    LDA  C  13      16
    
HET    BCL  D   1      51
    
HET    BCL  D   2      66
    
HET    BCL  D   3      66
    
HET    BCL  D   4      66
    
HET    BPH  D   5      52
    
HET    BPH  D   6      65
    
HET    FE2  D   7       1
    
HET    U10  D   8      32
    
HET    U10  D   9      18 

And I want to select these individually.
I can show all by saying "show sticks, (het)".
I realize this is partially my lack of understanding of how a pdb file is
put together, if there is a tutorial on that that someone could refer me to
that would be great as well.

Thanks,
Carly                                                      

RE: [PyMOL] moving/fitting

[Richard K. <rk...@Tr...>]

Hi Kristl,

You can change the mouse to "edit mode" from the Mouse menu.  Here's a =
link to a response from Warren to a similar question...

http://sourceforge.net/mailarchive/message.php?msg_id=3D2376446

hope that helps.

Richard



-----Original Message-----
From: Kristl Adams [mailto:kr...@ph...]=20
Sent: Saturday, November 23, 2002 11:40 AM
To: pym...@li...
Subject: [PyMOL] moving/fitting


I'd like to fit the porphyrin of the alpha subunit of Hemoglobin on top =
of
the porphyrin of myoglobin ( in order to compare the heme pockets ).  I =
am
a new user of Pymol and have been fiddling with it to become familiar,
but am having no luck in this area.  Please send any useful hints my =
way.

Thanks,
Kristl



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[PyMOL] A little script for massaging pdb files

[Michael G. L. <ml...@um...>]

The electron densities of Carbon, Nitrogen and Oxygen look basically the
same to crystallographers.  So, sometimes they get them confused in
pdb files.  In particular, one often has to flip the orientation of the
side chains in Asn or Gln.  Also, this means that the Nitrogens may be
placed incorrectly in His side chains.  Similarly, since x-ray
crystallographers cannot see Hydrogens, the crystal structure may not tell
you which Nitrogen(s) in the His residue should be protonated.  If you're
going to use the crystal structure in, for example, a molecular dynamics
calculation, it is critical that you get this stuff right.  The easiest
way to do this is to try out each possibility and see which one looks best
with respect to Hydrogen bonding.  Since PyMOL is so easy to script, I
wrote a little bit of code to automate this process.  You can find the
code at

http://www.umich.edu/~mlerner/mgzoom.py

and a little bit of explaination at

http://www.umich.edu/~mlerner/pymolscripts.html

It basically lets you scan through the Asn, Gln and His residues and pick
the proper orientation/protonation.  If I can figure out how, maybe I'll
turn it into a wizard.

I had a quick question that I came across when writing this script:

I was looking for some way to set a bond valence, and all I could find was
cycle_valence.  Is there something like set_valence?  My guess is that it
would look something like this:

/*========================================================================*/
void EditorSetValence(int valence)
{
  CEditor *I = &Editor;
  int sele0,sele1;

  if(I->Obj) {

    ObjectMoleculeVerifyChemistry(I->Obj); /* remember chemistry for later */

    sele0 = SelectorIndexByName(cEditorSele1);
    if(sele0>=0) {
      sele1 = SelectorIndexByName(cEditorSele2);
      if(sele1>=0) {
        /* bond mode */
        /* should we care if valence > 3? */
        ObjectMoleculeAdjustBonds(I->Obj,sele0,sele1,0,valence);
      }
    }
  }

}

But I didn't see it in layer3/Editor.c.  Is it somewhere else and I just
haven't found it?

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

[PyMOL] moving/fitting

[Kristl A. <kr...@ph...>]

I'd like to fit the porphyrin of the alpha subunit of Hemoglobin on top of
the porphyrin of myoglobin ( in order to compare the heme pockets ).  I am
a new user of Pymol and have been fiddling with it to become familiar,
but am having no luck in this area.  Please send any useful hints my way.

Thanks,
Kristl

[PyMOL] Selective Z-clipping

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

Dear Pymollers,

I am trying to display a cross-section of an active site pocket with a
ligand bound in the active site.  For the figure I would like to Z-clip the
active site residues (viewed as a surface representation), but not the
ligand. To accomplish this I would assume that I need to create two
different objects and Z-clip only one of them.  The problem is this: if I
create and display both objects and then execute a Z-clip  both of the
objects get clipped.  If I create one object, call for a Z-clip, then create
the second object, the Z-clip is over-ridden and both full structures
(without any Z-clipping) are displayed.

Any suggestions on how I can get selective Z-clipping

Thanks,

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] NULL-POINTER-ERROR: in RepSphere.c line 380

[B. C. <chevalib@u.washington.edu>]

pymol version 0.83

i'm receiving a similar error to those posted earlier; i get this error in
both windows and linux.  the molecules i'm loading are not huge (two
protein/dna complexes), and i can provide details as necessary.
interestingly, i can sometimes avoid this error by rebooting linux...but
only sometimes...

btw, great program warren.

RE: [PyMOL] ray tracing and cross-eyed stereo

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

Dottore Ambroggio: 

For sereo figures people usually  use a rotation angle of ~6 deg with
coinciding elements of the images spaced ca 60-65 mm apart (assuming normal
human physiology) You can either take one image then rotate the scene with
turn y,6 and take the other shot or sometimes it makes more sense to start
from the "center" and take images +- 3 degrees apart. I use the later
technique for electron density shots, gives  less artifacts.

Happy PyMol'ing

	Carsten

> -----Original Message-----
> From: Xavier I. Ambroggio [mailto:amb...@it...]
> Sent: Thursday, November 21, 2002 18:04
> To: PyM...@li...
> Subject: [PyMOL] ray tracing and cross-eyed stereo
> 
> 
> Pymolers,
> 
> I am trying to make an image (png file) in cross-eyed stereo, 
> but it seems
> that I cannot make the stereo image and ray trace. Does 
> anyone know either
> how to do this or how to manually make the image by making 
> two images with
> the proper angles/distance/etc.?
> 
> Thanks,
> Xavier
> 
> ____________________________________
> http://www.its.caltech.edu/~ambrosia
> 
> 
> 
> -------------------------------------------------------
> This sf.net email is sponsored by:ThinkGeek
> Welcome to geek heaven.
> http://thinkgeek.com/sf
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
> 

[PyMOL] ray tracing and cross-eyed stereo

[Xavier I. A. <amb...@it...>]

Pymolers,

I am trying to make an image (png file) in cross-eyed stereo, but it seems
that I cannot make the stereo image and ray trace. Does anyone know either
how to do this or how to manually make the image by making two images with
the proper angles/distance/etc.?

Thanks,
Xavier

____________________________________
http://www.its.caltech.edu/~ambrosia

[PyMOL] multiple h bonds

[Scott C. <cl...@uc...>]

PyMOL users,
	Is there a way to add multiple hydrogen bonds quickly and easily 
without having to type in an endless array of distance commands?

distance (/lc03A//D/1 and name NAI),(/lc03A//A/365 and name OE1)
distance (/lc03A//A/365 and name NE2),(/lc03A//L/1 and name O1G)
etc
etc..

Thanks,
Scott



==============================================
   Scott Classen, Ph.D.
   cl...@uc...
   University of California, Berkeley
   Department of Molecular & Cell Biology
   237 Hildebrand Hall #3206
   Berkeley, CA 94720-3206
   LAB 510.643.9491
   FAX 510.643.9290
==============================================

Re: [PyMOL] labels again

[Evan S. <st...@sa...>]

I label in stereo using Adobe Illustrator.

I place the labels at the same approximate position on the figure (aligning
them vertically) and then I adjust the horizontal position of the label on
the right figure until the label appears at the proper depth for the figure.

--
Evan Stein
Structural Biology Program
Skirball Institute / NYU School of Medicine
540 First Avenue Lab 3-4
New York, NY 10016

phone: (212) 263-8968
fax: (212) 263-8951
email: st...@sa...
URL: http://saturn.med.nyu.edu/~stein


> From: Ricardo Aparicio <apa...@if...>
> Date: Wed, 20 Nov 2002 15:37:46 +0000
> To: "pym...@li..." <pym...@li...>
> Subject: [PyMOL] labels again
> 
> Dear colleagues:
> 
> I've been looking for a way to add labels to my figures.
> After a search in the e-mail list files, I could draw cgo labels, although it
> would be a pain to
> orient them by hand using cmd.rotate and cmd.translate (too many figures).
> So, in the case of mono, I have used photoshop to include labels (superposing
> figures from PyMOL).
> 
> The main problem, however, is that I need stereo now and I see two
> possibilities:
> to use cgo labels in both figures
> or
> to use labels (photoshop) in only one figure of the stereo par.
> 
> 
> My questions are:
> 
> 1a) are there "news" about labels within PyMOL? Any recent improvement? (last
> e-mail in this issue
> was from august/25)? Any other clue I didn't see?
> 
> 1b) are there "news" concerning automatic orientation?
> 
> 2) is there a way to change color of cgo labels?
> 
> 3) is there a way to change font of cgo labels?
> 
> 4) do you have any reference (paper published or web) where I can see
> PyMOL-made figures containing
> labels?
> 
> 
> Thank you very much for your help.
> 
> 
> Regards,
> 
> Ricardo Aparicio
> PhD Student
> Sao Paulo - BR
> 
> 
> 
> 
> 
> -------------------------------------------------------
> This sf.net email is sponsored by: To learn the basics of securing
> your web site with SSL, click here to get a FREE TRIAL of a Thawte
> Server Certificate: http://www.gothawte.com/rd524.html
> _______________________________________________
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> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users

[PyMOL] labels again

[Ricardo A. <apa...@if...>]

Dear colleagues:

I've been looking for a way to add labels to my figures.
After a search in the e-mail list files, I could draw cgo labels, although it would be a pain to
orient them by hand using cmd.rotate and cmd.translate (too many figures).
So, in the case of mono, I have used photoshop to include labels (superposing figures from PyMOL).

The main problem, however, is that I need stereo now and I see two possibilities:
to use cgo labels in both figures
or
to use labels (photoshop) in only one figure of the stereo par.


My questions are:

1a) are there "news" about labels within PyMOL? Any recent improvement? (last e-mail in this issue
was from august/25)? Any other clue I didn't see?

1b) are there "news" concerning automatic orientation?

2) is there a way to change color of cgo labels?

3) is there a way to change font of cgo labels?

4) do you have any reference (paper published or web) where I can see PyMOL-made figures containing
labels?


Thank you very much for your help.


Regards,

Ricardo Aparicio
PhD Student
Sao Paulo - BR

Re: [PyMOL] editing question

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

Michael,

   What's going on would become clear if you turned on valence display.
Changing the name of a residue doesn't change the underlying chemical
representation.  Basically, you've got to change the location of the
double bond in the histidine ring, or eliminate it in the case of charged
his.

   You are using PyMOL in a new way -- I've never tried to do this myself,
but you should be able to unbond and then rebond the atoms in question
using the proper bond orders in order to get the effect you want.

Good luck,
Warren

 On Mon, 18 Nov 2002, Michael George Lerner
wrote:

>
> Hi,
>
> I'm trying to cycle through the various protonation states of a Histidine
> residue (HIE,HIP,HID).  I have resn and the residue number stored as
> 'curr_state' and 'i' respectively.  My first shot at a function looked
> basically like this (the real function has a a doc string and some gunk to
> set up curr_state and i):
>
>     cmd.remove('(hydro and neighbor %s/ND1,NE2)' % i)
>     if curr_state == 'HIE':
>         cmd.alter('%s/' % i,'resn="HID"')
>     elif curr_state == 'HID':
>         cmd.alter('%s/' % i,'resn="HIP"')
>     elif curr_state == 'HIP':
>         cmd.alter('%s/' % i,'resn="HIE"')
>     cmd.h_add('(%s/)'%i)
>     cmd.sort()
>
> After I run this, it looks like nothing has changed.  I can use something
> like
>
>     iterate (114/),print resn
>
> to see that the resn has in fact changed, but the hydrogens end up right
> where they were when I started.
>
> I've tried progressively more complex things, like this:
>
>     cmd.remove('(hydro and neighbor %s/ND1,NE2)' % i)
>     if curr_state == 'HIE':
>         print "Changing HIE to HID"
>         cmd.alter('%s/' % i,'resn="HID"')
>         cmd.alter('%s/ND1' % i,'formal_charge=1.0')
>         cmd.h_add('%s/ND1' % i)
>         cmd.alter('%s/NE2' % i,'formal_charge=0.0')
>         cmd.iterate('%s/ND1,NE2'%i,'print formal_charge,partial_charge')
>     elif curr_state == 'HID':
>         print "Changing HID to HIP"
>         cmd.alter('%s/' % i,'resn="HIP"')
>         cmd.alter('%s/ND1' % i,'formal_charge=1.0')
>         cmd.h_add('%s/ND1' % i)
>         cmd.alter('%s/NE2' % i,'formal_charge=1.0')
>         cmd.h_add('%s/NE2' % i)
>         cmd.iterate('%s/ND1,NE2'%i,'print formal_charge,partial_charge')
>     elif curr_state == 'HIP':
>         print "Changing HIP to HIE"
>         cmd.alter('%s/' % i,'resn="HIE"')
>         cmd.alter('%s/ND1' % i,'formal_charge=0.0')
>         cmd.alter('%s/NE2' % i,'formal_charge=1.0')
>         cmd.h_add('%s/NE2' % i)
>         cmd.iterate('%s/ND1,NE2'%i,'print formal_charge,partial_charge')
>     cmd.sort()
>
> But I think I may just be on the wrong track.  The last snippet *appears*
> to work for NE2 (and not for ND1), but I think that's just because the his
> was an HIE to begin with.
>
> Any hints?
>
> 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
>
>
>
> -------------------------------------------------------
> This sf.net email is sponsored by: To learn the basics of securing
> your web site with SSL, click here to get a FREE TRIAL of a Thawte
> Server Certificate: http://www.gothawte.com/rd524.html
> _______________________________________________
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> PyM...@li...
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>

Re: [PyMOL] (no subject)

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

Fei Xu wrote:
> HI! Dr. Delano:
> Would you like to tell me how I can control the size of the ball, if I
> pick an atom and show it like a ball?

Dear Fei Xu:

1. You select an atom
2. You display it as a ball
3. You type:
set sphere_scale = 2.0

Here, the number is the size proportional to an original size of 1.0.

Unfortunately, settings for individual objects are not functional yet.


Kristian

[PyMOL] (no subject)

[Fei Xu <fe...@ru...>]

HI! Dr. Delano:
Would you like to tell me how I can control the size of the ball, if I
pick an atom and show it like a ball?
Have a nice day!
Fei

[PyMOL] editing question

[Michael G. L. <ml...@um...>]

Hi,

I'm trying to cycle through the various protonation states of a Histidine
residue (HIE,HIP,HID).  I have resn and the residue number stored as
'curr_state' and 'i' respectively.  My first shot at a function looked
basically like this (the real function has a a doc string and some gunk to
set up curr_state and i):

    cmd.remove('(hydro and neighbor %s/ND1,NE2)' % i)
    if curr_state == 'HIE':
        cmd.alter('%s/' % i,'resn="HID"')
    elif curr_state == 'HID':
        cmd.alter('%s/' % i,'resn="HIP"')
    elif curr_state == 'HIP':
        cmd.alter('%s/' % i,'resn="HIE"')
    cmd.h_add('(%s/)'%i)
    cmd.sort()

After I run this, it looks like nothing has changed.  I can use something
like

    iterate (114/),print resn

to see that the resn has in fact changed, but the hydrogens end up right
where they were when I started.

I've tried progressively more complex things, like this:

    cmd.remove('(hydro and neighbor %s/ND1,NE2)' % i)
    if curr_state == 'HIE':
        print "Changing HIE to HID"
        cmd.alter('%s/' % i,'resn="HID"')
        cmd.alter('%s/ND1' % i,'formal_charge=1.0')
        cmd.h_add('%s/ND1' % i)
        cmd.alter('%s/NE2' % i,'formal_charge=0.0')
        cmd.iterate('%s/ND1,NE2'%i,'print formal_charge,partial_charge')
    elif curr_state == 'HID':
        print "Changing HID to HIP"
        cmd.alter('%s/' % i,'resn="HIP"')
        cmd.alter('%s/ND1' % i,'formal_charge=1.0')
        cmd.h_add('%s/ND1' % i)
        cmd.alter('%s/NE2' % i,'formal_charge=1.0')
        cmd.h_add('%s/NE2' % i)
        cmd.iterate('%s/ND1,NE2'%i,'print formal_charge,partial_charge')
    elif curr_state == 'HIP':
        print "Changing HIP to HIE"
        cmd.alter('%s/' % i,'resn="HIE"')
        cmd.alter('%s/ND1' % i,'formal_charge=0.0')
        cmd.alter('%s/NE2' % i,'formal_charge=1.0')
        cmd.h_add('%s/NE2' % i)
        cmd.iterate('%s/ND1,NE2'%i,'print formal_charge,partial_charge')
    cmd.sort()

But I think I may just be on the wrong track.  The last snippet *appears*
to work for NE2 (and not for ND1), but I think that's just because the his
was an HIE to begin with.

Any hints?

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