pymol-users Mailing List for PyMOL Molecular Graphics System

Hi David,

On Mon, Nov 29, 2010 at 10:33 AM, David A.  Horita <dh...@wf...> wrote:
> Hi - a couple align questions:
> 1.  How do I get a listing of which atoms are used for alignment/RMSD
> calculation when aligning one molecule to another via the align to molecule
> pulldown (especially if they're different proteins)

You can iterate over the the new alignment objects.  Here's an example,

# fetch some proteins
fetch 1rlw 1rsy, async=0

# align them, save to an alignment 'object'
align 1rlw, 1rsy, object=aln

# walk over the alignment object for each protein
# and print out the included alpha carbons
iterate aln and 1rlw and n. CA, print model, chain, resi, resn, name, elem
iterate aln and 1rsy and n. CA, print model, chain, resi, resn, name, elem

You can iterate across other properties as you see fit.


> 2.  Is it possible to write an alignment script, e.g., align mol2 and (name
> n,c,ca) and (resid 10-64), mol1 and ...
> where mol2 and mol1 are generic labels for the first, second, etc. molecules
> loaded?  I'm looking at NMR structure bundles where each conformer has a
> name from e.g., refined_1 to refined_16, and aligning each of them pairwise
> to the first in the set.  If I only load in a subset - say the 4 lowest
> energy, they may or may not include any given filename, so aligning them to
> an explicit name won't always work.

There's no default "molX" or equivalent.  I suggest you use the
"get_names" function.  In the following example, it'll return a list
of names of objects and align that to your target protein called
'target':

for conformerX in cmd.get_names("objects"):
  cmd.align(conformerX, "target")

As a more concrete example, the target is "3kus":

# fetch a multistate protein
fetch 1nmr 3kus, async=0, multiplex=1

python
for x in cmd.get_names("objects"):
  if "1nmr" in x:
    cmd.align(x, "/3kus//B")
python end

For any keywords here like "discrete," "multiplex," "cmd", be sure to
check the PyMOLWiki (http://pymolwiki.org) for more information.

Cheers,

-- Jason

> Thanks,
> David
>
> -----------------------------
> David A. Horita, Ph.D.
> Department of Biochemistry
> Wake Forest University School of Medicine
> Winston-Salem, NC 27157-1016
> Tel: 336 713-4194
> Fax: 336 716-7671
> email:  dh...@wf...
> web:  http://www1.wfubmc.edu/biochem/faculty/Horita.htm
>
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>



-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) Jas...@sc...
(o) +1 (603) 374-7120

Hi - a couple align questions:
1.  How do I get a listing of which atoms are used for alignment/RMSD calculation when aligning one molecule to another via the align to molecule pulldown (especially if they're different proteins)

2.  Is it possible to write an alignment script, e.g., align mol2 and (name n,c,ca) and (resid 10-64), mol1 and ...
where mol2 and mol1 are generic labels for the first, second, etc. molecules loaded?  I'm looking at NMR structure bundles where each conformer has a name from e.g., refined_1 to refined_16, and aligning each of them pairwise to the first in the set.  If I only load in a subset - say the 4 lowest energy, they may or may not include any given filename, so aligning them to an explicit name won't always work.

Thanks,
David

-----------------------------
David A. Horita, Ph.D.
Department of Biochemistry
Wake Forest University School of Medicine
Winston-Salem, NC 27157-1016
Tel: 336 713-4194
Fax: 336 716-7671
email:  dh...@wf...<mailto:dh...@wf...>
web:  " rel="nofollow">http://www1.wfubmc.edu/biochem/faculty/Horita.htm<http://www1.wfubmc.edu/biochem/faculty/Horita.htm/>

Hi PyMOL users,

I would like to know if PyMOL can be used in an immersive environment, 
like the CAVE.
The only material I have been able to find is the following:

"Porting Legacy Applications to immersive virtual environments - a case 
study" by K Gruchalla, J Marbach and M Dubin.
Recently Virtalis has done some driver plugin which is very costly and I 
would like to know if there is any cheaper option.
I would just like to run a demo initially and see how the system can be 
beneficial in a CAVE.
I have also read about the Virtalis Plugin for PyMOL, but this is quite 
expensive. Does anyone know of any cheaper option of how I can use PyMOL 
in a CAVE.

Thanks
TN

Hi all,

I like to announce two scripts that I put on pymolwiki today.

http://www.pymolwiki.org/index.php/AAindex
http://www.pymolwiki.org/index.php/Sidechaincenters

AAindex is useful to load numerical amino acid properties from the amino 
acid index database at http://www.genome.jp/aaindex/ into b-factors for 
coloring, selecting etc. The script also provides a Potential of Mean 
Force calculation (little tested) with contact potentials from aaindex3.

Sidechaincenters creates single pseudoatoms for each residue sidechain. 
This can be used for the PMF calculation.

Cheers,
   Thomas

Hi all,

I would like to know if is it possible to see VASP crystal structure
directly in pymol ? And is it possible to draw cell edge of a crystal in
pymol ?

I can easily write a script to convert POSCAR and CONTCAR VASP files
into standard xyz file but I would like to know if is it a way to read
directly this file in pymol.

I found this link on the web :
http://pymol.sourcearchive.com/documentation/1.2r1/vaspchgcarplugin_8c-source.html
but I do not know how to use it in pymol. When I try to open a file
CONTCAR and POSCAR are not in the liste of available format. I have this
version of pymol 
 PyMOL(TM) Molecular Graphics System, Version 1.2r2.
 Copyright (C) 2009 by DeLano Scientific LLC.

Thanks for your help

Germain

-- 
Maître de Conférence
Université de Pau et des pays de l'Adour
IPREM - ECP - CTR
ger...@un...
05 59 40 78 51
http://germain-salvato-vallverdu.blogspot.com/

Hi David,

It seems to me you are looking to include the PyMOL GUI window in your images.  If that's the case, you may want to create composite images.  Here's what I would do, for what it's worth:

1. Decide what dimensions (aspect ratio) you want for the final image and choose a viewport size that will achieve this once you include the rest of the window.

viewport 800,600

2. Take a screenshot of the PyMOL window.  Grab.app is useful for this on OS X.

3. After you have your image looking the way you want, save a ray-traced .png image using a size (and dpi) that's some multiple of your viewport size to give yourself the higher resolution.  For example, if you have 72 dpi screen resolution and want at least 300 dpi, multiply the viewport dimensions and screen resolution by 5.

    # this will print the same size as the 800 x 600 viewport @ 72 dpi
    png myimage.png, width=4000, height=3000, dpi=360, ray=1

4. Using an image editing/design program such as Illustrator or Inkscape, superimpose the two images and crop/tweak as necessary.

Good luck,
Jared

--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
New York, NY 10016
212-263-7898

On Nov 23, 2010, at 8:52 AM, David Hall wrote:

Dear all,

I want to take high resolution screenshots of the PyMol interface for
figures in a methods paper where PyMol is used for some steps.  Is
there a way to make the elements of the interface display 4 times as
large so I can get ~300 dpi images instead of 72 dpi?  I have access
to Linux, OS X, and Windows, so answers on any of these systems will
be useful.

Thanks,
David

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Hey David,

Not being an expert, the best I can tell you is to check this link :

http://www.pymolwiki.org/index.php/Png

Basically, first ray trace your image with the ray command setting the size:

*ray 1200, 1200*

Then export it to PNG with the png command setting the dpi in the process:

*png myfile.png, dpi=300*

This should make the trick I guess.

Best regards,

João

If you mean the GUI of PyMOL, I guess you can change your screen 
resolution and then make a screenshot.

hongbo
On 11/23/2010 02:52 PM, David Hall wrote:
> Dear all,
>
> I want to take high resolution screenshots of the PyMol interface for
> figures in a methods paper where PyMol is used for some steps.  Is
> there a way to make the elements of the interface display 4 times as
> large so I can get ~300 dpi images instead of 72 dpi?  I have access
> to Linux, OS X, and Windows, so answers on any of these systems will
> be useful.
>
> Thanks,
> David
>
> ------------------------------------------------------------------------------
> Increase Visibility of Your 3D Game App&  Earn a Chance To Win $500!
> Tap into the largest installed PC base&  get more eyes on your game by
> optimizing for Intel(R) Graphics Technology. Get started today with the
> Intel(R) Software Partner Program. Five $500 cash prizes are up for grabs.
> http://p.sf.net/sfu/intelisp-dev2dev
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...

Dear all,

I want to take high resolution screenshots of the PyMol interface for
figures in a methods paper where PyMol is used for some steps.  Is
there a way to make the elements of the interface display 4 times as
large so I can get ~300 dpi images instead of 72 dpi?  I have access
to Linux, OS X, and Windows, so answers on any of these systems will
be useful.

Thanks,
David

you may also want to check out:
http://www.pymolwiki.org/index.php/Set_Color

On Thu, Nov 18, 2010 at 12:26 PM, Prince, D Bryan <
DBr...@as...> wrote:

>
> Dear PyMol BBS:
>
> Is it possible to color all residues (for example, K) in a protein a
> particular, user determined color? Can this be done from the scripting
> line, I can't find it in the dropdown menus.
>
> Kind regards,
> Bryan
>
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-- 
Michael Zimmermann
Ph.D. student in Bioinformatics and Computational Biology
Department of Biochemistry, Biophysics and Molecular Biology
Iowa State University

You can try -

>color yellow, resn lys

it works
surajit



________________________________
From: "Prince, D Bryan" <DBr...@as...>
To: Jason Vertrees <jas...@sc...>; 
pym...@li...
Sent: Thu, November 18, 2010 12:26:55 PM
Subject: [PyMOL] coloring residues


Dear PyMol BBS:

Is it possible to color all residues (for example, K) in a protein a
particular, user determined color? Can this be done from the scripting
line, I can't find it in the dropdown menus. 

Kind regards, 
Bryan

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Dear PyMol BBS:

Is it possible to color all residues (for example, K) in a protein a
particular, user determined color? Can this be done from the scripting
line, I can't find it in the dropdown menus. 

Kind regards, 
Bryan

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Hi Seth and Jason,

I just tried out Jason's commands and while that works for this case I can't
verify that it fails in Seth's case.  While checking the command line options
for create, I did notice that, like the load command, the create command also
has a discrete flag.  It is not described in the help (i.e. when typing "help
create"), but it is listed in the PYMOL API syntax and it is clearly listed
when you type: "create ?".

So I would suggest that you should try your usual script but add a
"discrete=1" flag to it.

Cheers,
Rob


 On Tue, 16 Nov 2010 21:46:17 -0500 Jason Vertrees
<jas...@sc...> wrote:

> Hi Seth,
> 
> When using the "create" command, you need to specify target and source
> states.  Here's an example.  Let's assume 1oky and 1t46 are the same
> protein (they're really close, so good for this example).  They both
> have ligands, 1t46 has STI and 1oky has STU.  I can (1) load each
> structure. using fetch:
> 
> # fetch the proteins from the PDB, or local file system
> fetch 1t46 1oky, async=0
> 
> # align the two proteins (you may not need this step for your application)
> align 1t46, 1oky
> 
> and then (2) extract their small molecules, into a new multi-state
> object, called 'ligands" using the 'create' command:
> 
> # create the object called 'ligands' and put 'resn STI' from state 1
> into state 1
> create ligands, 1t46 and resn STI, 1, 1
> 
> # create the object called 'ligands,' which in PyMOL re-creating an
> object that already exists
> # will add another state, and put 'resn STU' from state 1 into state 2
> create ligands, 1oky and resn STU, 1, 2
> 
> Hide the first two objects and then use the arrow keys to switch from
> state 1 to state 2.
> 
> Cheers,
> 
> -- Jason
> 
> 
> 
> On Tue, Nov 16, 2010 at 12:51 PM, Seth Harris <se...@gm...> wrote:
> > Hi Jason,
> > The end result I am trying to get is a single multi-state object that has
> > a different small molecule stored in each state, so that you can use the
> > cursor keys and flip through the various ligands (i.e. states) all aligned
> > at a given binding site. So what Robert described generates such an
> > object, but does so at the point of loading the ligand from an external
> > file. I was just trying to see if there was a way to get there from
> > objects already loaded in pymol. For instance, I'd have a protein:small
> > molecule structure loaded and aligned, and I want to bring just the
> > aligned small molecule into one of the states of the multi-state object.
> > When I use the create command all kinds of extra bonds were being drawn
> > within a given ligand, along with atom colors changing unpredictably. I
> > assumed that different small molecules have matching atom names across
> > the various states and likely that was causing the trouble. But when
> > "load"ed with the discrete flag it avoids this. Essentially, I was
> > imagining something like the 'create' command along with the discrete
> > flag. I was searching for some pdb's to share and further explore this
> > with. I think it would happen with most any small molecule structure from
> > the PDB. Anyway, the workaround seemed to be that once I had loaded the
> > protein:small molecule, aligned it, I could save out the aligned small
> > molecule only in a temp file, and load it back in to the multi state
> > object with the discrete=1 and carry on through all the objects I wanted
> > and at the end delete the temp file. The part I thought was a bit clunky
> > was having to save the file back out to the file system in order to bring
> > it back in with the load command just to be able to get access to the
> > 'discrete' flag. That's where I thought I might be missing something if I
> > explained the case further. Thanks,
> > Seth

-- 
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor 
Botterell Hall Rm 644
Department of Biochemistry, Queen's University, 
Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821            Fax: 613-533-2497
<rob...@qu...>    http://pldserver1.biochem.queensu.ca/~rlc

Hi Seth,

When using the "create" command, you need to specify target and source
states.  Here's an example.  Let's assume 1oky and 1t46 are the same
protein (they're really close, so good for this example).  They both
have ligands, 1t46 has STI and 1oky has STU.  I can (1) load each
structure. using fetch:

# fetch the proteins from the PDB, or local file system
fetch 1t46 1oky, async=0

# align the two proteins (you may not need this step for your application)
align 1t46, 1oky

and then (2) extract their small molecules, into a new multi-state
object, called 'ligands" using the 'create' command:

# create the object called 'ligands' and put 'resn STI' from state 1
into state 1
create ligands, 1t46 and resn STI, 1, 1

# create the object called 'ligands,' which in PyMOL re-creating an
object that already exists
# will add another state, and put 'resn STU' from state 1 into state 2
create ligands, 1oky and resn STU, 1, 2

Hide the first two objects and then use the arrow keys to switch from
state 1 to state 2.

Cheers,

-- Jason



On Tue, Nov 16, 2010 at 12:51 PM, Seth Harris <se...@gm...> wrote:
> Hi Jason,
> The end result I am trying to get is a single multi-state object that has a
> different small molecule stored in each state, so that you can use the
> cursor keys and flip through the various ligands (i.e. states) all aligned
> at a given binding site. So what Robert described generates such an object,
> but does so at the point of loading the ligand from an external file. I was
> just trying to see if there was a way to get there from objects already
> loaded in pymol. For instance, I'd have a protein:small molecule structure
> loaded and aligned, and I want to bring just the aligned small molecule into
> one of the states of the multi-state object. When I use the create command
> all kinds of extra bonds were being drawn within a given ligand, along with
> atom colors changing unpredictably. I assumed that different small molecules
> have matching atom names across the various states and likely that was
> causing the trouble. But when "load"ed with the discrete flag it avoids
> this. Essentially, I was imagining something like the 'create' command along
> with the discrete flag.
> I was searching for some pdb's to share and further explore this with. I
> think it would happen with most any small molecule structure from the PDB.
> Anyway, the workaround seemed to be that once I had loaded the protein:small
> molecule, aligned it, I could save out the aligned small molecule only in a
> temp file, and load it back in to the multi state object with the discrete=1
> and carry on through all the objects I wanted and at the end delete the temp
> file. The part I thought was a bit clunky was having to save the file back
> out to the file system in order to bring it back in with the load command
> just to be able to get access to the 'discrete' flag. That's where I thought
> I might be missing something if I explained the case further.
> Thanks,
> Seth
>
> On Tue, Nov 16, 2010 at 5:37 AM, Jason Vertrees
> <jas...@sc...> wrote:
>>
>> Seth,
>>
>> I don't understand your question.  I think you're looking for the
>> "copy" or "extract" command
>> (http://www.pymolwiki.org/index.php/Extract).  If not, please try
>> rewording the question.
>>
>> Cheers,
>>
>> -- Jason
>>
>> On Fri, Nov 12, 2010 at 12:55 PM, Seth Harris <se...@gm...> wrote:
>> > Thanks Robert and Jason
>> > Indeed, I have different small molecules as Robert surmised and
>> > subsequent
>> > ones affect the connectivity of the earlier ones (and representations
>> > for
>> > some reasons, colors and spheres, etc. become unpredictable) when using
>> > the
>> > create command. I had noted that "discrete" flag for the load command,
>> > but
>> > not having separate files from these aligned in the right spot is there
>> > really nothing similar to do on the fly without saving out the newly
>> > aligned
>> > (using the surrounding protein) and extracted ligand into its own pdb
>> > file
>> > and loading that back in again with the discrete flag on? That will
>> > work,
>> > but seemed a bit clunky!
>> > Thanks again for the tips to that functional route!
>> > Cheers,
>> > Seth
>> >
>> >
>> > """
>> > Hi Seth,
>> >
>> > On Tue, 09 Nov 2010 22:54:59 -0500 Jason Vertrees
>> > <jas...@sc...> wrote:
>> >
>> >> Hi Seth,
>> >>
>> >> I haven't seen that (in this scenario).  Can you send me a few PDB
>> >> examples?
>> >>
>> >> Cheers,
>> >>
>> >> -- Jason
>> >>
>> >> On Mon, Nov 8, 2010 at 10:13 PM, Seth Harris <se...@gm...> wrote:
>> >> > Hi all,
>> >> > I feel I should know this one. I have a program looping through
>> >> > structures
>> >> > and bringing each small molecule into a single multi-state object so
>> >> > I
>> >> > can
>> >> > tab through the states.
>> >> > I do:
>> >> > create all_lig, this_ligand, 1, 1
>> >> > then go on to the next one:
>> >> > create all_lig, next_ligand, 1, 2
>> >> > and so on....
>> >> > however, the bonds get all messed up, presumably with atom names
>> >> > confused? I tried issuing a "rebuild all_lig" in between adding but
>> >> > that
>> >> > didn't seem to help. What am I missing?
>> >
>> > It sounds like you are loading a set of *different* structures into the
>> > multi-state object.  I don't think you can do this properly with the
>> > "create" command.  I think the only way to do this and retain the
>> > correct
>> > bonding information is to use the load command directly with the
>> > "discrete=1"
>> > option.
>> >
>> > So, you need to do:
>> >
>> > load this_ligand, all_lig, discrete=1
>> > load next_ligand, all_lig, discrete=1
>> >
>> > Cheers,
>> > Rob
>> >
>> > --
>> > Robert L. Campbell, Ph.D.
>> > Senior Research Associate/Adjunct Assistant Professor
>> > Botterell Hall Rm 644
>> > Department of Biochemistry, Queen's University,
>> > Kingston, ON K7L 3N6  Canada
>> > Tel: 613-533-6821            Fax: 613-533-2497
>> >
>> > ------------------------------------------------------------------------------
>> > Centralized Desktop Delivery: Dell and VMware Reference Architecture
>> > Simplifying enterprise desktop deployment and management using
>> > Dell EqualLogic storage and VMware View: A highly scalable, end-to-end
>> > client virtualization framework. Read more!
>> > http://p.sf.net/sfu/dell-eql-dev2dev
>> > _______________________________________________
>> > PyMOL-users mailing list (PyM...@li...)
>> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> > Archives: http://www.mail-archive.com/pym...@li...
>> >
>>
>>
>>
>> --
>> Jason Vertrees, PhD
>> PyMOL Product Manager
>> Schrodinger, LLC
>>
>> (e) Jas...@sc...
>> (o) +1 (603) 374-7120
>
>



-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) Jas...@sc...
(o) +1 (603) 374-7120

Thanks Robert and Jason

Indeed, I have different small molecules as Robert surmised and subsequent
ones affect the connectivity of the earlier ones (and representations for
some reasons, colors and spheres, etc. become unpredictable) when using the
create command. I had noted that "discrete" flag for the load command, but
not having separate files from these aligned in the right spot is there
really nothing similar to do on the fly without saving out the newly aligned
(using the surrounding protein) and extracted ligand into its own pdb file
and loading that back in again with the discrete flag on? That will work,
but seemed a bit clunky!

Thanks again for the tips to that functional route!

Cheers,
Seth



"""
Hi Seth,

On Tue, 09 Nov 2010 22:54:59 -0500 Jason Vertrees
<jas...@sc...> wrote:

> Hi Seth,
>
> I haven't seen that (in this scenario).  Can you send me a few PDB
examples?
>
> Cheers,
>
> -- Jason
>
> On Mon, Nov 8, 2010 at 10:13 PM, Seth Harris <se...@gm...> wrote:
> > Hi all,
> > I feel I should know this one. I have a program looping through
structures
> > and bringing each small molecule into a single multi-state object so I
can
> > tab through the states.
> > I do:
> > create all_lig, this_ligand, 1, 1
> > then go on to the next one:
> > create all_lig, next_ligand, 1, 2
> > and so on....
> > however, the bonds get all messed up, presumably with atom names
> > confused? I tried issuing a "rebuild all_lig" in between adding but that
> > didn't seem to help. What am I missing?

It sounds like you are loading a set of *different* structures into the
multi-state object.  I don't think you can do this properly with the
"create" command.  I think the only way to do this and retain the correct
bonding information is to use the load command directly with the
"discrete=1"
option.

So, you need to do:

load this_ligand, all_lig, discrete=1
load next_ligand, all_lig, discrete=1

Cheers,
Rob

--
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor
Botterell Hall Rm 644
Department of Biochemistry, Queen's University,
Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821            Fax: 613-533-2497

On Wed, Nov 10, 2010 at 8:55 AM, Robert Campbell
<rob...@qu...> wrote:
> So, you need to do:
>
> load this_ligand, all_lig, discrete=1
> load next_ligand, all_lig, discrete=1

Great point, Robert.  In PyMOL when you load without specifying the
discrete flag or set it to zero, any series of states is considered as
one actual object that varies in coordinates (eg. trajectories).  To
save space, PyMOL shares atomic information (except for coordinates).
When we use, "discrete=1" as in
  load myTrajectory.pdb, discrete=1
this makes each state its own object and does not share the atom information.

In Seth's case, it looks like that difference was confusing PyMOL.

Cheers,

-- Jason

On Wed, Nov 10, 2010 at 8:55 AM, Robert Campbell
<rob...@qu...> wrote:
> Hi Seth,
>
> On Tue, 09 Nov 2010 22:54:59 -0500 Jason Vertrees
> <jas...@sc...> wrote:
>
>> Hi Seth,
>>
>> I haven't seen that (in this scenario).  Can you send me a few PDB examples?
>>
>> Cheers,
>>
>> -- Jason
>>
>> On Mon, Nov 8, 2010 at 10:13 PM, Seth Harris <se...@gm...> wrote:
>> > Hi all,
>> > I feel I should know this one. I have a program looping through structures
>> > and bringing each small molecule into a single multi-state object so I can
>> > tab through the states.
>> > I do:
>> > create all_lig, this_ligand, 1, 1
>> > then go on to the next one:
>> > create all_lig, next_ligand, 1, 2
>> > and so on....
>> > however, the bonds get all messed up, presumably with atom names
>> > confused? I tried issuing a "rebuild all_lig" in between adding but that
>> > didn't seem to help. What am I missing?
>
> It sounds like you are loading a set of *different* structures into the
> multi-state object.  I don't think you can do this properly with the
> "create" command.  I think the only way to do this and retain the correct
> bonding information is to use the load command directly with the "discrete=1"
> option.
>
> So, you need to do:
>
> load this_ligand, all_lig, discrete=1
> load next_ligand, all_lig, discrete=1
>
> Cheers,
> Rob
>
> --
> Robert L. Campbell, Ph.D.
> Senior Research Associate/Adjunct Assistant Professor
> Botterell Hall Rm 644
> Department of Biochemistry, Queen's University,
> Kingston, ON K7L 3N6  Canada
> Tel: 613-533-6821            Fax: 613-533-2497
> <rob...@qu...>    http://pldserver1.biochem.queensu.ca/~rlc
>
> ------------------------------------------------------------------------------
> The Next 800 Companies to Lead America's Growth: New Video Whitepaper
> David G. Thomson, author of the best-selling book "Blueprint to a
> Billion" shares his insights and actions to help propel your
> business during the next growth cycle. Listen Now!
> http://p.sf.net/sfu/SAP-dev2dev
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>



-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) Jas...@sc...
(o) +1 (603) 374-7120

set label_digits, 3

On Wed, Nov 10, 2010 at 3:50 PM, Martin Hediger <ma...@bl...> wrote:

> Dear all
> Is it possible to increase the number of digits displayed when measuring
> the distance between two atoms?
>
> Thanks
> Martin
>
>
>
>
>
> ------------------------------------------------------------------------------
> The Next 800 Companies to Lead America's Growth: New Video Whitepaper
> David G. Thomson, author of the best-selling book "Blueprint to a
> Billion" shares his insights and actions to help propel your
> business during the next growth cycle. Listen Now!
> http://p.sf.net/sfu/SAP-dev2dev
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>

Dear all
Is it possible to increase the number of digits displayed when measuring 
the distance between two atoms?

Thanks
Martin

Chris,

I don't know much about MACs, but on Linux you can have a look at
/var/log/xorg.?.log or some similar log file. Take a look at the
equivalent log file. May be there is some clue as to why the emitter
won't work. Looks to me like a driver issue.

Good luck,

	Carsten


> -----Original Message-----
> From: Chris Richardson [mailto:dr...@gm...]
> Sent: Wednesday, November 10, 2010 6:49 AM
> To: pym...@li...
> Subject: [PyMOL] Stereo issues on Mac Pro with Quadro FX 4800
> 
> Dear All,
> 
> I'm trying to get stereo working in PyMOL with the following setup:
> 
> - Mac Pro (early 2010, MacPro 5,1) running 10.6.4
> - Quadro FX 4800 for Mac
> - nVidia drivers Retail_256.00.05a23
> - nVidia Pro emitter and glasses set connected by DIN and USB cables
> - ViewSonic Fuhzion VX2268WM, refresh 120Hz
> - MacPyMOL incentive product
> 
> The monitor, emitter and glasses are known to work when attached to a
> Linux desktop.
> 
> PyMOL runs, and displays the sort of image you'd expect for working
> stereo.    However, the emitter continues to flash red rather than
> going green.  On the console, PyMOL displays
> 
> OpenGL graphics engine:
>  GL_VENDOR: NVIDIA Corporation
>  GL_RENDERER: NVIDIA Quadro FX 4800 OpenGL Engine
>  GL_VERSION: 2.1 NVIDIA-1.6.21
> Adapting to Quadro hardware.
> Detected 16 CPU cores.  Enabled multithreaded rendering.
> OpenGL quad-buffer stereo 3D detected and enabled.
> 
> Can someone with experience of this setup suggest a way around these
> problems?  nVidia's support seems to have only a tenuous appreciation
> of the existence of the Mac platform.  The 4800 is quite* expensive,
> so I'm keen to get this working.
> 
> Regards,
> 
> Chris
> 
> * For "quite", read "cripplingly"
> 
>
-----------------------------------------------------------------------
> -------
> The Next 800 Companies to Lead America's Growth: New Video Whitepaper
> David G. Thomson, author of the best-selling book "Blueprint to a
> Billion" shares his insights and actions to help propel your
> business during the next growth cycle. Listen Now!
> http://p.sf.net/sfu/SAP-dev2dev
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives:
http://www.mail-archive.com/pym...@li...

Hi Seth,

On Tue, 09 Nov 2010 22:54:59 -0500 Jason Vertrees
<jas...@sc...> wrote:

> Hi Seth,
> 
> I haven't seen that (in this scenario).  Can you send me a few PDB examples?
> 
> Cheers,
> 
> -- Jason
> 
> On Mon, Nov 8, 2010 at 10:13 PM, Seth Harris <se...@gm...> wrote:
> > Hi all,
> > I feel I should know this one. I have a program looping through structures
> > and bringing each small molecule into a single multi-state object so I can
> > tab through the states.
> > I do:
> > create all_lig, this_ligand, 1, 1
> > then go on to the next one:
> > create all_lig, next_ligand, 1, 2
> > and so on....
> > however, the bonds get all messed up, presumably with atom names
> > confused? I tried issuing a "rebuild all_lig" in between adding but that
> > didn't seem to help. What am I missing?

It sounds like you are loading a set of *different* structures into the
multi-state object.  I don't think you can do this properly with the
"create" command.  I think the only way to do this and retain the correct
bonding information is to use the load command directly with the "discrete=1"
option.

So, you need to do:

load this_ligand, all_lig, discrete=1
load next_ligand, all_lig, discrete=1

Cheers,
Rob

-- 
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor 
Botterell Hall Rm 644
Department of Biochemistry, Queen's University, 
Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821            Fax: 613-533-2497
<rob...@qu...>    http://pldserver1.biochem.queensu.ca/~rlc

Dear All,

I'm trying to get stereo working in PyMOL with the following setup:

- Mac Pro (early 2010, MacPro 5,1) running 10.6.4
- Quadro FX 4800 for Mac
- nVidia drivers Retail_256.00.05a23
- nVidia Pro emitter and glasses set connected by DIN and USB cables
- ViewSonic Fuhzion VX2268WM, refresh 120Hz
- MacPyMOL incentive product

The monitor, emitter and glasses are known to work when attached to a
Linux desktop.

PyMOL runs, and displays the sort of image you'd expect for working
stereo.    However, the emitter continues to flash red rather than
going green.  On the console, PyMOL displays

OpenGL graphics engine:
 GL_VENDOR: NVIDIA Corporation
 GL_RENDERER: NVIDIA Quadro FX 4800 OpenGL Engine
 GL_VERSION: 2.1 NVIDIA-1.6.21
Adapting to Quadro hardware.
Detected 16 CPU cores.  Enabled multithreaded rendering.
OpenGL quad-buffer stereo 3D detected and enabled.

Can someone with experience of this setup suggest a way around these
problems?  nVidia's support seems to have only a tenuous appreciation
of the existence of the Mac platform.  The 4800 is quite* expensive,
so I'm keen to get this working.

Regards,

Chris

* For "quite", read "cripplingly"

Hi Seth,

I haven't seen that (in this scenario).  Can you send me a few PDB examples?

Cheers,

-- Jason

On Mon, Nov 8, 2010 at 10:13 PM, Seth Harris <se...@gm...> wrote:
> Hi all,
> I feel I should know this one. I have a program looping through structures
> and bringing each small molecule into a single multi-state object so I can
> tab through the states.
> I do:
> create all_lig, this_ligand, 1, 1
> then go on to the next one:
> create all_lig, next_ligand, 1, 2
> and so on....
> however, the bonds get all messed up, presumably with atom names confused? I
> tried issuing a "rebuild all_lig" in between adding but that didn't seem to
> help. What am I missing?
> Thanks,
> Seth
>
>
> ------------------------------------------------------------------------------
> The Next 800 Companies to Lead America's Growth: New Video Whitepaper
> David G. Thomson, author of the best-selling book "Blueprint to a
> Billion" shares his insights and actions to help propel your
> business during the next growth cycle. Listen Now!
> http://p.sf.net/sfu/SAP-dev2dev
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>



-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) Jas...@sc...
(o) +1 (603) 374-7120

Hi Martin,

set retain_order
set pdb_retain_ids

Cheers,

-- Jason

On Tue, Nov 9, 2010 at 4:30 AM, Martin Hediger <ma...@bl...> wrote:
> Dear all
> It occured to me that PyMOL is resequencing a structure when saving. I
> am trying to interpolate between two structures where it is critical to
> have identical sequence in both structures. Is it possible submit a
> <DO_NOT_RESEQUENCE>-option to the save command?
>
> Thanks for your help
> Martin
>
> ------------------------------------------------------------------------------
> The Next 800 Companies to Lead America's Growth: New Video Whitepaper
> David G. Thomson, author of the best-selling book "Blueprint to a
> Billion" shares his insights and actions to help propel your
> business during the next growth cycle. Listen Now!
> http://p.sf.net/sfu/SAP-dev2dev
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>



-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) Jas...@sc...
(o) +1 (603) 374-7120

Dear all
It occured to me that PyMOL is resequencing a structure when saving. I 
am trying to interpolate between two structures where it is critical to 
have identical sequence in both structures. Is it possible submit a 
<DO_NOT_RESEQUENCE>-option to the save command?

Thanks for your help
Martin

Hi all,

I feel I should know this one. I have a program looping through structures
and bringing each small molecule into a single multi-state object so I can
tab through the states.

I do:
create all_lig, this_ligand, 1, 1
then go on to the next one:
create all_lig, next_ligand, 1, 2
and so on....

however, the bonds get all messed up, presumably with atom names confused? I
tried issuing a "rebuild all_lig" in between adding but that didn't seem to
help. What am I missing?

Thanks,
Seth