pymol-users — Collaborative support and tips for PyMOL users

[PyMOL] Participation

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

All PyMOL users please read.

> From: Alan Wilter Sousa da Silva [mailto:al...@bi...]
> 	PyMol is really amazing.  Besides what we can do with it now,
> there is a great potential of evolution.

That is the key difference between PyMOL and any comparable
closed-source project.  PyMOL can and will evolve rapidly, but what it
evolves into will be determined in large part by the users who support
it, through investments of effort and/or funding.  The project has
unprecedented potential (in the molecular computing field), but USERS
MUST CONTRIBUTE for this potential to be realized in reasonable time
(ie. 1-5 years).

Some of you may have noticed recently that I have been changing my
message.  In the past, I encouraged people to think of PyMOL as a free
and open package with no strings attached.  But now the project has
grown so large, and the needs so great, that PyMOL requires steady
involvement from users at all levels in order to remain healthly. =20

In addition, I seek to raise sufficient funding to begin hiring
individuals  (sporadically) to perform discrete tasks.  Though my
personal development time is limited since I am full-time scientist &
manager myself, I believe I can effectively act as a coordinator of
outside efforts, if provided with capital from new and existing users.

In essence, I am trying to build a virtual distributed software company,
with no regular employees, with free products, where customers closely
interact with developers and each other via the internet, and where
voluntary funding is used to cover costs.  I know this sounds a bit
crazy, but writing a free and unrestricted molecular graphics program in
my spare time wasn't exactly conventional thinking, either.  If this
effort is successful, then the world of molecular computing will be
forever changed for the better.

Thus, I urge all of you to start thinking of PyMOL as an ongoing process
-- one which needs regular funding and involvement in order to thrive,
but that will continue  generating value by making remarkable
capabilities available to all students, scientists, and companies, IF
properly nourished.  Although PyMOL remains free and unrestricted
open-source software, I will be leaning on all users (stakeholders,
really) to "do their part" in making it as successful and powerful as it
can be.

The current gaping hole in PyMOL is documentation.  The manual is far
behind PyMOL's recent version.  Those who have learned to use the
package through trial and error should consider transferring that
information to a web site where others can access it.  I can review such
documents for accuracy and provide additional useful information, but
someone needs to take a leadership role in PyMOL documentation, since I
cannot.  M

The second biggest hole is a robust user interface.  Be assured that it
*is* part of the plan.  A cross-platform wxPython-based interface is
being designed, but the native OSX port comes first. =20

There are at least a dozen other areas which require attention, from
rigorous testing to peer-to-peer support. =20

Thank you for your time in reading this message, and please join me in
exploring a new paradigm for development of research & educational
software for the biological and chemical sciences.

Cheers,

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

[PyMOL] About Surface

[Alan W. S. da S. <al...@bi...>]

Hi List,

=09PyMol is really amazing.  Besides what we can do with it now,
there is a great potential of evolution.
=09I'm particularly interested in how pymol generate surface (a
internal algorithm?) and how to compare it to vdW, solvent, Connolly and
MSMS surfaces.  Moreover, I know Delano has plans to integrate
Electrostatic Potential calculation in PyMol but I would like to know if
we will be able to map the elec. pot. over such surface.
=09Also, can I improve the surface resolution and make it
transparent?

-----------------------
Alan Wilter S. da Silva
-----------------------
 Laborat=F3rio de F=EDsica Biol=F3gica
  Instituto de Biof=EDsica Carlos Chagas Filho
   Universidade do Brasil/UFRJ
    Rio de Janeiro, Brasil

RE: [PyMOL] selecting atoms from a mask

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

Ricardo,

Your suggestion sounds great -- enable creation of atom selections based
on map value.  Here is a further refinement:

select (prot and map1 < 1)
select (prot and map1 1 3)
select (prot and map1 >=3D 3)

select (prot and map1 =3D 5)

Unfortunately, the code isn't yet written, but it won't take much
work...

Comments?

- Warren


> -----Original Message-----
> From: Ricardo Aparicio [mailto:apa...@if...]
> Sent: Wednesday, March 06, 2002 6:16 AM
> To: pym...@li...
> Subject: [PyMOL] selecting atoms from a mask
>=20
>=20
> Dear users,
>=20
> I would like to select atoms from file.pdb which are - at the=20
> same time
> - inside the volume of a map.
>=20
> In other words, I would like to make to make a selection like:
>=20
> select file.pdb AND map.ccp4
>=20
>=20
> I would like to know what would be the correct way to do it in PyMOL.
>=20
> Many thanks in advance,
>=20
>=20
> Ricardo Aparicio
> PhD Student
> Brazil
>=20
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20

[PyMOL] selecting atoms from a mask

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

Dear users,

I would like to select atoms from file.pdb which are - at the same time
- inside the volume of a map.

In other words, I would like to make to make a selection like:

select file.pdb AND map.ccp4


I would like to know what would be the correct way to do it in PyMOL.

Many thanks in advance,


Ricardo Aparicio
PhD Student
Brazil

[PyMOL] hydrogen bonds

[Letizia B. <bar...@ph...>]

Hi,

I am a new PyMOL user and I am impressed indeed by the characteristics of this program!

Since I am about preparing a paper, I would like to include some pictures prepared with PyMOL.

I have a complex ligand/protein and I would like to show the hydrogen bonds interaction between them.

I looked at the manual, but I was not able to find this information.

Any help is appreciated.  Thanks.

Maria Letizia

--
Maria Letizia Barreca, Ph.D.
Dipartimento Farmaco-Chimico
Universita'degli Studi di Messina
Viale Annunziata 98168 MESSINA ITALY
Phone: +39 090 6766464
Fax:   +39 090 355613
email: bar...@ph...

[PyMOL] RE: update coordinates

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

> From: Jianhua Fu

> 	I am trying to use Pymol to manipulate protein=20
> coordinates.  Basically, how can I rotate or translate a=20
> model and save out the transformed coordinates in pdb?  It isn't
> clear in the manual on this.  Thanks in advance.
>=20

1. Load PDB file
[1b. Hide meshes & surfaces; just show lines, sticks, or ribbons]
[1c. Unpick any picked atoms by clicking the "unpick" button.]

2. Select "3 Button Editing" from the Mouse menu

3. Shift-left-click-and-drag on any atom to rotate

4. Shift-middle-click-and-drag on any atom to translate

5. Ctrl-shift-middle-click on any atom to change the origin of rotation
   or use the "origin" command

6. Save your transformed structure to a PDB file.

    save test.pdb

CTRL-Z will undo the last transformation=20
CTRL-A will redo the last transformation

Cheers,
Warren

RE: [PyMOL] picking atoms on a Win 2000 machine

[Flip H. <fl...@ke...>]

Thanks Warren,

I can set my depth cue to 24-bit (I'm running Pymol on a sony vaio SR1K
laptop) and this works fine. Great package! I'll be waiting for the
minimiser so I can do RSR on my laptop!

Flip

-----Original Message-----
From: DeLano, Warren [mailto:wa...@su...]
Sent: Friday, March 01, 2002 18:58
To: Flip Hoedemaeker; pym...@li...
Subject: RE: [PyMOL] picking atoms on a Win 2000 machine


Hi Flip,

   This can happen on some graphics cards if the color depth isn't high
enough.  If you're in 16-bit color, try switching to 32 bit color using
the start->settings->control-panel->display->settings->colors, and then
restart PyMOL.  If this is still happening with 32-bit color, then
you've found a genuine bug, so please let me know what your exact PyMOL
version and hardware configuration is.

Cheers,
Warren


--
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



> -----Original Message-----
> From: Flip Hoedemaeker [mailto:fl...@ke...]
> Sent: Friday, March 01, 2002 9:10 AM
> To: pym...@li...
> Subject: [PyMOL] picking atoms on a Win 2000 machine
>
>
> Hi,
>
> I seem to have a problem with picking atoms with the "ctrl
> middle" mouse
> option. When I click on a specific atom a different atom is actually
> selected, usually far away in the structure. The same happens
> with the "ctrl
> left" option (+lb). Can somebody tell me what is going on?
>
> Flip
>
>
>
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>

RE: [PyMOL] superimpose

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

Michael,

   The 'fit' command will do atom-for-atom RMS alignments, but all atom
attributes must match within each object (segment, chain, residue id,
residue name, atom name, etc.) for this to succeed.  As a result, the
'fit' command can be tricky to use.  Several 'alter' commands and a
'sort', are often needed to get the attributes to match before fitting.
'fit' only works for chemically identical models.

   PyMOL's fitting abilities are improving: the upcoming version (v0.80)
will have the ability to do an on-the-fly sequence-alignment followed by
an optimized structure alignment, saving considerable time and hassle. =20

Cheers,
Warren

--
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



> -----Original Message-----
> From: Michael S. Cosgrove [mailto:co...@co...]
> Sent: Sunday, March 03, 2002 11:08 AM
> To: pym...@li...
> Subject: [PyMOL] superimpose
>=20
>=20
> Dear Sir,
>=20
> Does Pymol have the capability to superimpose molecules? If so how?
>=20
> Thanks,
>=20
> Michael
>=20
> Michael S. Cosgrove, Ph.D.
> Postdoctoral Fellow
> Johns Hopkins School of Medicine
> Department of Biophysics and Biophysical Chemistry
> 725 N. Wolfe Street, WBSB 603
> Baltimore MD, 21205
>=20
>=20
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20

[PyMOL] superimpose

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

Dear Sir,

Does Pymol have the capability to superimpose molecules? If so how?

Thanks,

Michael

Michael S. Cosgrove, Ph.D.
Postdoctoral Fellow
Johns Hopkins School of Medicine
Department of Biophysics and Biophysical Chemistry
725 N. Wolfe Street, WBSB 603
Baltimore MD, 21205

[PyMOL] autotools

[Ben C. <ac...@em...>]

Warren,

Would you have any interest in an autoconf/automake build setup for
pymol?  I have done some preliminary work on such a system this week,
mostly to learn how to use the GNU autotools.  The code is still
pretty rough, but if you think that you might be interested in
incorporating it, I will continue polishing.

Cheers,

Ben

RE: [PyMOL] Mac OS X?

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

Albion, you're looking for the GNU/Darwin version of PyMOL=20

http://gnu-darwin.sourceforge.net/gdc/

which currently doesn't support hardware acceleration (just
unaccelerated MesaGL).  Although the mac is supported, it is not an
optimal PyMOL platform.

The Makefile in the distro hasn't yet been used successfully -- it's an
adaptation from the original (very unstable) port, with some suggestions
from Jamie Cate thrown in.  I'm still waiting for some current Mac
hardware to arrive, so release of an official hardware-accelerated Mac
version of PyMOL is at least ~1-2 months off. =20

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

> From: Albion Baucom [mailto:ba...@bi...]

> I dont see an OS X package on the sourceforge site, and the=20
> source tarball
> has a "Rules.make" that claims it was never sucessfully=20
> compiled on Mac OS
> X. Is OS X still a work in progress or did I miss something?
>=20
>=20

[PyMOL] Mac OS X?

[Albion B. <ba...@bi...>]

I dont see an OS X package on the sourceforge site, and the source tarball
has a "Rules.make" that claims it was never sucessfully compiled on Mac OS
X. Is OS X still a work in progress or did I miss something?

Thanks

Albion

Albion E. Baucom
http://www.cse.ucsc.edu/~baucom

RE: [PyMOL] RNA and Pseudo-atom Models

[Albion B. <ba...@bi...>]

On Thu, 28 Feb 2002, DeLano, Warren wrote:

> Nice to hear from you Albion, glad to see you're finally getting a
> chance to try the package.

Yes, it looks to be my answer to movie making if I can get it to read my
model files!

> Great -- PyMOL should be up to the task provided that you've got a fast
> machine with tons of RAM.

Dual 800MHz G4 with 1.5GB of RAM. That is the best I can do for now. 

> > Ideally I would like to move seperate objects 
> > in the view
> > separeately, that is have things "dock" in the movies. I dont know if
> > PyMol will do this yet ...
> 
> Yes, it can do this using the translate, origin, and rotate commands.
> Unfortunately the docs are incomplete, so I recommend you take a look at
> the Python code in modules/pymol/editing.py (rotate, translate) and
> viewing.py (origin) for the specific calling conventions.  

OK.

> def rotate(axis='x',angle=0.0,selection="all",
>            state=0,camera=1,object=None):
> def translate(vector=[0.0,0.0,0.0],selection="all",
>               state=0,camera=1,object=None):
> def origin(selection="(all)",object=None,position=None):
> 
> Here's a key bit of information for these commands:  If you pass the
> object name using 'object=...', then you'll translate the entire object
> matrix.  If instead you pass in a selection with object still equal to
> NULL, then you'll translate the atom coordinates within the object.  

OK, does that mean one is non-reversable (coordinates change), and one
that is (only the object translates, original coordinates remain)?
 
> > Now, the rRNA I have is phosphorus atom only, with some 
> > allatom proteins
> > some CA-only proteins.
> 
> Ugh -- this is something PyMOL doesn't yet handle well, and you're the
> third person to draw my attention to this in the last couple weeks!

Yah, this has been the one thing making me stick with Mike Carson's
Ribbons. It handles these models like no other program (and RNA at all for
that matter!). I am convinced your program could serve me better if I
could get it to read those pseudo-atoms.

> There is no bond definition file (yet -- this will be changed in the
> future).  Except for HETATMS, PyMOL connects atoms based on proximity,
> not dictionary lookups.  The quick-and-dirty solution is to add explicit
> CONECT records for the atoms into the PDB file for the phosphates.

OK, that is a start.
  
> Nope, PyMOL won't be fooled by such trickery.  It will only draw ribbons
> between phosphates separated by six bonds (i.e. in real nucleic acids).
> Minor code changes will be required to accomplish what you're looking
> for. You might be able to comment-out the line in RepCartoon.c, but I
> haven't tested the idea. 
> 
> Look for:
>   if(!ObjectMoleculeCheckBondSep(obj,a1,a2,6))...

OK.
 
> > My only workaround ideas now are to take the pseudo-atom 
> > model, use CNS
> > (generate.inp) to build in the rest of the bases, use that to generate
> > the cartoon, and undisplay the stick representation (which of 
> > course will
> > have completely bogus conformations). Im not sure what biases 
> > the built in
> > bases will impose on the cartoon if PyMol uses them to interpolate the
> > ribbon.
> 
> Unfortunately for now you'll have to provide full coordinates in order
> to get ribbons.  This is probably a decent way to go.

Yah, to generate the intervening atoms and then undisplay them at render
time. I will try the above code changes and the workaround and compare the
results.
 
> > At some point I would like to draw pseudo-bonds between base-paired
> > pseudo-atoms, but I will see if I can do the above before that.
> 
> Such bonds can be drawn using the dist command.

OK. But these are distance representations, not true bonds right? How
about primitives using a precompiled object file to simulate the bonds?
Could I mix the PDB and object files in the same scene?

Also, I have breaks in the cartoon at modified base-pairs, particularly
with tRNA's. Is there way to remedy this without swapping for standard
bases? Again, I am plan only to render the cartoon with pseudo-basepair
bonds in the final scene, so the all atom stick representation is
irrelevant. I can use MidasPlus and "swapna" to replace the offending
bases, but Im not sure that is necessary.

Thanks a lot!

Albion

Albion E. Baucom
http://www.cse.ucsc.edu/~baucom

RE: [PyMOL] picking atoms on a Win 2000 machine

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

Hi Flip,

   This can happen on some graphics cards if the color depth isn't high
enough.  If you're in 16-bit color, try switching to 32 bit color using
the start->settings->control-panel->display->settings->colors, and then
restart PyMOL.  If this is still happening with 32-bit color, then
you've found a genuine bug, so please let me know what your exact PyMOL
version and hardware configuration is.

Cheers,
Warren


--
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



> -----Original Message-----
> From: Flip Hoedemaeker [mailto:fl...@ke...]
> Sent: Friday, March 01, 2002 9:10 AM
> To: pym...@li...
> Subject: [PyMOL] picking atoms on a Win 2000 machine
>=20
>=20
> Hi,
>=20
> I seem to have a problem with picking atoms with the "ctrl=20
> middle" mouse
> option. When I click on a specific atom a different atom is actually
> selected, usually far away in the structure. The same happens=20
> with the "ctrl
> left" option (+lb). Can somebody tell me what is going on?
>=20
> Flip
>=20
>=20
>=20
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20

[PyMOL] picking atoms on a Win 2000 machine

[Flip H. <fl...@ke...>]

Hi,

I seem to have a problem with picking atoms with the "ctrl middle" mouse
option. When I click on a specific atom a different atom is actually
selected, usually far away in the structure. The same happens with the "ctrl
left" option (+lb). Can somebody tell me what is going on?

Flip

RE: [PyMOL] RNA and Pseudo-atom Models

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

Busy day on the list : ) I'll take this one...

> From: Albion Baucom [mailto:ba...@bi...]

Nice to hear from you Albion, glad to see you're finally getting a
chance to try the package.

> I want to make high resolution, smooth (high frame rate)=20
> playing movies of
> the Ribosome.=20

Great -- PyMOL should be up to the task provided that you've got a fast
machine with tons of RAM.

> Ideally I would like to move seperate objects=20
> in the view
> separeately, that is have things "dock" in the movies. I dont know if
> PyMol will do this yet ...

Yes, it can do this using the translate, origin, and rotate commands.
Unfortunately the docs are incomplete, so I recommend you take a look at
the Python code in modules/pymol/editing.py (rotate, translate) and
viewing.py (origin) for the specific calling conventions. =20

def rotate(axis=3D'x',angle=3D0.0,selection=3D"all",
           state=3D0,camera=3D1,object=3DNone):
def translate(vector=3D[0.0,0.0,0.0],selection=3D"all",
              state=3D0,camera=3D1,object=3DNone):
def origin(selection=3D"(all)",object=3DNone,position=3DNone):

Here's a key bit of information for these commands:  If you pass the
object name using 'object=3D...', then you'll translate the entire =
object
matrix.  If instead you pass in a selection with object still equal to
NULL, then you'll translate the atom coordinates within the object. =20

This functionality is still primitive, but I think it will do the
job...play around with them for a while, see if you can get them to do
what you need.

> Now, the rRNA I have is phosphorus atom only, with some=20
> allatom proteins
> some CA-only proteins.

Ugh -- this is something PyMOL doesn't yet handle well, and you're the
third person to draw my attention to this in the last couple weeks!
=20
> PyMol opens the psueudo-atom rRNA as a cloud of atoms,=20
> presumably because
> it does not know how to bond these files. That is my first=20
> question. How,
> and what do I modify (bond definition file) to make it bond=20
> the adjacent
> atoms of the phosphorus only backbone?=20

There is no bond definition file (yet -- this will be changed in the
future).  Except for HETATMS, PyMOL connects atoms based on proximity,
not dictionary lookups.  The quick-and-dirty solution is to add explicit
CONECT records for the atoms into the PDB file for the phosphates.
=20
> My second question for now is once I bond it, will Pymol be=20
> able to render
> a cartoon using the P atoms to interpolate?

Nope, PyMOL won't be fooled by such trickery.  It will only draw ribbons
between phosphates separated by six bonds (i.e. in real nucleic acids).
Minor code changes will be required to accomplish what you're looking
for. You might be able to comment-out the line in RepCartoon.c, but I
haven't tested the idea.=20

Look for:
  if(!ObjectMoleculeCheckBondSep(obj,a1,a2,6))...

> My only workaround ideas now are to take the pseudo-atom=20
> model, use CNS
> (generate.inp) to build in the rest of the bases, use that to generate
> the cartoon, and undisplay the stick representation (which of=20
> course will
> have completely bogus conformations). Im not sure what biases=20
> the built in
> bases will impose on the cartoon if PyMol uses them to interpolate the
> ribbon.

Unfortunately for now you'll have to provide full coordinates in order
to get ribbons.  This is probably a decent way to go.

> At some point I would like to draw pseudo-bonds between base-paired
> pseudo-atoms, but I will see if I can do the above before that.

Such bonds can be drawn using the dist command.

Cheers,
Warren

[PyMOL] RNA and Pseudo-atom Models

[Albion B. <ba...@bi...>]

I am new to PyMol and spent the day getting use to the controls, learning
the interface and reading the manual.

Now, I have a few questions. Before that though I want to let everyone
know why I want to use PyMol

I want to make high resolution, smooth (high frame rate) playing movies of
the Ribosome. Ideally I would like to move seperate objects in the view
separeately, that is have things "dock" in the movies. I dont know if
PyMol will do this yet ...

Now, the rRNA I have is phosphorus atom only, with some allatom proteins
some CA-only proteins.

PyMol opens the psueudo-atom rRNA as a cloud of atoms, presumably because
it does not know how to bond these files. That is my first question. How,
and what do I modify (bond definition file) to make it bond the adjacent
atoms of the phosphorus only backbone? 

My second question for now is once I bond it, will Pymol be able to render
a cartoon using the P atoms to interpolate?

My only workaround ideas now are to take the pseudo-atom model, use CNS
(generate.inp) to build in the rest of the bases, use that to generate
the cartoon, and undisplay the stick representation (which of course will
have completely bogus conformations). Im not sure what biases the built in
bases will impose on the cartoon if PyMol uses them to interpolate the
ribbon.

At some point I would like to draw pseudo-bonds between base-paired
pseudo-atoms, but I will see if I can do the above before that.

Thanks!

Albion

Albion E. Baucom
http://www.cse.ucsc.edu/~baucom

Re: [PyMOL] image resolution

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

Wow, I've really been posting to this list a lot today. I guess 
free-time to post is what results when I happen to be working with a 
column with an agonizingly slow flow-through.

So anyway, since I didn't want to post both the question and my own 
interpretation of the answer in the same message, here's my stab at 
the problem.

It sounds like you're trying to execute the commands Warren 
referenced you to from within PyMol itself. Unless I'm mistaken, you 
should instead create a file "povray.py" (your python script for 
outputting the povray .pov file) that contains entire

import string
f=open("test.pov",'w')
f.write(string.join(cmd.get_povray(),'\n'))
f.close()

So here's what the above script does line by line...although it's not 
very conventional, I've preceded each line of the script with "**", 
and the comment of what that line accomplishes with a "#".

**import string
# I'm not totally familiar with Python, but I'm guessing this 
contains the tools you need to wrote what is known as "strings", 
basically just text rather than numbers

**f=open("test.pov",'w')
# create a file named test.pov (the POVRay file that you will render 
from) and prepare to write to it

**f.write(string.join(cmd.get_povray(),'\n'))
# in a nutshell, this fills test.pov with the actual guts of your 
POVRay file. The problem with cmd.get_povray() is that when Warren 
says it returns a "tuple of strings", he really means "enough strings 
to fill a multi-megabyte file". Before I went to PyMol, I used to 
make 20MB MegaPOVRay include files for images of molecular surfaces. 
If you don't stuff this massive bit of text to a file, it's not much 
use to you.

**f.close()
# we're all done, so go ahead and close test.pov

So once you've made  your script (povray.py), you should get your 
molecule all ready, and then execute povray.py. This will create the 
file test.pov, containing all of the coordinates POVRay will need to 
do the raytracing.

Well, that was my shot at it! Anyone else have something to add?

Jacob

>I was just in contact with Bronwyn Carlisle, who is having some 
>problems posting questions to the PyMol mailing list. He had the 
>following question and asked me to post it for him:
>
>::begin B. Carlisle quote::
>Also, I'd like to use POVRay to render pics, but I have POVRay for MacOS
>already and don't want to lose it, and when I try to install POVRay for
>XFree86 it won't do it because of the previous version.  Is there any
>way around this?  It would be nice if Pymol would export POV files like
>Swiss PDB viewer does!
>
>And this is what he said:
>
>cmd.get_povray() will return a tuple of strings containing PovRay input.
>Just write that out to a file:
>
># povray.py
>
>import string
>f=open("test.pov",'w')
>f.write(string.join(cmd.get_povray(),'\n'))
>f.close()
>
>I am not at all familiar with these sorts of commands - I have used Unix
>a little but I'm mostly a Mac person and this Linux/python stuff is
>totally foreign to me.  So I'm not sure if I can just go
>cmd.get_povray() or if I have to do the whole
>import string
>f=open("test.pov",'w')
>f.write(string.join(cmd.get_povray(),'\n'))
>f.close()
>thing.  I sort of figured that the 4 line version includes saving it to
>file - but I have no idea where it would end up!  And in any case I
>tried both and in each case it tells me:
>
>Traceback (most recent call last):
>File "/usr/local/pymol/modules/pymol/parser.py", line 208, in parse
>exec(com2[nest],pymol_names,pymol_names)
>File "<string>", line 1, in ?
>AttributeError: get_povray
>
>after the line containing cmd.get_povray.  I am assuming that python
>doesn't understand get_povray without being told to?  So how do I tell
>it to?  Or whatever.
>
>Bronwyn Carlisle
>Biochemistry Department
>University of Otago
>Dunedin
>New Zealand
>
>Tel 64 3 479 7704
>::end B. Carlisle quote::
>--
>Jacob Corn
>Gladstone Institute of Neurological Disease
>415.695.3745
>jc...@gl...
>
>_______________________________________________
>PyMOL-users mailing list
>PyM...@li...
>https://lists.sourceforge.net/lists/listinfo/pymol-users

-- 
Jacob Corn
Gladstone Institute of Neurological Disease
415.695.3745
jc...@gl...

Re: [PyMOL] image resolution

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

I was just in contact with Bronwyn Carlisle, who is having some 
problems posting questions to the PyMol mailing list. He had the 
following question and asked me to post it for him:

::begin B. Carlisle quote::
Also, I'd like to use POVRay to render pics, but I have POVRay for MacOS
already and don't want to lose it, and when I try to install POVRay for
XFree86 it won't do it because of the previous version.  Is there any
way around this?  It would be nice if Pymol would export POV files like
Swiss PDB viewer does!

And this is what he said:

cmd.get_povray() will return a tuple of strings containing PovRay input.
Just write that out to a file:

# povray.py

import string
f=open("test.pov",'w')
f.write(string.join(cmd.get_povray(),'\n'))
f.close()

I am not at all familiar with these sorts of commands - I have used Unix
a little but I'm mostly a Mac person and this Linux/python stuff is
totally foreign to me.  So I'm not sure if I can just go
cmd.get_povray() or if I have to do the whole
import string
f=open("test.pov",'w')
f.write(string.join(cmd.get_povray(),'\n'))
f.close()
thing.  I sort of figured that the 4 line version includes saving it to
file - but I have no idea where it would end up!  And in any case I
tried both and in each case it tells me:

Traceback (most recent call last):
File "/usr/local/pymol/modules/pymol/parser.py", line 208, in parse
exec(com2[nest],pymol_names,pymol_names)
File "<string>", line 1, in ?
AttributeError: get_povray

after the line containing cmd.get_povray.  I am assuming that python
doesn't understand get_povray without being told to?  So how do I tell
it to?  Or whatever.

Bronwyn Carlisle
Biochemistry Department
University of Otago
Dunedin
New Zealand

Tel 64 3 479 7704
::end B. Carlisle quote::
-- 
Jacob Corn
Gladstone Institute of Neurological Disease
415.695.3745
jc...@gl...

Re: [PyMOL] image resolution

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

(I'm responding to the whole list, just in case others weren't on the 
list or missed Warren's info on this when he posted it a while ago)

It's actually quite easy to make 300dpi (or any other dpi) images in 
PyMol. Just take the number of inches (ie - 8.5 inches) and multiply 
it by the number of pixels you need in that inch (ie - 300dpi), and 
that's the number of pixels you need to use for that particular 
dimension when you render.
For example:
8.5x11in image at 300dpi = 2550x3300 pixels
so use the command

ray 2550,3300

to render such an image. Take note, though, that PyMol probably won't 
display your rendered image, since it will be far too large to fit in 
the viewing window. You can then either save the image using the GUI, 
or use the "png" command (ie - "png protein.png") from the command 
line. Then take this HUUUUGE image into an editor like Photoshop and 
increase the image dpi from 72dpi to 300dpi. The print dimensions of 
your image should end up at the desired values you calculated for.

Remember, though, that most printers won't print all the way to the 
edge of a page (most leave a 0.5-1" margin between the edge of the 
image and the edge of the page). If you have a good printer, it will 
probably do a pretty good job of resizing the image to fit within the 
margins. However, you might want to take the margins into account 
when making your calculations. As always, the best way to find out 
what will work best with your particular situation is 
experimentation. Try it all and see what strikes your fancy the most.

Jacob

>Hello!
>
>I am working on making images for publication and
>need to create 8.5X11in images at 300dpi resolution.
>Is there a way to control the resolution and
>size of images exported from pymol?
>
>Thanks
>
>Joel M. Harp
>
>
>
>_______________________________________________
>PyMOL-users mailing list
>PyM...@li...
>https://lists.sourceforge.net/lists/listinfo/pymol-users

-- 
Jacob Corn
Gladstone Institute of Neurological Disease
415.695.3745
jc...@gl...

[PyMOL] image resolution

[Joel H. <jh...@un...>]

Hello!

I am working on making images for publication and
need to create 8.5X11in images at 300dpi resolution.
Is there a way to control the resolution and
size of images exported from pymol?

Thanks

Joel M. Harp

RE: [PyMOL] independent objects

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

1. Load two objects

2. Put the mouse into "editing" mode. =20

3. Click "unpick" to clear the picked atom selections (if they exist).

4. To rotate, shift-left-click-and-drag on an atom.

5. To translate, shift-middle-click-and-drag on an atom.

Rotation occurs about the origin.  You can change this by
control-shift-middle-clicking on any atom.

Note that if you attempt to rotate or translate while picked atom
selections exist, you will only transform a fragment.

Also note that you need to hide meshes and surfaces while performing
these kinds of transformations in order to preserve responsiveness,
since geometries are recalculated after each transformation.  As of yet,
PyMOL can't do manual transformations without recalculating geometries,
but that will change.  For the time being, this will likely preclude
manual docking of surfaces except with very small objects.

Also note that spheres can't be picked directly, though you can pick
lines or sticks hidden underneath the spheres.

Cheers,
Warren

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

> From: Michael S. Cosgrove, Ph.D. [mailto:co...@co...]

> Dear sir,
> I was wondering if there was a way to manipulate independent=20
> objects in=20
> Pymol. For example, is there a way to fix one object while rotating=20
> another? This would be useful for manually docking two surfaces, or=20
> creating a movie of a ligand binding to its binding site.
>=20
> Thanks,
>=20
> Michael
>=20
>=20
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20

[PyMOL] independent objects

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

Dear sir,
I was wondering if there was a way to manipulate independent objects in 
Pymol. For example, is there a way to fix one object while rotating 
another? This would be useful for manually docking two surfaces, or 
creating a movie of a ligand binding to its binding site.

Thanks,

Michael

RE: [PyMOL] selections

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

Due to the degeneracy of the PyMOL selection language, there are many
ways.

Say we want 79 to 85 and 89 to 94 in chain A...

# the most concise way is=20

select name2, a/79:85+89:94/

# but alternatives include:

select name2, ( a/79:85/ or a/89:94/ )
select name2, ( chain a and (resi 79:85 or resi 89:94 ))

# hyphens (-) work just as well as colons (:) in the above...

select name2, a/79-85+89-94/

- Warren

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

> From: Michael S. Cosgrove, Ph.D. [mailto:co...@co...]

> Hi, I am new to pymol. I was wondering if someone could help me with=20
> selecting multiple noncontinuous residues with the same name.=20
> For example,=20
> I have tried the following:
> select name1, a/79/ .....# to select a single residue,
> select name2, a/79:85/ ......# to select a continuous string=20
> of residues,
> How do I select a collection of noncontinuous of residues=20
> that can be given=20
> the same name (i.e. name3)
>=20
> Thanks,
>=20
> Michael

RE: [PyMOL] Sphere Scale Preference

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

Fergus,

Like other settings, sphere_scale is either global or object-specific,
not atomic.=20

To change the sphere size for specific atoms, use the "alter" command
with the "vdw" property over the selection.  For example:

alter (resi 10),vdw=3Dvdw*2.0

- Warren

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


> -----Original Message-----
> From: Fergus Binnie [mailto:f.b...@au...]
> Sent: Monday, February 25, 2002 12:06 PM
> To: pym...@li...
> Subject: [PyMOL] Sphere Scale Preference
>=20
>=20
> Dear Sir
>=20
> How can I alter the sphere_scale to affect only specific named=20
> selections. At present, changing the scale alters all the loaded=20
> molecules at the same time.
>=20
> Thankyou
>=20
> Fergus Binnie
> University of Auckland=20
>=20
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20