pymol-users — Collaborative support and tips for PyMOL users

Re: [PyMOL] Setting transparency for CGOs

[Lari <lar...@he...>]

Hi,

I've done this by rendering two images (actually 4 to get stereo). One wi=
thout
the CGOs and one with them. Then I overlaid them with photoshop and chang=
ed the
trasnparency of the CGO containing layer. I just used triangles and it lo=
oked
rather nice.

~Lari~

_______________________________________
Lari Lehti=F6
University of Helsinki
Institute of Biotechnology
Macromolecular X-ray crystallography
P.O.Box 65
00014 HY
Finland
http://www.biocenter.helsinki.fi/~lehtio/
_______________________________________


Quoting tan...@st...:

# Hi everybody,
#=20
# i've just created many CGOs, which show up solid surfaces like spheres =
and
# ellipsoids. Is it possible to set the transparency of some CGO's to i.e=
. 0.5
# and leave the others solid?
# I've checked out the reference and the manual, and found something like=
:
#=20
# set transparency=3D0.5, object
#=20
# But this actually does not work for CGO's.
# Any ideas....
#=20
# Yusuf
#=20
#=20
# --
# Yusuf Tanrikulu
# Bioinformatics Diploma Student
# Department of Biosciences
# Johann-Wolfgang-Goethe Univerity Frankfurt
# Siesmayerstrasse 70
# 60326 Frankfurt am Main
# - Germany -
# tan...@bi...
#=20
#=20
# -------------------------------------------------------
# SF.Net email is Sponsored by the Better Software Conference & EXPO
# September 19-22, 2005 * San Francisco, CA * Development Lifecycle Pract=
ices
# Agile & Plan-Driven Development * Managing Projects & Teams * Testing &=
 QA
# Security * Process Improvement & Measurement * http://www.sqe.com/bsce5=
sf
# _______________________________________________
# PyMOL-users mailing list
# PyM...@li...
# https://lists.sourceforge.net/lists/listinfo/pymol-users
#=20

[PyMOL] Setting transparency for CGOs

[<tan...@st...>]

Hi everybody,

i've just created many CGOs, which show up solid surfaces like spheres and
ellipsoids. Is it possible to set the transparency of some CGO's to i.e. 0.5
and leave the others solid?
I've checked out the reference and the manual, and found something like:

set transparency=0.5, object

But this actually does not work for CGO's.
Any ideas....

Yusuf


--
Yusuf Tanrikulu
Bioinformatics Diploma Student
Department of Biosciences
Johann-Wolfgang-Goethe Univerity Frankfurt
Siesmayerstrasse 70
60326 Frankfurt am Main
- Germany -
tan...@bi...

Re: [PyMOL] Creating PDB files from Primary Sequence

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

Hi Blanton,

* Blanton Tolbert <bla...@ur...> [2005-08-11 11:53] wrote:
> Hi pymolers
> 
> is it possible to generate a template nucleic acid structures from 
> sequence in pymol?

Not as far as I've found.  There are other programs that can do this:

"B" (aka "Biomer") (http://www.scripps.edu/mb/case/Biomer/)

 NAMOT (http://namot.lanl.gov/)

"3DNA" (http://rutchem.rutgers.edu/~olson/3DNA/)

Cheers,
Rob
-- 
Robert L. Campbell, Ph.D.                         <rl...@po...>
Senior Research Associate                            phone: 613-533-6821
Dept. of Biochemistry, Queen's University,             fax: 613-533-2497
Kingston, ON K7L 3N6  Canada       http://adelie.biochem.queensu.ca/~rlc
    PGP Fingerprint: 9B49 3D3F A489 05DC B35C  8E33 F238 A8F5 F635 C0E2

Re: [PyMOL] Creating PDB files from Primary Sequence

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

Hi,

I just felt like making a correction to the language I used.  It seems a
few words went missing!

* Robert Campbell <rl...@po...> [2005-08-11 11:28] wrote:
> I had already written a script to do this, but making it easier to
> specify the exact phi/psi angles to use.  I borrowed bits of the

I meant to say that "I had already written a script to do this, but had
not put it on my web site. It is there now. It does the same sort of
operation, but makes it easier to specify the exact phi/psi angles to
use."

Brain is now re-engaged, before typing commences.

Cheers,
Rob
-- 
Robert L. Campbell, Ph.D.                         <rl...@po...>
Senior Research Associate                            phone: 613-533-6821
Dept. of Biochemistry, Queen's University,             fax: 613-533-2497
Kingston, ON K7L 3N6  Canada       http://adelie.biochem.queensu.ca/~rlc
    PGP Fingerprint: 9B49 3D3F A489 05DC B35C  8E33 F238 A8F5 F635 C0E2

Re: [PyMOL] Creating PDB files from Primary Sequence

[Blanton T. <bla...@ur...>]

Hi pymolers

is it possible to generate a template nucleic acid structures from 
sequence in pymol?


Blanton Tolbert
PhD Candidate
University of Rochester
Biophysics and Structural Biology
575 Elmwood Ave
Rochester, NY 14642




Blanton Tolbert
PhD Candidate
University of Rochester
Biophysics and Structural Biology
575 Elmwood Ave
Rochester, NY 14642

Re: [PyMOL] Creating PDB files from Primary Sequence

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

Hi folks,

* Warren DeLano <wa...@de...> [2005-08-10 16:41] wrote:
> James,
> 
> > PyMol would allow one to enter a peptide sequence (generally short in
> > length) to create a template structure that can then be used 
> 
> Just hold down ALT/OPTION and type in the peptide sequence.  The
> numbering will be arbitrary, but at least you'll have something to work
> with.
> 
> >From a script, you can hack this as follows:
> 
> for aa in "DCAHWLGELVWCT": cmd._alt(string.lower(aa))

I had already written a script to do this, but making it easier to
specify the exact phi/psi angles to use.  I borrowed bits of the
editor.py file already within PyMOL and created a new front end to it.
There are two versions.

build_seq.py builds a stretch of residues with the same phi/psi angles:

  build_seq QGAADLESLGQYF, ss=helix 
or
  build_seq QGAADLESLGQYF, phi=-75, psi=-35 

while build_seq_phi_psi.py reads a file containing the sequence and
phi/psi angles to use for each residue:

  build_seq_phi_psi filename

where filename contains lines like:

  Q 30. 50.
  G -57. 60.
  A 120. 30.
  A -50. 60.
  D -57. 60.
  L -119. 113.
  E -119. 113.


For both scripts a new object named for the first residue is created (gln in this
case), unless you've picked an atom to build from, thus creating a pk1
selection.  Then the sequence is added onto that atom.

Both scripts are downloadable from my PyMOL scripts site (under the
section called "modelling").

  http://adelie.biochem.queensu.ca/~rlc/work/pymol

Cheers,
Rob
-- 
Robert L. Campbell, Ph.D.                         <rl...@po...>
Senior Research Associate                            phone: 613-533-6821
Dept. of Biochemistry, Queen's University,             fax: 613-533-2497
Kingston, ON K7L 3N6  Canada       http://adelie.biochem.queensu.ca/~rlc
    PGP Fingerprint: 9B49 3D3F A489 05DC B35C  8E33 F238 A8F5 F635 C0E2

Re: [PyMOL] Creating PDB files from Primary Sequence

[James R. G. <jam...@ma...>]

Thanks for the prompt responses, Warren and Joe! Works like a charm!

Now, I just wish that my Kensington Expert Mouse could function as a  
true three button mouse...is there a keystroke that mimics the third  
mouse button?

Thanks again,
james

Re: [PyMOL] Creating PDB files from Primary Sequence

[Joel T. <joe...@ot...>]

Hi James,

Sounds like you want a homology model type set up, ie generate 
coordinates based on a template. Modeller can do this and an easier way 
is via the  swissmodel

http://swissmodel.expasy.org//SWISS-MODEL.html

If however you want a relatively random structure then pymol _can_ do 
this. Click on builder (top right og GUI) and then select protein. From 
here you can generate any sequence you want. You can then export this 
and use the program of your choice to run dynamics etc

Hope this helps

J

James R. Graham wrote:

> Hello,
>
> This may be slightly off-topic, but I was wondering whether PyMol  
> would allow one to enter a peptide sequence (generally short in  
> length) to create a template structure that can then be used for  
> structural refinements (minimizations, etc.) elsewhere.
>
> If PyMol cannot do this, is anyone aware of any program (preferably  
> Mac OS X or linux compatible) that would be able to do this?
>
> Any info would be greatly appreciated.
>
> And apologies if this question is too far off-topic.
>
> Regards,
> james
>
>
>
>
> -------------------------------------------------------
> SF.Net email is Sponsored by the Better Software Conference & EXPO
> September 19-22, 2005 * San Francisco, CA * Development Lifecycle 
> Practices
> Agile & Plan-Driven Development * Managing Projects & Teams * Testing 
> & QA
> Security * Process Improvement & Measurement * http://www.sqe.com/bsce5sf
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>

-- 
Joel Tyndall, PhD

Lecturer
National School of Pharmacy
University of Otago
PO Box 913 Dunedin
New Zealand                     

Pukenga
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 913 Otepoti
Aotearoa

Ph / Waea               +64 3 4797293 
Fax / Waeawhakaahua     +64 3 4797034

RE: [PyMOL] Creating PDB files from Primary Sequence

[Warren D. <wa...@de...>]

James,

> PyMol would allow one to enter a peptide sequence (generally short in
> length) to create a template structure that can then be used=20

Just hold down ALT/OPTION and type in the peptide sequence.  The
numbering will be arbitrary, but at least you'll have something to work
with.

From a script, you can hack this as follows:

for aa in "DCAHWLGELVWCT": cmd._alt(string.lower(aa))

Cheers,
Warren


--
Warren L. DeLano, Ph.D.                    =20
Principal Scientist

. DeLano Scientific LLC =20
. 400 Oyster Point Blvd., Suite 213          =20
. South San Francisco, CA 94080 USA  =20
. Biz:(650)-872-0942  Tech:(650)-872-0834    =20
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:wa...@de...     =20
=20

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> James R. Graham
> Sent: Wednesday, August 10, 2005 4:36 PM
> To: pym...@li...
> Subject: [PyMOL] Creating PDB files from Primary Sequence
>=20
> Hello,
>=20
> This may be slightly off-topic, but I was wondering whether=20
> PyMol would allow one to enter a peptide sequence (generally short in
> length) to create a template structure that can then be used=20
> for structural refinements (minimizations, etc.) elsewhere.
>=20
> If PyMol cannot do this, is anyone aware of any program=20
> (preferably Mac OS X or linux compatible) that would be able=20
> to do this?
>=20
> Any info would be greatly appreciated.
>=20
> And apologies if this question is too far off-topic.
>=20
> Regards,
> james
>=20
>=20
>=20
>=20
> -------------------------------------------------------
> SF.Net email is Sponsored by the Better Software Conference &=20
> EXPO September 19-22, 2005 * San Francisco, CA * Development=20
> Lifecycle Practices Agile & Plan-Driven Development *=20
> Managing Projects & Teams * Testing & QA Security * Process=20
> Improvement & Measurement * http://www.sqe.com/bsce5sf=20
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
>=20

[PyMOL] Creating PDB files from Primary Sequence

[James R. G. <jam...@ma...>]

Hello,

This may be slightly off-topic, but I was wondering whether PyMol  
would allow one to enter a peptide sequence (generally short in  
length) to create a template structure that can then be used for  
structural refinements (minimizations, etc.) elsewhere.

If PyMol cannot do this, is anyone aware of any program (preferably  
Mac OS X or linux compatible) that would be able to do this?

Any info would be greatly appreciated.

And apologies if this question is too far off-topic.

Regards,
james

Re: [PyMOL] Rendering large surfaces

[Peter A. M. <pa...@co...>]

> I have been trying to coax Pymol to raytrace or output to pov
> (make_pov.py) some very large surfaces and I am unable to. It works for
> ~33,000 atoms, but chokes on ~61,000. I would like to get up to >100,000.
>
> Anybody have some good tips? I have tried adjusting hash_max, but I
> think this my be a more basic problem.

Good tips, maybe not...but I'll give it a shot (~30,000 atoms is about as
much as I've had to use with pymol, and never tried povray export):

It could be that the conversion from pymol to povray is done in memory,
and that's exceeding the max list size that the python interpreter (or
physical memory) can handle.  It might be possible to rework the script so
that the conversion is done in on smaller groups (resides/atoms maybe) at
the same time as file writing.  This would depend on povray being able to
to clipping, otherwise the final rendering would come out wrong.

Of course, I could be wrong about the memory problem.  When you say
chokes, does pymol slow down, raise an exception, or crash?

Hopefully somebody who's more farmiliar with povray or the specifics of
the pymol->povray conversion can comment on whether or not this is
actually likely to be the problem or not.


Pete


Pete Meyer
Fu Lab
BMCB grad student
Cornell University

RE: [PyMOL] multi distance object to single distance objects

[Warren D. <wa...@de...>]

Dan,

Sorry, that is not currently possible.  In order to get individual
distances, you need to create them one by one using a nested loop.
Something like:

for at1 in cmd.index("resi 10"): \
   for at2 in cmd.index("resi 11"): \
       cmd.dist(None, "%s`%d"%at1, "%s`%d"%at2)

Cheers,
Warren

--
Warren L. DeLano, Ph.D.                    =20
Principal Scientist

. DeLano Scientific LLC =20
. 400 Oyster Point Blvd., Suite 213          =20
. South San Francisco, CA 94080 USA  =20
. Biz:(650)-872-0942  Tech:(650)-872-0834    =20
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:wa...@de...     =20
=20

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> Daniel Hasenpusch
> Sent: Tuesday, August 09, 2005 5:04 PM
> To: pym...@li...
> Subject: [PyMOL] multi distance object to single distance objects
>=20
> Hi,
> =20
> I used the distance command:
> =20
>  cmd.dist(" (/mol1///1/C)","(/mol1///2/C*)").
> =20
> In pymol it creates a new distance object with all distances=20
> from C in Residue 1 to every C in Residue 2.
> How can I split this object to single distance objects?=20
> Or there are better possibilities because I want to write the=20
> distances into an extra file, but I only get the last=20
> distance as result.
> =20
> Thanks in advance,
>=20
> Daniel
> =20
>=20

RE: [PyMOL] Before the release of PyMol 0.99: Nucleotides and CGO

[Warren D. <wa...@de...>]

> The question is: how can I then delete the created MyColor=20
> object? I tried the cmd.delete command, it does not generate=20
> an error but apparently the color is still defined... Any idea?!

Colors can't be undefined, and that would especially be true if an =
object is still using a given color, since colors in PyMOL are based on =
lookups.  MyColor isn't so much an object as an entry in the global =
color table.

Cheers,
Warren

--
Warren L. DeLano, Ph.D.                    =20
Principal Scientist

. DeLano Scientific LLC =20
. 400 Oyster Point Blvd., Suite 213          =20
. South San Francisco, CA 94080 USA  =20
. Biz:(650)-872-0942  Tech:(650)-872-0834    =20
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:wa...@de...     =20
=20

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> Gr=E9gori Gerebtzoff
> Sent: Wednesday, August 10, 2005 10:43 AM
> To: pym...@li...
> Subject: RE: [PyMOL] Before the release of PyMol 0.99:=20
> Nucleotides and CGO
>=20
> Same script, but with hydrogen bonds between nucleotides.
>=20
> Load the pdb file 127D, run the script and type 'DrawNT' in=20
> PyMol command line...
>=20
> =20
>=20
> =20
>=20
> I have a question, maybe Warren you can answer:
>=20
> I wanted to use the set_color command to define a new color=20
> for the Hydrogen bonds (MyRGBColor =3D [x,y,z] and then=20
> cmd.set_color("MyColor", MyRGBColor))
>=20
> And finally apply the created color to the Hydrogen bonds=20
> (cmd.distance('MyDistance', Selection1, Selection2) and then=20
> cmd.color("MyColor", "MyDistance"))
>=20
> The question is: how can I then delete the created MyColor=20
> object? I tried the cmd.delete command, it does not generate=20
> an error but apparently the color is still defined... Any idea?!
>=20
> =20
>=20
> =20
>=20
> =20
>=20
> Cheers,
>=20
>=20
> Greg
>=20
> =20
>=20
> =20
>=20
> =20
>=20
> =20
>=20
> from pymol import cmd
>=20
> from pymol.cgo import *
>=20
> from Numeric import *
>=20
> import sys,re
>=20
> =20
>=20
> # COLOR SETTINGS:
>=20
> AColor=3D[0.2,1,0.2]
>=20
> TColor=3D[1,0.2,0.2]
>=20
> CColor=3D[0.3,0.3,1]
>=20
> GColor=3D[1,0.55,0.15]
>=20
> HColor=3D"magenta"
>=20
> =20
>=20
> def DrawNT(select=3D"all"):
>=20
>     CurrentView =3D cmd.get_view(1)
>=20
>     CurrentResi =3D 0
>=20
>     FirstRun =3D 1
>=20
>     NTPlate =3D [BEGIN,TRIANGLE_FAN]
>=20
> =20
>=20
> # THYMINE
>=20
>     BaseT =3D cmd.get_model("resn T")
>=20
>     for atoms in BaseT.atom:
>=20
>         if (CurrentResi !=3D atoms.resi):
>=20
>             CurrentResi =3D atoms.resi
>=20
>             if FirstRun =3D=3D 0:
>=20
>                 NTPlate.append(END)
>=20
>                 NTPlate.extend([BEGIN,TRIANGLE_FAN])
>=20
>                 NTPlate.extend([COLOR]+TColor)
>=20
>             else:
>=20
>                 NTPlate.extend([COLOR]+TColor)
>=20
>                 FirstRun =3D 0
>=20
>         if (atoms.name =3D=3D "N1") or (atoms.name =3D=3D "C2") or=20
> (atoms.name =3D=3D "N3") or (atoms.name =3D=3D "C4") or (atoms.name=20
> =3D=3D "C5") or (atoms.name =3D=3D "C6"):       =20
>=20
>             NTPlate.extend([VERTEX] + atoms.coord)
>=20
>         if atoms.name =3D=3D "N3":
>=20
>             Sel1 =3D=20
> '%s/%s/%s/%s'%(atoms.segi,atoms.chain,atoms.resi,atoms.name)
>=20
>             cmd.select('Sel2','%s around 3.1 and name N1 and=20
> not chain %s'%(Sel1,atoms.chain))
>=20
>             cmd.distance('Dst', Sel1, "Sel2")
>=20
>         elif atoms.name =3D=3D "O4":
>=20
>             Sel1 =3D=20
> '%s/%s/%s/%s'%(atoms.segi,atoms.chain,atoms.resi,atoms.name)
>=20
>             cmd.select('Sel2','%s around 3.1 and name N6 and=20
> not chain %s'%(Sel1,atoms.chain))
>=20
>             cmd.distance('Dst', Sel1, "Sel2")
>=20
> # ADENINE
>=20
>     BaseA =3D cmd.get_model("resn A")
>=20
>     for atoms in BaseA.atom:
>=20
>         if (CurrentResi !=3D atoms.resi):
>=20
>             CurrentResi =3D atoms.resi
>=20
>             if FirstRun =3D=3D 0:
>=20
>                 NTPlate.append(END)
>=20
>                 NTPlate.extend([BEGIN,TRIANGLE_FAN])
>=20
>                 NTPlate.extend([COLOR]+AColor)
>=20
>             else:
>=20
>                 NTPlate.extend([COLOR]+AColor)
>=20
>                 FirstRun =3D 0
>=20
>         if (atoms.name =3D=3D "N1") or (atoms.name =3D=3D "C2") or=20
> (atoms.name =3D=3D "N3") or (atoms.name =3D=3D "C4") or (atoms.name=20
> =3D=3D "C5") or (atoms.name =3D=3D "C6"):           =20
>=20
>             NTPlate.extend([VERTEX] + atoms.coord)
>=20
>             if (atoms.name =3D=3D "C4"):
>=20
>                 TmpC4 =3D atoms.coord
>=20
>             elif (atoms.name =3D=3D "C5"):
>=20
>                 TmpC5 =3D atoms.coord
>=20
>         elif (atoms.name =3D=3D "N7"):
>=20
>             NTPlate.append(END)
>=20
>             NTPlate.extend([BEGIN,TRIANGLE_FAN])
>=20
>             NTPlate.extend([COLOR]+AColor)
>=20
>             NTPlate.extend([VERTEX] + TmpC4)
>=20
>             NTPlate.extend([VERTEX] + TmpC5)
>=20
>             NTPlate.extend([VERTEX] + atoms.coord)
>=20
>         elif (atoms.name =3D=3D "C8") or (atoms.name =3D=3D "N9"):
>=20
>             NTPlate.extend([VERTEX] + atoms.coord)
>=20
> =20
>=20
> # CYTOSINE
>=20
>     BaseC =3D cmd.get_model("resn C")
>=20
>     for atoms in BaseC.atom:
>=20
>         if (CurrentResi !=3D atoms.resi):
>=20
>             CurrentResi =3D atoms.resi
>=20
>             if FirstRun =3D=3D 0:
>=20
>                 NTPlate.append(END)
>=20
>                 NTPlate.extend([BEGIN,TRIANGLE_FAN])
>=20
>                 NTPlate.extend([COLOR]+CColor)
>=20
>             else:
>=20
>                 NTPlate.extend([COLOR]+CColor)
>=20
>                 FirstRun =3D 0
>=20
>         if (atoms.name =3D=3D "N1") or (atoms.name =3D=3D "C2") or=20
> (atoms.name =3D=3D "N3") or (atoms.name =3D=3D "C4") or (atoms.name=20
> =3D=3D "C5") or (atoms.name =3D=3D "C6"):       =20
>=20
>             NTPlate.extend([VERTEX] + atoms.coord)
>=20
>         if atoms.name =3D=3D "O2":
>=20
>             Sel1 =3D=20
> '%s/%s/%s/%s'%(atoms.segi,atoms.chain,atoms.resi,atoms.name)
>=20
>             cmd.select('Sel2','%s around 3.1 and name N2 and=20
> not chain %s'%(Sel1,atoms.chain))
>=20
>             cmd.distance('Dst', Sel1, "Sel2")
>=20
>         elif atoms.name =3D=3D "N3":
>=20
>             Sel1 =3D=20
> '%s/%s/%s/%s'%(atoms.segi,atoms.chain,atoms.resi,atoms.name)
>=20
>             cmd.select('Sel2','%s around 3.1 and name N1 and=20
> not chain %s'%(Sel1,atoms.chain))
>=20
>             cmd.distance('Dst', Sel1, "Sel2")
>=20
>         elif atoms.name =3D=3D "N4":
>=20
>             Sel1 =3D=20
> '%s/%s/%s/%s'%(atoms.segi,atoms.chain,atoms.resi,atoms.name)
>=20
>             cmd.select('Sel2','%s around 3.1 and name O6 and=20
> not chain %s'%(Sel1,atoms.chain))
>=20
>             cmd.distance('Dst', Sel1, "Sel2")
>=20
> =20
>=20
> # GUANINE
>=20
>     BaseG =3D cmd.get_model("resn G")
>=20
>     for atoms in BaseG.atom:
>=20
>         if (CurrentResi !=3D atoms.resi):
>=20
>             CurrentResi =3D atoms.resi
>=20
>             if FirstRun =3D=3D 0:
>=20
>                 NTPlate.append(END)
>=20
>                 NTPlate.extend([BEGIN,TRIANGLE_FAN])
>=20
>                 NTPlate.extend([COLOR]+GColor)
>=20
>             else:
>=20
>                 NTPlate.extend([COLOR]+GColor)
>=20
>                 FirstRun =3D 0
>=20
>         if (atoms.name =3D=3D "N1") or (atoms.name =3D=3D "C2") or=20
> (atoms.name =3D=3D "N3") or (atoms.name =3D=3D "C4") or (atoms.name=20
> =3D=3D "C5") or (atoms.name =3D=3D "C6"):
>=20
>             NTPlate.extend([VERTEX] + atoms.coord)
>=20
>             if (atoms.name =3D=3D "C4"):
>=20
>                 TmpC4 =3D atoms.coord
>=20
>             elif (atoms.name =3D=3D "C5"):
>=20
>                 TmpC5 =3D atoms.coord
>=20
>         elif (atoms.name =3D=3D "N7"):
>=20
>             NTPlate.append(END)
>=20
>             NTPlate.extend([BEGIN,TRIANGLE_FAN])
>=20
>             NTPlate.extend([COLOR]+GColor)
>=20
>             NTPlate.extend([VERTEX] + TmpC4)
>=20
>             NTPlate.extend([VERTEX] + TmpC5)
>=20
>             NTPlate.extend([VERTEX] + atoms.coord)
>=20
>         elif (atoms.name =3D=3D "C8") or (atoms.name =3D=3D "N9"):
>=20
>             NTPlate.extend([VERTEX] + atoms.coord)
>=20
>     NTPlate.append(END)
>=20
>     cmd.load_cgo(NTPlate,"PLAIN_NT")
>=20
>     cmd.select("chain1", "name C3*+C4*+C5*+O5*+P+O3*")
>=20
>     cmd.show("cartoon", "chain1")
>=20
>     cmd.cartoon("dumbbell", "chain1")
>=20
>     cmd.set("cartoon_nucleic_acid_mode", 1, "chain1")
>=20
>     cmd.delete("chain1")
>=20
>     cmd.hide("label", "Dst")
>=20
>     cmd.color(HColor, "Dst")
>=20
>     cmd.delete("Sel2")
>=20
>     cmd.set_view(CurrentView)
>=20
> cmd.extend("DrawNT",DrawNT)
>=20
>=20

RE: [PyMOL] multi distance object to single distance objects

[<gre...@un...>]

Hi Daniel,

=20

This problem has been tackled several times, maybe have a look at the
following URLs, it might help you getting started:

=20

http://www.rubor.de/bioinf/tips_python.html#msdist

http://sourceforge.net/mailarchive/message.php?msg_id=3D2914266

And also don=92t forget the =91search=92 feature of the PyMOL Mailing =
List:

http://sourceforge.net/search/?type_of_search=3Dmlists
<http://sourceforge.net/search/?type_of_search=3Dmlists&forum_id=3D60&gro=
up_id=3D4
546&words=3Dcmd.distance> =
&forum_id=3D60&group_id=3D4546&words=3Dcmd.distance

=20

=20

Cheers,


Greg

=20

=20

-----Original Message-----
From: pym...@li...
[mailto:pym...@li...] On Behalf Of Daniel
Hasenpusch
Sent: lundi, 8. ao=FBt 2005 20:51
To: pym...@li...
Subject: [PyMOL] multi distance object to single distance objects

=20

Hi,

=20

I used the distance command:

=20

 cmd.dist(" (/mol1///1/C)","(/mol1///2/C*)").

=20

In pymol it creates a new distance object with all distances from C in
Residue 1 to every C in Residue 2.

How can I split this object to single distance objects?=20

Or there are better possibilities because I want to write the distances =
into
an extra file, but I only get the last distance as result.

=20

Thanks in advance,

Daniel

=20

RE: [PyMOL] Before the release of PyMol 0.99: Nucleotides and CGO

[<gre...@un...>]

Same script, but with hydrogen bonds between nucleotides.

Load the pdb file 127D, run the script and type =91DrawNT=92 in PyMol =
command
line=85

=20

=20

I have a question, maybe Warren you can answer:

I wanted to use the set_color command to define a new color for the =
Hydrogen
bonds (MyRGBColor =3D [x,y,z] and then cmd.set_color(=93MyColor=94, =
MyRGBColor))

And finally apply the created color to the Hydrogen bonds
(cmd.distance('MyDistance', Selection1, Selection2) and then
cmd.color("MyColor", "MyDistance"))

The question is: how can I then delete the created MyColor object? I =
tried
the cmd.delete command, it does not generate an error but apparently the
color is still defined=85 Any idea?!

=20

=20

=20

Cheers,


Greg

=20

=20

=20

=20

from pymol import cmd

from pymol.cgo import *

from Numeric import *

import sys,re

=20

# COLOR SETTINGS:

AColor=3D[0.2,1,0.2]

TColor=3D[1,0.2,0.2]

CColor=3D[0.3,0.3,1]

GColor=3D[1,0.55,0.15]

HColor=3D=94magenta=94

=20

def DrawNT(select=3D"all"):

    CurrentView =3D cmd.get_view(1)

    CurrentResi =3D 0

    FirstRun =3D 1

    NTPlate =3D [BEGIN,TRIANGLE_FAN]

=20

# THYMINE

    BaseT =3D cmd.get_model("resn T")

    for atoms in BaseT.atom:

        if (CurrentResi !=3D atoms.resi):

            CurrentResi =3D atoms.resi

            if FirstRun =3D=3D 0:

                NTPlate.append(END)

                NTPlate.extend([BEGIN,TRIANGLE_FAN])

                NTPlate.extend([COLOR]+TColor)

            else:

                NTPlate.extend([COLOR]+TColor)

                FirstRun =3D 0

        if (atoms.name =3D=3D "N1") or (atoms.name =3D=3D "C2") or =
(atoms.name =3D=3D
"N3") or (atoms.name =3D=3D "C4") or (atoms.name =3D=3D "C5") or =
(atoms.name =3D=3D
"C6"):       =20

            NTPlate.extend([VERTEX] + atoms.coord)

        if atoms.name =3D=3D "N3":

            Sel1 =3D
'%s/%s/%s/%s'%(atoms.segi,atoms.chain,atoms.resi,atoms.name)

            cmd.select('Sel2','%s around 3.1 and name N1 and not chain
%s'%(Sel1,atoms.chain))

            cmd.distance('Dst', Sel1, "Sel2")

        elif atoms.name =3D=3D "O4":

            Sel1 =3D
'%s/%s/%s/%s'%(atoms.segi,atoms.chain,atoms.resi,atoms.name)

            cmd.select('Sel2','%s around 3.1 and name N6 and not chain
%s'%(Sel1,atoms.chain))

            cmd.distance('Dst', Sel1, "Sel2")

# ADENINE

    BaseA =3D cmd.get_model("resn A")

    for atoms in BaseA.atom:

        if (CurrentResi !=3D atoms.resi):

            CurrentResi =3D atoms.resi

            if FirstRun =3D=3D 0:

                NTPlate.append(END)

                NTPlate.extend([BEGIN,TRIANGLE_FAN])

                NTPlate.extend([COLOR]+AColor)

            else:

                NTPlate.extend([COLOR]+AColor)

                FirstRun =3D 0

        if (atoms.name =3D=3D "N1") or (atoms.name =3D=3D "C2") or =
(atoms.name =3D=3D
"N3") or (atoms.name =3D=3D "C4") or (atoms.name =3D=3D "C5") or =
(atoms.name =3D=3D
"C6"):           =20

            NTPlate.extend([VERTEX] + atoms.coord)

            if (atoms.name =3D=3D "C4"):

                TmpC4 =3D atoms.coord

            elif (atoms.name =3D=3D "C5"):

                TmpC5 =3D atoms.coord

        elif (atoms.name =3D=3D "N7"):

            NTPlate.append(END)

            NTPlate.extend([BEGIN,TRIANGLE_FAN])

            NTPlate.extend([COLOR]+AColor)

            NTPlate.extend([VERTEX] + TmpC4)

            NTPlate.extend([VERTEX] + TmpC5)

            NTPlate.extend([VERTEX] + atoms.coord)

        elif (atoms.name =3D=3D "C8") or (atoms.name =3D=3D "N9"):

            NTPlate.extend([VERTEX] + atoms.coord)

=20

# CYTOSINE

    BaseC =3D cmd.get_model("resn C")

    for atoms in BaseC.atom:

        if (CurrentResi !=3D atoms.resi):

            CurrentResi =3D atoms.resi

            if FirstRun =3D=3D 0:

                NTPlate.append(END)

                NTPlate.extend([BEGIN,TRIANGLE_FAN])

                NTPlate.extend([COLOR]+CColor)

            else:

                NTPlate.extend([COLOR]+CColor)

                FirstRun =3D 0

        if (atoms.name =3D=3D "N1") or (atoms.name =3D=3D "C2") or =
(atoms.name =3D=3D
"N3") or (atoms.name =3D=3D "C4") or (atoms.name =3D=3D "C5") or =
(atoms.name =3D=3D
"C6"):       =20

            NTPlate.extend([VERTEX] + atoms.coord)

        if atoms.name =3D=3D "O2":

            Sel1 =3D
'%s/%s/%s/%s'%(atoms.segi,atoms.chain,atoms.resi,atoms.name)

            cmd.select('Sel2','%s around 3.1 and name N2 and not chain
%s'%(Sel1,atoms.chain))

            cmd.distance('Dst', Sel1, "Sel2")

        elif atoms.name =3D=3D "N3":

            Sel1 =3D
'%s/%s/%s/%s'%(atoms.segi,atoms.chain,atoms.resi,atoms.name)

            cmd.select('Sel2','%s around 3.1 and name N1 and not chain
%s'%(Sel1,atoms.chain))

            cmd.distance('Dst', Sel1, "Sel2")

        elif atoms.name =3D=3D "N4":

            Sel1 =3D
'%s/%s/%s/%s'%(atoms.segi,atoms.chain,atoms.resi,atoms.name)

            cmd.select('Sel2','%s around 3.1 and name O6 and not chain
%s'%(Sel1,atoms.chain))

            cmd.distance('Dst', Sel1, "Sel2")

=20

# GUANINE

    BaseG =3D cmd.get_model("resn G")

    for atoms in BaseG.atom:

        if (CurrentResi !=3D atoms.resi):

            CurrentResi =3D atoms.resi

            if FirstRun =3D=3D 0:

                NTPlate.append(END)

                NTPlate.extend([BEGIN,TRIANGLE_FAN])

                NTPlate.extend([COLOR]+GColor)

            else:

                NTPlate.extend([COLOR]+GColor)

                FirstRun =3D 0

        if (atoms.name =3D=3D "N1") or (atoms.name =3D=3D "C2") or =
(atoms.name =3D=3D
"N3") or (atoms.name =3D=3D "C4") or (atoms.name =3D=3D "C5") or =
(atoms.name =3D=3D
"C6"):

            NTPlate.extend([VERTEX] + atoms.coord)

            if (atoms.name =3D=3D "C4"):

                TmpC4 =3D atoms.coord

            elif (atoms.name =3D=3D "C5"):

                TmpC5 =3D atoms.coord

        elif (atoms.name =3D=3D "N7"):

            NTPlate.append(END)

            NTPlate.extend([BEGIN,TRIANGLE_FAN])

            NTPlate.extend([COLOR]+GColor)

            NTPlate.extend([VERTEX] + TmpC4)

            NTPlate.extend([VERTEX] + TmpC5)

            NTPlate.extend([VERTEX] + atoms.coord)

        elif (atoms.name =3D=3D "C8") or (atoms.name =3D=3D "N9"):

            NTPlate.extend([VERTEX] + atoms.coord)

    NTPlate.append(END)

    cmd.load_cgo(NTPlate,"PLAIN_NT")

    cmd.select("chain1", "name C3*+C4*+C5*+O5*+P+O3*")

    cmd.show("cartoon", "chain1")

    cmd.cartoon("dumbbell", "chain1")

    cmd.set("cartoon_nucleic_acid_mode", 1, "chain1")

    cmd.delete("chain1")

    cmd.hide("label", "Dst")

    cmd.color(HColor, "Dst")

    cmd.delete("Sel2")

    cmd.set_view(CurrentView)

cmd.extend("DrawNT",DrawNT)

[PyMOL] Rendering large surfaces

[Frank M. <fm...@mr...>]

I have been trying to coax Pymol to raytrace or output to pov 
(make_pov.py) some very large surfaces and I am unable to. It works for 
~33,000 atoms, but chokes on ~61,000. I would like to get up to >100,000.

Anybody have some good tips? I have tried adjusting hash_max, but I 
think this my be a more basic problem.

Thanks in advance

-- 
Frank Murphy

MRC LMB
Structural Studies Division
Hills Road
Cambridge CB2 2QH

LAB  +44 1223 402295
MOB +44 7779 224206
FAX   +44 1223 213556

[PyMOL] multi distance object to single distance objects

[Daniel H. <Spo...@gm...>]

Hi,

I used the distance command:

 cmd.dist(" (/mol1///1/C)","(/mol1///2/C*)").

In pymol it creates a new distance object with all distances from C in =
Residue 1 to every C in Residue 2.
How can I split this object to single distance objects?=20
Or there are better possibilities because I want to write the distances =
into an extra file, but I only get the last distance as result.

Thanks in advance,

Daniel

[PyMOL] nuccyl's URL has changed!

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

Dear PyMOL users,

Recently I moved, and so has nuccyl's home page. Please update your =20
bookmarks to:

     http://www.biosci.ki.se/groups/ljo/software/nuccyl.html

With best regards,

Luca

-----------------------------------------------------
Luca Jovine, Ph.D.
Karolinska Institutet
Department of Biosciences at Novum
Center for Structural Biochemistry (CSB)
H=E4lsov=E4gen 7-9, S-141 57 Huddinge, Sweden
Voice: +46.(0)8.6083-301  FAX: +46.(0)8.6089-290
E-mail: luc...@bi... - luc...@ma...
W3: http://www.biosci.ki.se/groups/ljo/
-----------------------------------------------------

[PyMOL] multi distance object to single distance objects

[Daniel H. <Dan...@gm...>]

Hi,

I used the distance command:

 cmd.dist(" (/mol1///1/C)","(/mol1///2/C*)").

In pymol it creates a new distance object with all distances from C in =
Residue 1 to every C in Residue 2.
How can I split this object to single distance objects?=20
Or there are better possibilities because I want to write the distances =
into an extra file, but I only get the last distance as result.

Thanks in advance,

Daniel

[PyMOL] Before the release of PyMol 0.99: Nucleotides and CGO

[<gre...@un...>]

Hello List,

=20

Maybe useful, maybe not=85 Here is a small py script for filling =
nucleotides
with colored CGO objects. I just tried it on the pdb file 127D.

Of course not as efficient as Nuccyl!!! But I couldn=92t find out how to =
run
perl scripts on my Windows-running PC, and this is exactly (and only) =
what I
needed.

=20

Just run the script, and type =91DrawNT=92 in the PyMol command line.

=20

Cheers,


Greg

=20

=20

=20

=20

=20

from pymol import cmd

from pymol.cgo import *

from Numeric import *

import sys,re

=20

# COLOR SETTINGS:

AColor=3D[0.2,1,0.2]

TColor=3D[1,0.2,0.2]

CColor=3D[0.3,0.3,1]

GColor=3D[1,0.55,0.15]

=20

def DrawNT(select=3D"all"):

    CurrentView =3D cmd.get_view(1)

    CurrentResi =3D 0

    FirstRun =3D 1

    NTPlate =3D [BEGIN,TRIANGLE_FAN]

=20

# THYMINE

    BaseT =3D cmd.get_model("resn T")

    for atoms in BaseT.atom:

        if (CurrentResi !=3D atoms.resi):

            CurrentResi =3D atoms.resi

            if FirstRun =3D=3D 0:

                NTPlate.append(END)

                NTPlate.extend([BEGIN,TRIANGLE_FAN])

                NTPlate.extend([COLOR]+TColor)

            else:

                NTPlate.extend([COLOR]+TColor)

                FirstRun =3D 0

        if (atoms.name =3D=3D "N1") or (atoms.name =3D=3D "C2") or =
(atoms.name =3D=3D
"N3") or (atoms.name =3D=3D "C4") or (atoms.name =3D=3D "C5") or =
(atoms.name =3D=3D
"C6"):       =20

            NTPlate.extend([VERTEX] + atoms.coord)

=20

# ADENINE

    BaseA =3D cmd.get_model("resn A")

    for atoms in BaseA.atom:

        if (CurrentResi !=3D atoms.resi):

            CurrentResi =3D atoms.resi

            if FirstRun =3D=3D 0:

                NTPlate.append(END)

                NTPlate.extend([BEGIN,TRIANGLE_FAN])

                NTPlate.extend([COLOR]+AColor)

            else:

                NTPlate.extend([COLOR]+AColor)

                FirstRun =3D 0

        if (atoms.name =3D=3D "N1") or (atoms.name =3D=3D "C2") or =
(atoms.name =3D=3D
"N3") or (atoms.name =3D=3D "C4") or (atoms.name =3D=3D "C5") or =
(atoms.name =3D=3D
"C6"):           =20

            NTPlate.extend([VERTEX] + atoms.coord)

            if (atoms.name =3D=3D "C4"):

                TmpC4 =3D atoms.coord

            elif (atoms.name =3D=3D "C5"):

                TmpC5 =3D atoms.coord

        elif (atoms.name =3D=3D "N7"):

            NTPlate.append(END)

            NTPlate.extend([BEGIN,TRIANGLE_FAN])

            NTPlate.extend([COLOR]+AColor)

            NTPlate.extend([VERTEX] + TmpC4)

            NTPlate.extend([VERTEX] + TmpC5)

            NTPlate.extend([VERTEX] + atoms.coord)

        elif (atoms.name =3D=3D "C8") or (atoms.name =3D=3D "N9"):

            NTPlate.extend([VERTEX] + atoms.coord)

=20

# CYTOSINE

    BaseC =3D cmd.get_model("resn C")

    for atoms in BaseC.atom:

        if (CurrentResi !=3D atoms.resi):

            CurrentResi =3D atoms.resi

            if FirstRun =3D=3D 0:

                NTPlate.append(END)

                NTPlate.extend([BEGIN,TRIANGLE_FAN])

                NTPlate.extend([COLOR]+CColor)

            else:

                NTPlate.extend([COLOR]+CColor)

                FirstRun =3D 0

        if (atoms.name =3D=3D "N1") or (atoms.name =3D=3D "C2") or =
(atoms.name =3D=3D
"N3") or (atoms.name =3D=3D "C4") or (atoms.name =3D=3D "C5") or =
(atoms.name =3D=3D
"C6"):       =20

            NTPlate.extend([VERTEX] + atoms.coord)

=20

# GUANINE

    BaseG =3D cmd.get_model("resn G")

    for atoms in BaseG.atom:

        if (CurrentResi !=3D atoms.resi):

            CurrentResi =3D atoms.resi

            if FirstRun =3D=3D 0:

                NTPlate.append(END)

                NTPlate.extend([BEGIN,TRIANGLE_FAN])

                NTPlate.extend([COLOR]+GColor)

            else:

                NTPlate.extend([COLOR]+GColor)

                FirstRun =3D 0

        if (atoms.name =3D=3D "N1") or (atoms.name =3D=3D "C2") or =
(atoms.name =3D=3D
"N3") or (atoms.name =3D=3D "C4") or (atoms.name =3D=3D "C5") or =
(atoms.name =3D=3D
"C6"):

            NTPlate.extend([VERTEX] + atoms.coord)

            if (atoms.name =3D=3D "C4"):

                TmpC4 =3D atoms.coord

            elif (atoms.name =3D=3D "C5"):

                TmpC5 =3D atoms.coord

        elif (atoms.name =3D=3D "N7"):

            NTPlate.append(END)

            NTPlate.extend([BEGIN,TRIANGLE_FAN])

            NTPlate.extend([COLOR]+GColor)

            NTPlate.extend([VERTEX] + TmpC4)

            NTPlate.extend([VERTEX] + TmpC5)

            NTPlate.extend([VERTEX] + atoms.coord)

        elif (atoms.name =3D=3D "C8") or (atoms.name =3D=3D "N9"):

            NTPlate.extend([VERTEX] + atoms.coord)

    NTPlate.append(END)

    cmd.load_cgo(NTPlate,"PLAIN_NT")

    cmd.select("chain1", "name C3*+C4*+C5*+O5*+P+O3*")

    cmd.show("cartoon", "chain1")

    cmd.cartoon("dumbbell", "chain1")

    cmd.delete("chain1")

    cmd.set_view(CurrentView)

cmd.extend("DrawNT",DrawNT)

Re: [PyMOL] sessions and movies

[Nadine A. <nad...@ho...>]

Hi again,

Joel, thank you for your additionnal help and suggestions. I unfortunately 
cannot avoid deleting the structures, as there are far too many of them, and 
having them all loaded at the same time really slows pymol down. I do seem 
to have found a solution, and one last problem that I hope someone will be 
able to help me with.

To consecutively load the session files that I had saved, I wrote a *.py 
script which I call from a terminal with: pymol -l my_script.py
The script has the following structure:

from pymol import cmd
cmd.set("security", value=0)
cmd.load("/.../1st_session.pse")
raw_input() # wait until key pressed
cmd.load("/.../2nd_session.pse")
etc...

This alloys me to restore a saved session, then move onto the next one when 
desired.

I would however like to make one last improvement, and here again ask for 
advice: I want to be able to change the view while observing a session, then 
obtain the same view for the next session. I have tried inserting:
my_view=cmd.get_view()
and:
cmd.set_view(my_view)
before and after cmd.load(), and this does work, but usually causes the next 
structure to be loaded with its original view and then shifted to the 
desired view (the protein appears to jump from one position to the next). I 
say usually because this is not always the case even when running the same 
file twice. Does anyone know how to avoid this, or how I could combine the 
load and set commands as one, so as to load each structure in the right 
position?

Thanks again for all the help. It is very much appreciated.

Nadine


>
>Hi Nadine,
>
>USing the scene/.psw files allows you to manipulate the structures as per 
>usual within the show. It pre4sents the graphical viwer in a full screen 
>mode without the right hand menu. So deleting molecules (probably a bad 
>thing)...it would be better if you could just undisplay them. I have just 
>tried doing this with two separate proteins (see attached) and the scene 
>function works fine. No sure about scripting.
>
>Hope this helps
>
>J
>
>Nadine Atwood wrote:
>
>>Hi,
>>
>>Thank you for your reply, Joel. I have followed that advice, downloaded 
>>v0.98 and tried using the scene function, but I didn't mention yesterday 
>>that I load and delete several dozen *.pdb files during the original movie 
>>and this appears to be a problem as the scene function does not restore 
>>deleted data. (Basically I want to take a few shots of the first 
>>structure, then move on to the second and delete the first, take a few 
>>more shots and move on to the third, etc. When I call the first scene, 
>>after deleting the first structure, the result is empty.) Do you have any 
>>other suggestions? I also did not specify that I am hoping to find a 
>>solution that will allow the structures to be manipulated as usual (not 
>>just a static representation of the structures at a given time). I do not 
>>know if this is or is not the case when using a *.psw with embedded 
>>scenes.
>>
>>Would it maybe be possible to write a script containing load commands for 
>>each of the different *.pse (or *.psw - I'm not sure of the difference 
>>between the 2) files, seperated by some kind of "wait until key pressed" 
>>command. If so, what is the second command?
>>
>>As for the other problem I mentionned, it doesn't happen with v0.98.
>>
>>Thanks again.
>>
>>Nadine
>>
>>
>>
>>>
>>>Hi Nadine,
>>>
>>>To answer the first part, there is a much easier way...use the scene 
>>>function in 0.98 version. This allows you to jump between individual 
>>>"screenshots". You can then save this as a .psw file and view it as full 
>>>screen or embed it in powerpoint. (See my previous post "Pymol scenes to 
>>>movies"). Essentaially you set up view 1 and hit append, then view 2 , 
>>>append etc. you can then scroll thru your views.
>>>
>>>The second question, can't help.
>>>
>>>Cheers
>>>
>>>J
>>>
>>>Nadine Atwood wrote:
>>>
>>>>
>>>>Hi,
>>>>
>>>>I have come across a problem that I cannot find a way around and would 
>>>>greatly appreciate some help. I have made a movie showing several 
>>>>protein models and numerous distances to illustrate residue interactions 
>>>>in different structures. This movie is rather long, and I wanted to make 
>>>>a very short version containing certain "screenshots" of the original. I 
>>>>have created *.pse files corresponding to the frames I would want in the 
>>>>short movie, but cannot find a way of loading these in a script. (I can 
>>>>view them "manually" by opening them one at a time through the command 
>>>>line, but that rather defeats the point.) I wanted to load these using 
>>>>mset and mdo commands, but of course, as soon as I load the first one, 
>>>>PyMOL's memory returns to the state that was saved and the new movie is 
>>>>deleted. I suppose I need to save these files in another format, but 
>>>>have not been able to find anything that seems appropriate.
>>>>
>>>>I have also encountered another small problem that I do not need a 
>>>>solution to but thought I would mention as it might be a bug (though it 
>>>>could be due to my very amateurish programming): when running the long 
>>>>movie (which creates and deletes a large number of distances), if the 
>>>>movie is stopped and then start again, some distances (I suppose 
>>>>corresponding to commands given in frames where the movie was stopped) 
>>>>are not deleted, whereas if the movie is run without interruption, all 
>>>>distances are handled correctly. (I am using version 0.97)
>>>>
>>>>I am not very computer literate, so a simple explanation would be 
>>>>fantastic.    ;)
>>>>Thanks for your advice.
>>>>
>>>>Nadine
>>>>

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RE: [PyMOL] volume approximation

[Peter T. <pet...@bi...>]

Hi Ormus,

Not sure if this can easily be done in PyMol, but I used HydroNMR and
HydroPro for something similar for the process of analysing the =
hydrodynamic
properties of molecules. As far as I remember they don't work with
overlapping spheres but fill the space of a molecule with spheres of =
equal
size.

See Torre, Huertas and Carrasco (2000) Journal of Magnetic Resonance, =
147,
138pp

or=20

http://leonardo.fcu.um.es/macromol/programs/hydronmr/hydronmr.htm

Peter

--=20
Dr Peter Teriete
Laboratory of Molecular Biophysics
Department of Biochemistry
University of Oxford
South Parks Rd.
Oxford
OX1 3QU
=20
Tel: +44 1865 275742
Fax: +44 1865 275182


-----Original Message-----
From: pym...@li...
[mailto:pym...@li...] On Behalf Of ormus cama
Sent: 05 August 2005 01:04
To: pym...@li...
Subject: [PyMOL] volume approximation



hi, i am looking for some advice. i would like to create a set of
overlapping spheres whose combined volume approximates the=20
actual volume of a protein of interest. obviously, i am looking for a
reduced representation. ideally, i am talking about no=20
more than a handful of spheres. these spheres should all be equally =
sized
and the degree of overlap between spheres should be=20
consistent across all of them (that is, they should all overlap all
neighboring spheres equally). i'm trying to construct an=20
algorithm that would take in the pdb coordinates of the protein to be
approximated and output a set of points corresponding to=20
the origins of the spheres required to fill the volume of the original
protein to some determined degree of accuracy (eg. >=20
90%).

i'm relatively new to pymol, but of all the molecular visualization =
programs
i have looked at, it seems best suited to the=20
task at hand. has anyone done anything even remotely like this? can =
anyone
offer insight as to whether i can do this within=20
pymol and, if so, where i might look (wiki, documenation, etc) to get
started?

thanks in advance, ormus


--=20
India.com free e-mail - www.india.com.=20
Check out our value-added Premium features, such as an extra 20MB for =
mail
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-------------------------------------------------------
SF.Net email is Sponsored by the Better Software Conference & EXPO =
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[PyMOL] volume approximation

[ormus c. <or...@in...>]

hi, i am looking for some advice. i would like to create a set of overlappi=
ng spheres whose combined volume approximates the=20
actual volume of a protein of interest. obviously, i am looking for a reduc=
ed representation. ideally, i am talking about no=20
more than a handful of spheres. these spheres should all be equally sized a=
nd the degree of overlap between spheres should be=20
consistent across all of them (that is, they should all overlap all neighbo=
ring spheres equally). i'm trying to construct an=20
algorithm that would take in the pdb coordinates of the protein to be appro=
ximated and output a set of points corresponding to=20
the origins of the spheres required to fill the volume of the original prot=
ein to some determined degree of accuracy (eg. >=20
90%).

i'm relatively new to pymol, but of all the molecular visualization program=
s i have looked at, it seems best suited to the=20
task at hand. has anyone done anything even remotely like this? can anyone =
offer insight as to whether i can do this within=20
pymol and, if so, where i might look (wiki, documenation, etc) to get start=
ed?

thanks in advance, ormus


--=20
India.com free e-mail - www.india.com.=20
Check out our value-added Premium features, such as an extra 20MB for mail =
storage, POP3, e-mail forwarding, and ads-free mailboxes!

RE: [PyMOL] comments ?

[Warren D. <wa...@de...>]

That's by design...we can't allow calling of Python from p1m files.

--
Warren L. DeLano, Ph.D.                    =20
Principal Scientist

. DeLano Scientific LLC =20
. 400 Oyster Point Blvd., Suite 213          =20
. South San Francisco, CA 94080 USA  =20
. Biz:(650)-872-0942  Tech:(650)-872-0834    =20
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:wa...@de...     =20
=20

> -----Original Message-----
> From: Sebastien Moretti [mailto:seb...@ig...]=20
> Sent: Thursday, August 04, 2005 12:17 AM
> To: Warren DeLano; pymol-users
> Subject: Re: [PyMOL] comments ?
>=20
> > Yes -- this is a bug -- thanks for pointing it out.
> >=20
> > Cheers,
> > Warren
> >=20
> >=20
>=20
> It seems that the 'print "..."' commands is unrecognized in=20
> p1m files too.
>=20
> >>
> >>>But, '#' doesn't work in p1m file.
> >>>    Error: unrecognized keyword: #second The # line
> >>
> >>involves an error
> >>
> >>>but the script goes on.
> >>
> >>I think indeed you found a bug with the parsing of p1m files.
> >>I have the same behaviour on my Linux computer.
> >>
> >>Nice choice of colors by the way.
> >>
> >>Cheers,
> >>
> >>Zac
>=20
> --
> S=E9bastien Moretti
> http://www.igs.cnrs-mrs.fr/
> CNRS - IGS
> 31 chemin Joseph Aiguier
> 13402 Marseille cedex
>=20
>=20
>=20

Re: [PyMOL] sessions and movies

[Nadine A. <nad...@ho...>]

Hi,

Thank you for your reply, Joel. I have followed that advice, downloaded 
v0.98 and tried using the scene function, but I didn't mention yesterday 
that I load and delete several dozen *.pdb files during the original movie 
and this appears to be a problem as the scene function does not restore 
deleted data. (Basically I want to take a few shots of the first structure, 
then move on to the second and delete the first, take a few more shots and 
move on to the third, etc. When I call the first scene, after deleting the 
first structure, the result is empty.) Do you have any other suggestions? I 
also did not specify that I am hoping to find a solution that will allow the 
structures to be manipulated as usual (not just a static representation of 
the structures at a given time). I do not know if this is or is not the case 
when using a *.psw with embedded scenes.

Would it maybe be possible to write a script containing load commands for 
each of the different *.pse (or *.psw - I'm not sure of the difference 
between the 2) files, seperated by some kind of "wait until key pressed" 
command. If so, what is the second command?

As for the other problem I mentionned, it doesn't happen with v0.98.

Thanks again.

Nadine



>
>Hi Nadine,
>
>To answer the first part, there is a much easier way...use the scene 
>function in 0.98 version. This allows you to jump between individual 
>"screenshots". You can then save this as a .psw file and view it as full 
>screen or embed it in powerpoint. (See my previous post "Pymol scenes to 
>movies"). Essentaially you set up view 1 and hit append, then view 2 , 
>append etc. you can then scroll thru your views.
>
>The second question, can't help.
>
>Cheers
>
>J
>
>Nadine Atwood wrote:
>
>>
>>Hi,
>>
>>I have come across a problem that I cannot find a way around and would 
>>greatly appreciate some help. I have made a movie showing several protein 
>>models and numerous distances to illustrate residue interactions in 
>>different structures. This movie is rather long, and I wanted to make a 
>>very short version containing certain "screenshots" of the original. I 
>>have created *.pse files corresponding to the frames I would want in the 
>>short movie, but cannot find a way of loading these in a script. (I can 
>>view them "manually" by opening them one at a time through the command 
>>line, but that rather defeats the point.) I wanted to load these using 
>>mset and mdo commands, but of course, as soon as I load the first one, 
>>PyMOL's memory returns to the state that was saved and the new movie is 
>>deleted. I suppose I need to save these files in another format, but have 
>>not been able to find anything that seems appropriate.
>>
>>I have also encountered another small problem that I do not need a 
>>solution to but thought I would mention as it might be a bug (though it 
>>could be due to my very amateurish programming): when running the long 
>>movie (which creates and deletes a large number of distances), if the 
>>movie is stopped and then start again, some distances (I suppose 
>>corresponding to commands given in frames where the movie was stopped) are 
>>not deleted, whereas if the movie is run without interruption, all 
>>distances are handled correctly. (I am using version 0.97)
>>
>>I am not very computer literate, so a simple explanation would be 
>>fantastic.    ;)
>>Thanks for your advice.
>>
>>Nadine
>>

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