pymol-users Mailing List for PyMOL Molecular Graphics System

Hi M=E1ire,

	PyMOL requires the other mainchain atoms to be present in order to
generate a nice cartoon representation.  The only exception to this is =
if
you're willing to work with a simple tube, in which case you can enable =
the
cartoon_trace setting ("set cartoon_trace,on"), followed by "cartoon =
loop"
or "cartoon tube".

	Unfortunately, there is no good workaround to this at present...

Cheers,
Warren


--
mailto:wa...@de...
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154=20
Fax   (650)-593-4020
 =20

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> mai...@gs...
> Sent: Thursday, May 27, 2004 9:06 AM
> To: pym...@li...
> Subject: [PyMOL] Cartoons from ca co-ordinates only
>=20
> Hi,
> I'm trying to create a movie showing mainchain and sidechain=20
> movements between two different states of a protein.
> I've generated the intermediate files, but they contain 
> the ca positions and not the other mainchain atom positions=20
> of the residues which are moving.
> I've specified the ss, but can not get a cartoon=20
> representation in pymol.
> Is not having the n, c and o the problem and is there a work round?
>=20
> M=E1ire Convery
> Protein Structure Section
> Computational and Structural Sciences
> Stevenage
>=20
>=20
>=20
>=20
>=20
>=20
> -------------------------------------------------------
> This SF.Net email is sponsored by: Oracle 10g Get certified=20
> on the hottest thing ever to hit the market... Oracle 10g.=20
> Take an Oracle 10g class now, and we'll give you the exam FREE.
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> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20

Hi,
I'm trying to create a movie showing mainchain and sidechain movements
between two different states of a protein.
I've generated the intermediate files, but they contain only the ca
positions and not the other mainchain atom positions of the residues wh=
ich
are moving.
I've specified the ss, but can not get a cartoon representation in pymo=
l.
Is not having the n, c and o the problem and is there a work round?

M=E1ire Convery
Protein Structure Section
Computational and Structural Sciences
Stevenage

=

Hi Torin,

Are you by chance trying to write an image without rendering? That will 
only work if you have something on display. Rendering and subsequent 
writing of an image should not pose a problem from within a script.

Cheers,

Tsjerk


 On Thu, 27 May 2004, Torin Huzil wrote:

> I am attempting to have a script output a png image of a set of pdb files 
> that I have in a directory.  I can get the images out of pymol when using 
> it in gui mode, but when I attempt to run in command line mode I get the 
> following error:
> 
> ScenePNG-WARNING: writing a blank image buffer.
> libpng error: Image width or height is zero in IHDR
>  ScenePNG-Error: error writing "PDB_Snapshot_iter_000001.pdb.png"! Please 
> check directory...
> 
> This happens on both Linux and Mac
> 
> Any help is appreciated.
> 
> -------------------------------------------------------
> J. Torin Huzil
> 
> 
> -------------------------------------------------------
> This SF.Net email is sponsored by: Oracle 10g
> Get certified on the hottest thing ever to hit the market... Oracle 10g. 
> Take an Oracle 10g class now, and we'll give you the exam FREE.
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> PyMOL-users mailing list
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> https://lists.sourceforge.net/lists/listinfo/pymol-users
> 

-- 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-- :)
-- :) 	Tsjerk A. Wassenaar, M.Sc.
-- :) 	Molecular Dynamics Group
-- :) 	Dept. of Biophysical Chemistry
-- :) 	University of Groningen
-- :) 	Nijenborgh 4
-- :) 	9747 AG Groningen
-- :) 	The Netherlands
-- :)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-- :)
-- :) 	Hi! I'm a .signature virus!
-- :) 	Copy me into your ~/.signature to help me spread!
-- :)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Hi Kaushik,

If you have a pdb file with the charges in the b-factor field, you can use 
Robert Campbells color_b.py to color your atoms accordingly.
Maybe you would have to adapt the code a bit to get a good color scheme 
for that.

Cheers,

Tsjerk

On Wed, 26 May 2004, Kaushik Raha wrote:

> Hi, Is there a way to color atoms by charge in PyMOL? Can PyMOL read 
> the charges in a PDB file use those charges to color the  atoms?
> 
> Thanks,
> Kaushik.
> 
> 
> 
> -------------------------------------------------------
> This SF.Net email is sponsored by: Oracle 10g
> Get certified on the hottest thing ever to hit the market... Oracle 10g. 
> Take an Oracle 10g class now, and we'll give you the exam FREE.
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> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
> 

-- 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-- :)
-- :) 	Tsjerk A. Wassenaar, M.Sc.
-- :) 	Molecular Dynamics Group
-- :) 	Dept. of Biophysical Chemistry
-- :) 	University of Groningen
-- :) 	Nijenborgh 4
-- :) 	9747 AG Groningen
-- :) 	The Netherlands
-- :)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-- :)
-- :) 	Hi! I'm a .signature virus!
-- :) 	Copy me into your ~/.signature to help me spread!
-- :)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

I am attempting to have a script output a png image of a set of pdb files 
that I have in a directory.  I can get the images out of pymol when using 
it in gui mode, but when I attempt to run in command line mode I get the 
following error:

ScenePNG-WARNING: writing a blank image buffer.
libpng error: Image width or height is zero in IHDR
 ScenePNG-Error: error writing "PDB_Snapshot_iter_000001.pdb.png"! Please 
check directory...

This happens on both Linux and Mac

Any help is appreciated.

-------------------------------------------------------
J. Torin Huzil

Hi, Is there a way to color atoms by charge in PyMOL? Can PyMOL read 
the charges in a PDB file use those charges to color the  atoms?

Thanks,
Kaushik.

Hello,

I'm a master biology french student.
I'm looking for subroutines of pymol that color selected surfaces of spec=
ific=20
amino acid from a pdb file.
I have the code source of Pymol.=20

Could you help me to find such subroutines ?

Cheers,

J=E9r=F4me LANE

Hi Robert,

On 2004-05-24 13:46 you wrote:
> 
> I probably have a very stupid question.
> How do I run the color_b.py script using the latest PYMOL on windows?
> Just clicking on it does not work, I also tried to run it by calling it from
> within pymol but this did not work either.

Sorry if the instructions aren't clear.  I don't often work with
windows, so I forget that windows users may not think the way we
UNIX-types do.  I type more than I click!

In general, *many* python scripts for use with PyMOL are used in a
two-step process. You "run" the script from the PyMOL command line (i.e.
in the external GUI window, or within the OpenGL window, it doesn't
matter), by issuing the "run" command (hmmm, confusing nomenclature
here!):

  run color_b.py

This just loads the color_b function into PyMOL. The "run" command is
running the python script, but in the case of most of my scripts, that
just defines a function that can be called repeatedly in PyMOL. Then
you can use it like a standard PyMOL command, again typing in the PyMOL
command line:

  color_b object
  
or with optional parameters such as:

  color_b object, grad=bwr, b0=5, b1=10

Let me know if this still isn't clear.  This is typical of external
python scripts that are to be run from PyMOL; unless the script does
something you are only likely to do once it should be written as a
function that can be called multiple times after loading it.  

You can even get help after doing "run color_b.py" by typing "help
color_b".  You should see a description of what it does and how to use
it.

In fact, for the scripts that I use often, I include the "run
scriptname.py" commands in my .pymolrc file so that they are included
automatically.

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

Tsjerk,
This is what I tried

1) load a small pdb files (10 atoms)
2) run graph.py
3) graph  all, star, 1, 0.10,[1,0,0], [0,0,1],[[1,0,0],[0,1,0],[0,0,1]],
"graph"

This is what I am getting
*************************************
Traceback (most recent call last):
  File "C:\Program Files\PyMOL/modules\pymol\parser.py", line 139, in parse
    result=apply(kw[nest][0],args[nest],kw_args[nest])
  File "C:/Documents and Settings/amit/Desktop/graph.py", line 230, in graph

obj.extend(shapefunctions[shape](sel.atom[i].coord,size,r,rgb1,rgb2,mtx))
  File "C:/Documents and Settings/amit/Desktop/graph.py", line 58, in star
    i[0] = mvmult(mtx,i[0])
  File "C:/Documents and Settings/amit/Desktop/graph.py", line 7, in mvmult
    return [ a[0][0]*b[0]+a[0][1]*b[1]+a[0][2]*b[2],
TypeError: can't multiply sequence to non-int
*************************************

Is this something to do with the end of line? Need to use special character
for line continuation when line is broken into several lines?

Please let me know

Thanks
--Amit




-----Original Message-----
From: pym...@li...
[mailto:pym...@li...]On Behalf Of Amit
Chourasia
Sent: Monday, May 24, 2004 2:31 PM
To: PyM...@li...
Subject: RE: [PyMOL] 3d plotting in pymol


Tsjerk,
	Thanks for providing the script. I was going through the code. It seems to
have a a lot of potential for easy expansion.
I am not able to use it though. Could you please provide a little
descriptive documentation for using this.

--Amit



-----Original Message-----
From: Tsjerk Wassenaar [mailto:t.a...@ch...]
Sent: Monday, May 24, 2004 4:59 AM
To: am...@sd...; PyM...@li...
Subject: Re: [PyMOL] 3d plotting in pymol



Hi Amit (and other users),

Here's a script which can be used to put marks on the positions of every
atom in a selection. There are several types of marks included now, e.g.
cube, rhombic dodecahedron, tetrahedron, plus and star. Using a matrix
operator these can be extended a bit, to 2D counterparts for example, or
to elongated or rotated shapes. I should still include some
documentation but in brief the usage is as follows:

graph selection = '(all)', shape = 'plus' | 'sphere' | 'star' |
'tetrahedron' | 'dodecahedron', size = 1, r = 0.10, rgb1 = [1,0,0], rgb2
= [0,0,1], mtx = [[1,0,0],[0,1,0],[0,0,1]], name = "graph"

Selection should be obvious, as is shape. Size is a relative indicator
for the size, though at present I haven't fixed things such that a size
1 tetrahedron matches a size 1 dodecahedron. r is the radius of the
lines. rgb1 and rgb2 are the start and end color for each line. mtx is
the matrix operator, which works on the original shape centered around
the origin (before translation to the point of the atom from the selection).

Hope this already works a bit as wanted. I'll be trying to make it a bit
better in the future ;)

Cheers,

Tsjerk

Amit Chourasia wrote:

>Tsjerk,
>
>Great I'll look forward to see your script.
>By that time I'll also gain some familiarity with Python.
>
>For spline related stuff I found this in archive.
>set ribbon_trace,1
>This will create ribbons for arbitrary atoms, but they should be seperate
>objects if we dont want them connected by one ribbon.
>
>Have a nice time in Rome. I wish to travel to Venice sometime.
>
>Thanks and Regards
>--Amit
>
>
>
>-----Original Message-----
>From: Tsjerk Wassenaar [mailto:t.a...@ch...]
>Sent: Thursday, May 13, 2004 3:04 AM
>To: am...@sd...
>Subject: Re: [PyMOL] 3d plotting in pymol
>
>
>
>Hi Amit,
>
>This isn't too difficult actually, and I have done something alike
>recently. What it comes down to is to write some python extensions and
>have definitions for the CGO shapes you want to use. Then you can read
>the coordinates for the atoms ( sel =
>cmd.get_selection("selection_string")  and reading coordinates from
>sel.atom[i].coord ) and add these coordinates to your CGO object. Doing
>this for all atoms and loading it back into pymol would give you what
>you want. I'm not completely sure where I have the script I wrote. But I
>can have a look in about a week (when I get back from Rome) and write
>the script if it hasn't been done already (the feature sounds cool
>enough ;) ).
>
>Wouldn't have ideas on the spline at this moment.
>
>Cheers,
>
>Tsjerk
>
>Amit Chourasia wrote:
>
>
>
>>Hi,
>>I am trying to use pymol as a 3d plotting tool.
>>
>>I have few questions
>>
>>1)Is there a way to add represenation in pymol. ?
>>For instance I would like to see the atom as a triangle or nhedron.
>>I was going through CGO objects that looks promising to what I want to
>>accomplish. What I am looking for is to add represenation module and
>>use them.
>>
>>2)Is there a method to represent a group of atoms connected by cartoon
>>even if the chains are not biologically feasable. What I am looking
>>for is you have bunch of points(atoms) through which the ribbon should
>>pass like a spline curve.
>>
>>Any inputs and pointers would be most appreciated.
>>
>>Thanks
>>--Amit
>>
>>
>>
>>
>>
>>
>
>
>
>--
>~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>-- :)
>-- :) 	Tsjerk A. Wassenaar, M.Sc.
>-- :) 	Molecular Dynamics Group
>-- :) 	Dept. of Biophysical Chemistry
>-- :) 	University of Groningen
>-- :) 	Nijenborgh 4
>-- :) 	9747 AG Groningen
>-- :) 	The Netherlands
>-- :)
>~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>-- :)
>-- :) 	Hi! I'm a .signature virus!
>-- :) 	Copy me into your ~/.signature to help me spread!
>-- :)
>~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>
>
>
>


--
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-- :)
-- :) 	Tsjerk A. Wassenaar, M.Sc.
-- :) 	Molecular Dynamics Group
-- :) 	Dept. of Biophysical Chemistry
-- :) 	University of Groningen
-- :) 	Nijenborgh 4
-- :) 	9747 AG Groningen
-- :) 	The Netherlands
-- :)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-- :)
-- :) 	Hi! I'm a .signature virus!
-- :) 	Copy me into your ~/.signature to help me spread!
-- :)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~




-------------------------------------------------------
This SF.Net email is sponsored by: Oracle 10g
Get certified on the hottest thing ever to hit the market... Oracle 10g.
Take an Oracle 10g class now, and we'll give you the exam FREE.
http://ads.osdn.com/?ad_id=3149&alloc_id=8166&op=click
_______________________________________________
PyMOL-users mailing list
PyM...@li...
https://lists.sourceforge.net/lists/listinfo/pymol-users

Tsjerk,
	Thanks for providing the script. I was going through the code. It seems to
have a a lot of potential for easy expansion.
I am not able to use it though. Could you please provide a little
descriptive documentation for using this.

--Amit



-----Original Message-----
From: Tsjerk Wassenaar [mailto:t.a...@ch...]
Sent: Monday, May 24, 2004 4:59 AM
To: am...@sd...; PyM...@li...
Subject: Re: [PyMOL] 3d plotting in pymol



Hi Amit (and other users),

Here's a script which can be used to put marks on the positions of every
atom in a selection. There are several types of marks included now, e.g.
cube, rhombic dodecahedron, tetrahedron, plus and star. Using a matrix
operator these can be extended a bit, to 2D counterparts for example, or
to elongated or rotated shapes. I should still include some
documentation but in brief the usage is as follows:

graph selection = '(all)', shape = 'plus' | 'sphere' | 'star' |
'tetrahedron' | 'dodecahedron', size = 1, r = 0.10, rgb1 = [1,0,0], rgb2
= [0,0,1], mtx = [[1,0,0],[0,1,0],[0,0,1]], name = "graph"

Selection should be obvious, as is shape. Size is a relative indicator
for the size, though at present I haven't fixed things such that a size
1 tetrahedron matches a size 1 dodecahedron. r is the radius of the
lines. rgb1 and rgb2 are the start and end color for each line. mtx is
the matrix operator, which works on the original shape centered around
the origin (before translation to the point of the atom from the selection).

Hope this already works a bit as wanted. I'll be trying to make it a bit
better in the future ;)

Cheers,

Tsjerk

Amit Chourasia wrote:

>Tsjerk,
>
>Great I'll look forward to see your script.
>By that time I'll also gain some familiarity with Python.
>
>For spline related stuff I found this in archive.
>set ribbon_trace,1
>This will create ribbons for arbitrary atoms, but they should be seperate
>objects if we dont want them connected by one ribbon.
>
>Have a nice time in Rome. I wish to travel to Venice sometime.
>
>Thanks and Regards
>--Amit
>
>
>
>-----Original Message-----
>From: Tsjerk Wassenaar [mailto:t.a...@ch...]
>Sent: Thursday, May 13, 2004 3:04 AM
>To: am...@sd...
>Subject: Re: [PyMOL] 3d plotting in pymol
>
>
>
>Hi Amit,
>
>This isn't too difficult actually, and I have done something alike
>recently. What it comes down to is to write some python extensions and
>have definitions for the CGO shapes you want to use. Then you can read
>the coordinates for the atoms ( sel =
>cmd.get_selection("selection_string")  and reading coordinates from
>sel.atom[i].coord ) and add these coordinates to your CGO object. Doing
>this for all atoms and loading it back into pymol would give you what
>you want. I'm not completely sure where I have the script I wrote. But I
>can have a look in about a week (when I get back from Rome) and write
>the script if it hasn't been done already (the feature sounds cool
>enough ;) ).
>
>Wouldn't have ideas on the spline at this moment.
>
>Cheers,
>
>Tsjerk
>
>Amit Chourasia wrote:
>
>
>
>>Hi,
>>I am trying to use pymol as a 3d plotting tool.
>>
>>I have few questions
>>
>>1)Is there a way to add represenation in pymol. ?
>>For instance I would like to see the atom as a triangle or nhedron.
>>I was going through CGO objects that looks promising to what I want to
>>accomplish. What I am looking for is to add represenation module and
>>use them.
>>
>>2)Is there a method to represent a group of atoms connected by cartoon
>>even if the chains are not biologically feasable. What I am looking
>>for is you have bunch of points(atoms) through which the ribbon should
>>pass like a spline curve.
>>
>>Any inputs and pointers would be most appreciated.
>>
>>Thanks
>>--Amit
>>
>>
>>
>>
>>
>>
>
>
>
>--
>~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>-- :)
>-- :) 	Tsjerk A. Wassenaar, M.Sc.
>-- :) 	Molecular Dynamics Group
>-- :) 	Dept. of Biophysical Chemistry
>-- :) 	University of Groningen
>-- :) 	Nijenborgh 4
>-- :) 	9747 AG Groningen
>-- :) 	The Netherlands
>-- :)
>~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>-- :)
>-- :) 	Hi! I'm a .signature virus!
>-- :) 	Copy me into your ~/.signature to help me spread!
>-- :)
>~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>
>
>
>


--
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-- :)
-- :) 	Tsjerk A. Wassenaar, M.Sc.
-- :) 	Molecular Dynamics Group
-- :) 	Dept. of Biophysical Chemistry
-- :) 	University of Groningen
-- :) 	Nijenborgh 4
-- :) 	9747 AG Groningen
-- :) 	The Netherlands
-- :)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-- :)
-- :) 	Hi! I'm a .signature virus!
-- :) 	Copy me into your ~/.signature to help me spread!
-- :)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Hi Amit (and other users),

Here's a script which can be used to put marks on the positions of every 
atom in a selection. There are several types of marks included now, e.g. 
cube, rhombic dodecahedron, tetrahedron, plus and star. Using a matrix 
operator these can be extended a bit, to 2D counterparts for example, or 
to elongated or rotated shapes. I should still include some 
documentation but in brief the usage is as follows:

graph selection = '(all)', shape = 'plus' | 'sphere' | 'star' | 
'tetrahedron' | 'dodecahedron', size = 1, r = 0.10, rgb1 = [1,0,0], rgb2 
= [0,0,1], mtx = [[1,0,0],[0,1,0],[0,0,1]], name = "graph"

Selection should be obvious, as is shape. Size is a relative indicator 
for the size, though at present I haven't fixed things such that a size 
1 tetrahedron matches a size 1 dodecahedron. r is the radius of the 
lines. rgb1 and rgb2 are the start and end color for each line. mtx is 
the matrix operator, which works on the original shape centered around 
the origin (before translation to the point of the atom from the selection).

Hope this already works a bit as wanted. I'll be trying to make it a bit 
better in the future ;)

Cheers,

Tsjerk

Amit Chourasia wrote:

>Tsjerk,
>
>Great I'll look forward to see your script.
>By that time I'll also gain some familiarity with Python.
>
>For spline related stuff I found this in archive.
>set ribbon_trace,1
>This will create ribbons for arbitrary atoms, but they should be seperate
>objects if we dont want them connected by one ribbon.
>
>Have a nice time in Rome. I wish to travel to Venice sometime.
>
>Thanks and Regards
>--Amit
>
>
>
>-----Original Message-----
>From: Tsjerk Wassenaar [mailto:t.a...@ch...]
>Sent: Thursday, May 13, 2004 3:04 AM
>To: am...@sd...
>Subject: Re: [PyMOL] 3d plotting in pymol
>
>
>
>Hi Amit,
>
>This isn't too difficult actually, and I have done something alike
>recently. What it comes down to is to write some python extensions and
>have definitions for the CGO shapes you want to use. Then you can read
>the coordinates for the atoms ( sel =
>cmd.get_selection("selection_string")  and reading coordinates from
>sel.atom[i].coord ) and add these coordinates to your CGO object. Doing
>this for all atoms and loading it back into pymol would give you what
>you want. I'm not completely sure where I have the script I wrote. But I
>can have a look in about a week (when I get back from Rome) and write
>the script if it hasn't been done already (the feature sounds cool
>enough ;) ).
>
>Wouldn't have ideas on the spline at this moment.
>
>Cheers,
>
>Tsjerk
>
>Amit Chourasia wrote:
>
>  
>
>>Hi,
>>I am trying to use pymol as a 3d plotting tool.
>>
>>I have few questions
>>
>>1)Is there a way to add represenation in pymol. ?
>>For instance I would like to see the atom as a triangle or nhedron.
>>I was going through CGO objects that looks promising to what I want to
>>accomplish. What I am looking for is to add represenation module and
>>use them.
>>
>>2)Is there a method to represent a group of atoms connected by cartoon
>>even if the chains are not biologically feasable. What I am looking
>>for is you have bunch of points(atoms) through which the ribbon should
>>pass like a spline curve.
>>
>>Any inputs and pointers would be most appreciated.
>>
>>Thanks
>>--Amit
>>
>>
>>
>>
>>    
>>
>
>
>
>--
>~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>-- :)
>-- :) 	Tsjerk A. Wassenaar, M.Sc.
>-- :) 	Molecular Dynamics Group
>-- :) 	Dept. of Biophysical Chemistry
>-- :) 	University of Groningen
>-- :) 	Nijenborgh 4
>-- :) 	9747 AG Groningen
>-- :) 	The Netherlands
>-- :)
>~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>-- :)
>-- :) 	Hi! I'm a .signature virus!
>-- :) 	Copy me into your ~/.signature to help me spread!
>-- :)
>~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>
>
>  
>


-- 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-- :)
-- :) 	Tsjerk A. Wassenaar, M.Sc.
-- :) 	Molecular Dynamics Group
-- :) 	Dept. of Biophysical Chemistry
-- :) 	University of Groningen
-- :) 	Nijenborgh 4
-- :) 	9747 AG Groningen
-- :) 	The Netherlands
-- :)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-- :)
-- :) 	Hi! I'm a .signature virus!
-- :) 	Copy me into your ~/.signature to help me spread!
-- :)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Hi Tony & Friends,

	I just wanted to draw your attention to the fact that rTools should
(in theory) work with the 0.95 OSX-X11 hybrid version, which has an native
Aqua-based OpenGL window and an X11-based Tcl/Tk gui.  I specifically
created that version to insure that Mac users wouldn't be left unable to use
external code such as this.  PyMOLX11Hybrid is not quite as convenient as
MacPyMOL since it requires a running instance of X11, but it is much easier
to install than the Fink version of PyMOL and should provide the same
compatibility.

http://pymol.sourceforge.net/obtaining.html

Cheers,
Warren

--
mailto:wa...@de...
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154 
Fax   (650)-593-4020
  

> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf Of 
> Tony Giannetti
> Sent: Friday, May 21, 2004 11:50 PM
> To: Olve Peersen
> Cc: pym...@li...
> Subject: Re: [PyMOL] Rtools Question
> 
> Hey Olve,
>     Not a prob, and since this is a common problem I will 
> post my answer to the list.  Kelley Moreman actually did a 
> lot of this legwork so I give props to him.  You are correct, 
> the rTools that you can download from the web does not work 
> on MacPyMol directly.  Kelley was able to obtain an earlier 
> version of the script that does work.  I've attached it and 
> it's called movie.py.
> Very simply, you put it in the same directory as the MacPyMol 
> executable file (in the Mac system this is simply where the 
> MacPyMol icon is located; you don't even have to open the 
> archive.  Once PyMol is loaded, type 'run movie.py' and 
> everything is loaded.  You can then input commands like 
> mvSinrot and mvMov and all those great commands.  Enclosed 
> are other files from Kelley including more detailed setup 
> instructions and a description of how the animation commands work.
> 
> It's pretty easy once you get started.  In about 2 days I 
> constructed the movie for my thesis defense that can 
> currently be viewed at:
> 
> www.its.caltech.edu/~tonyg/smaller_fpnhyp.mov
> 
> Of course moving objects independently of scene rotations 
> isn't trivial, though it apparently can be done (Kelley and 
> Warren have tips on this).  For this movie, anything that 
> moves was rendered with the rest of the scene objects turned 
> off and then spliced into background scenes using photoshop scripts.
> 
> Hope this helps you, and other Mac users.
>         Tony
> 
> On 5/21/04 11:12 PM, "Olve Peersen" 
> <Olv...@Co...> wrote:
> 
> > Tony,
> >   I was wondering if you could e-mail me or post the details of how 
> > you got rTools to work with MacPymol as opposed to X11 
> pymol for the 
> > Mac.  I've fiddled with it a bit, but I cannot seem to get 
> the movie 
> > commands to work.
> > 
> > Thanks,
> > 
> > Olve Peersen
> > 
> > 
> > On May 15, 2004, at 11:25 PM, Tony Giannetti wrote:
> > 
> >> Hello all,
> >>     This may have already been answered but I don't see it in the 
> >> archives.
> >> I've got rTools working under MacPyMol and the effects are great.  
> >> I'm working with a scene that has many objects loaded at 
> once and I 
> >> want to have some of them move independently over each 
> other.  So far 
> >> I can only get rTools to apply rotations/translations to the whole 
> >> scene, but not to individual objects.  I can probably work around 
> >> this using the alpha channel and then pasting the rendered images 
> >> back onto the original scene in photoshop, but I'm wondering if 
> >> there's a command scheme that will allow object one to rotate and 
> >> translate according to rTools commands without altering the other 
> >> objects in the scene.  Thanks much,
> >>         Tony
> >> 
> >> 
> >> 
> >> 
> >> -------------------------------------------------------
> >> This SF.Net email is sponsored by: SourceForge.net 
> Broadband Sign-up 
> >> now for SourceForge Broadband and get the fastest
> >> 6.0/768 connection for only $19.95/mo for the first 3 months!
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> >> PyMOL-users mailing list
> >> PyM...@li...
> >> https://lists.sourceforge.net/lists/listinfo/pymol-users
> >> 
> > 
> > -------------------------------------------------------
> > Olve Peersen
> > Assistant Professor
> > Dept. of Biochemistry & Molecular Biology 1870 Campus Delivery 
> > Colorado State University Ft. Collins, CO  80523-1870
> > -------------------------------------------------------
> > 970.491-0433    Office
> > 970.491-0271    Lab
> > 970.491-0494    Fax
> > -------------------------------------------------------
> > 
> > 
> 
> 

Hey Olve,
    Not a prob, and since this is a common problem I will post my answer to
the list.  Kelley Moreman actually did a lot of this legwork so I give props
to him.  You are correct, the rTools that you can download from the web does
not work on MacPyMol directly.  Kelley was able to obtain an earlier version
of the script that does work.  I've attached it and it's called movie.py.
Very simply, you put it in the same directory as the MacPyMol executable
file (in the Mac system this is simply where the MacPyMol icon is located;
you don't even have to open the archive.  Once PyMol is loaded, type 'run
movie.py' and everything is loaded.  You can then input commands like
mvSinrot and mvMov and all those great commands.  Enclosed are other files
from Kelley including more detailed setup instructions and a description of
how the animation commands work.

It's pretty easy once you get started.  In about 2 days I constructed the
movie for my thesis defense that can currently be viewed at:

www.its.caltech.edu/~tonyg/smaller_fpnhyp.mov

Of course moving objects independently of scene rotations isn't trivial,
though it apparently can be done (Kelley and Warren have tips on this).  For
this movie, anything that moves was rendered with the rest of the scene
objects turned off and then spliced into background scenes using photoshop
scripts.

Hope this helps you, and other Mac users.
        Tony

On 5/21/04 11:12 PM, "Olve Peersen" <Olv...@Co...> wrote:

> Tony,
>   I was wondering if you could e-mail me or post the details of how
> you got rTools to work with MacPymol as opposed to X11 pymol for the
> Mac.  I've fiddled with it a bit, but I cannot seem to get the movie
> commands to work.
> 
> Thanks,
> 
> Olve Peersen
> 
> 
> On May 15, 2004, at 11:25 PM, Tony Giannetti wrote:
> 
>> Hello all,
>>     This may have already been answered but I don't see it in the
>> archives.
>> I've got rTools working under MacPyMol and the effects are great.  I'm
>> working with a scene that has many objects loaded at once and I want
>> to have
>> some of them move independently over each other.  So far I can only get
>> rTools to apply rotations/translations to the whole scene, but not to
>> individual objects.  I can probably work around this using the alpha
>> channel
>> and then pasting the rendered images back onto the original scene in
>> photoshop, but I'm wondering if there's a command scheme that will
>> allow
>> object one to rotate and translate according to rTools commands without
>> altering the other objects in the scene.  Thanks much,
>>         Tony
>> 
>> 
>> 
>> 
>> -------------------------------------------------------
>> This SF.Net email is sponsored by: SourceForge.net Broadband
>> Sign-up now for SourceForge Broadband and get the fastest
>> 6.0/768 connection for only $19.95/mo for the first 3 months!
>> http://ads.osdn.com/?ad_id=2562&alloc_id=6184&op=click
>> _______________________________________________
>> PyMOL-users mailing list
>> PyM...@li...
>> https://lists.sourceforge.net/lists/listinfo/pymol-users
>> 
> 
> -------------------------------------------------------
> Olve Peersen
> Assistant Professor
> Dept. of Biochemistry & Molecular Biology
> 1870 Campus Delivery
> Colorado State University
> Ft. Collins, CO  80523-1870
> -------------------------------------------------------
> 970.491-0433    Office
> 970.491-0271    Lab
> 970.491-0494    Fax
> -------------------------------------------------------
> 
> 

hi -- pink squares are a result of the selection process; try "deselect" 
to remove them.
cameron

=== Greg C wrote (on 05/21/2004 12:38 PM): ===

>
> I am having difficulty in displaying only one of 2 chains in a PDB 
> file.  The file is basically a homodimer, but I want to only display 
> one of the monomers.  I can hide one of the two chains by selecting it 
> and then hiding it, but the problem is that I am left with one chain 
> and a collection of pink dots.  So is there a way of hiding the chain 
> without selecting it (and thereby gettingthe dots) or is there a way 
> of getting rid of the dots post selection/hiding?
>
>  
>
> THANKS
>
> -Greg
>
> Greg Caputo* *Ph.D.
>
> Postdoctoral Research Associate
>
> Department of Medical Biochemistry & Genetics
>
> Texas A&M University
>
> College Station, TX 77840
>
> (979) 862 3188 (lab)
>
> (979) 324 8645 (cell)
>
>
> ------------------------------------------------------------------------
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> _______________________________________________ PyMOL-users mailing 
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> https://lists.sourceforge.net/lists/listinfo/pymol-users 


-- 
Cameron Mura
UCSD

<html><div style='background-color:'><P><BR>I am having difficulty in displaying only one of 2 chains in a PDB file.&nbsp; The file is basically a homodimer, but I want to only display one of the monomers.&nbsp; I can hide one of the two chains by selecting it and then hiding it, but the problem is that I am left with one chain and a collection of pink dots.&nbsp; So is there a way of hiding the chain without selecting it (and thereby gettingthe dots) or is there a way of getting rid of the dots post selection/hiding?</P>
<P>&nbsp;</P>
<P>THANKS</P>
<P>-Greg<BR><BR></P>
<DIV>
<P><IMG height=2 src="http://graphics.hotmail.com/greypixel.gif" width="100%" vspace=9><FONT face="Verdana, Geneva, Arial, Sans-serif">Greg Caputo<STRONG> </STRONG>Ph.D. <IMG height=19 src="http://graphics.hotmail.com/i.p.embeer.gif" width=19></FONT></P>
<P><FONT face="Verdana, Geneva, Arial, Sans-serif">Postdoctoral Research Associate </FONT></P>
<P><FONT face="Verdana, Geneva, Arial, Sans-serif">Department of Medical Biochemistry &amp; Genetics </FONT></P>
<P><FONT face="Verdana, Geneva, Arial, Sans-serif">Texas A&amp;M University </FONT></P>
<P><FONT face="Verdana, Geneva, Arial, Sans-serif">College Station, TX 77840</FONT></P>
<P><FONT face="Verdana, Geneva, Arial, Sans-serif">(979) 862 3188 (lab)</FONT></P>
<P><FONT face=Verdana>(979) 324 8645 (cell)</FONT></P>
<P><IMG height=2 src="http://graphics.hotmail.com/greypixel.gif" width="100%" vspace=9></P></DIV></div><br clear=all><hr> <a href="FREE" rel="nofollow">http://g.msn.com/8HMBENUS/2734??PS=47575">FREE pop-up blocking with the new MSN Toolbar – get it now!</a> </html>

Hi Camille and Daniel,

I heard my name mentioned, so I'll join in!

* Daniel Rigden <dr...@li...> [2004-05-21 16:43] wrote:
> Hi Camille
> 
> The Espript server is the easiest way I know.  Go here
> 
> http://prodes.toulouse.inra.fr/ESPript/cgi-bin/ESPript.cgi
> 
> choose Execute then Expert mode.  SUpply an alignment and a
> supplementary pdb file then execute.  You get back an annotated
> alignment + the pdb file with a conservation score in the b-factor
> column.  The only trouble can be making that the top sequence in your
> alignment matches exactly the sequence of the structure (no missing
> loops etc).  You can read this new pdb file into Pymol and colour easily
> with Robert Campbell's script color_b.py which you get here
> 
> http://adelie.biochem.queensu.ca/~rlc/work/pymol/
> 
> Good luck
> 
> Daniel
> 
> On Fri, 2004-05-21 at 15:28, ca...@mr... wrote:
> > Hello PyMol community!
> > 
> > is there any way to display sequence conservation on the surface of a 
> > protein?
> > i.e. to use the info I have in a sequence alignment.
> > 
> > do I have to do this by hand?
> > 
> > Thanks,
> > 	Camille

I have a little python routine for calculating the sequence variability
(a measure that has apparently been commonly used in the immunoglobulin
community -- Thanks for the tip Dave!), but it requires that you already
have your sequences in lists (or strings) and already aligned.  My
seq_convert.py routines could be used for reading files with these
individual sequences, or you could use biopython to read, say, a Fasta
alignment file.  

Variability is defined as:

(Number of different residue types at a location)/(Frequence of the most
common at that location)

Ok, so I quickly added the sequence reading capability and added
variability.py to my web site (where you can find seq_convert.py also):

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

Create three plain text sequence files (really short examples here!)
that look like:

SGKSGMDVAI

AKCIGPDDAL

ARCS-MDVAL

Then run it with:

  variability.py test1.seq test2.seq test3.seq 

giving:
    1 S A A   2   2   0.667  3.000
    2 G K R   3   1   0.333  9.000
    3 K C C   2   2   0.667  3.000
    4 S I S   2   2   0.667  3.000
    5 G G -   2   2   0.667  3.000
    6 M P M   2   2   0.667  3.000
    7 D D D   1   3   1.000  1.000
    8 V D V   2   2   0.667  3.000
    9 A A A   1   3   1.000  1.000
   10 I L L   2   2   0.667  3.000

That is, the sequences written in vertical columns followed by:

the number of different amino acids found at the position
the number of the most commonly observed at that position
the frequency of the most common
the variability

You would then need to extract the variability data (e.g. with awk, or
modify the script to write only that) and modify your B-factors within
PyMOL using my data2bfactor.py script followed by colouring on B-factor
either with the spectrum command or my color_b.py script.

This was kind of a quick hack, so it isn't as user-friendly as it could
be! It would be ideal to get the alignment out of PyMOL that is created
with the align command but I haven't found a way to get at it.

Hope that helps,
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

Even easier than Espript is ConSurf
http://consurf.tau.ac.il/

You can either supply your own PDB or use one from RCSB. You can also
supply your own alignment or let Consurf build one from a PSI-BLAST
run.

The server returns several outputs, including:
*The alignment it used to generate the surface conservation (in case
you had it build one automatically)
*A nice list of each residue in your favorite protein, the relative
conservation (scale of 1-10) of that position, and what other residues
are found at that position in other organisms. This list is, frankly,
incredibly handy.
*PDB with the B-factor column replaced with relative conservation. If
you open this PDB and run the color_b script
(http://adelie.biochem.queensu.ca/~rlc/work/pymol/) with a two-color
ramped gradient (eg - white->green) you'll have a very intuitive view
of potential "hot spots".

Enjoy!

-- 
Jacob Corn
UC Berkeley - Berger Lab
Lab: 510-643-9491
Cell: 925-408-8579
jc...@uc...

Friday, May 21, 2004, 8:28:45 AM, you wrote:
cmlcau> Hello PyMol community!

cmlcau> is there any way to display sequence conservation on the surface of a
cmlcau> protein?
cmlcau> i.e. to use the info I have in a sequence alignment.

cmlcau> do I have to do this by hand?

cmlcau> Thanks,
cmlcau> 	Camille



cmlcau> -------------------------------------------------------
cmlcau> This SF.Net email is sponsored by: Oracle 10g
cmlcau> Get certified on the hottest thing ever to hit the market... Oracle 10g.
cmlcau> Take an Oracle 10g class now, and we'll give you the exam FREE.
cmlcau> http://ads.osdn.com/?ad_id=3149&alloc_id=8166&op=click
cmlcau> _______________________________________________
cmlcau> PyMOL-users mailing list
cmlcau> PyM...@li...
cmlcau> https://lists.sourceforge.net/lists/listinfo/pymol-users

Randy,

	For some reason this approach has turned out to be unstable, so I've
basically placed it on "unsupported" status until someone with a better
understanding of Python interactive mode than me can take a look at it.  

	Are you aware that the PyMOL command line is also a Python command
line?  You can just use PyMOL interactively in that fashion.

PyMOL>print 1+1
2
PyMOL>from random import random
PyMOL>print random()
0.739460642143


	The only major difference is that the default namespace for PyMOL is
"pymol" not "__main__"

PyMOL>print __name__
pymol


Cheers,
Warrne


--
mailto:wa...@de...
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154 
Fax   (650)-593-4020
  

> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf Of 
> Randy Heiland
> Sent: Friday, May 21, 2004 8:11 AM
> To: pym...@li...
> Subject: [PyMOL] using from native Python
> 
> Can I use PyMOL from native Python?  I'm aware of using the 
> command-line version, but this doesn't let me take an 
> interpretive approach, with which I'd like to experiment.
> 
> I googled and found that one could supposedly do this:
> 
> >>> import pymol
> >>> pymol.finish_launching()
> 
> However, I simply get a seg fault when attempting this (and 
> can supply more details on that if necessary).  Can someone 
> confirm that this works for them?
> 
> I'm running Python 2.3.2 on Linux and PyMOL 0.95.
> 
> Thanks, Randy
> 
> 
> 
> -------------------------------------------------------
> This SF.Net email is sponsored by: Oracle 10g Get certified 
> on the hottest thing ever to hit the market... Oracle 10g. 
> Take an Oracle 10g class now, and we'll give you the exam FREE.
> http://ads.osdn.com/?ad_id=3149&alloc_id=8166&op=click
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
> 

Hi Camille

The Espript server is the easiest way I know.  Go here

http://prodes.toulouse.inra.fr/ESPript/cgi-bin/ESPript.cgi

choose Execute then Expert mode.  SUpply an alignment and a
supplementary pdb file then execute.  You get back an annotated
alignment + the pdb file with a conservation score in the b-factor
column.  The only trouble can be making that the top sequence in your
alignment matches exactly the sequence of the structure (no missing
loops etc).  You can read this new pdb file into Pymol and colour easily
with Robert Campbell's script color_b.py which you get here

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

Good luck

Daniel

On Fri, 2004-05-21 at 15:28, ca...@mr... wrote:
> Hello PyMol community!
> 
> is there any way to display sequence conservation on the surface of a 
> protein?
> i.e. to use the info I have in a sequence alignment.
> 
> do I have to do this by hand?
> 
> Thanks,
> 	Camille
> 
> 
> 
> -------------------------------------------------------
> This SF.Net email is sponsored by: Oracle 10g
> Get certified on the hottest thing ever to hit the market... Oracle 10g. 
> Take an Oracle 10g class now, and we'll give you the exam FREE.
> http://ads.osdn.com/?ad_id=3149&alloc_id=8166&op=click
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
-- 
Dr Daniel John Rigden                     Tel:(+44) 151 795 4467
School of Biological Sciences             FAX:(+44) 151 795 4414
Room 101, Biosciences Building
University of Liverpool
Crown St.,
Liverpool L69 7ZB, U.K.

Hello PyMol community!

is there any way to display sequence conservation on the surface of a 
protein?
i.e. to use the info I have in a sequence alignment.

do I have to do this by hand?

Thanks,
	Camille

Hi,

Having difficulty with the sphere_transparency and stick_transparency 
options in ray-traced figures. When I try to set the transparency to 1 
(or close to 1) the object just appears darker in the ray trace (not 
transparent). The effect I'm trying to achieve is to have things fade 
in and out during a movie. Is this is a known problem with these 
settings or am I missing something obvious?

Alex Gutteridge
European Bioinformatics Institute
Cambridge CB10 1SD
UK

Tel: 01223 492550
Email: al...@eb...

Can I use PyMOL from native Python?  I'm aware of using the command-line
version, but this doesn't let me take an interpretive approach, with
which I'd like to experiment.

I googled and found that one could supposedly do this:

>>> import pymol
>>> pymol.finish_launching()

However, I simply get a seg fault when attempting this (and can supply
more details on that if necessary).  Can someone confirm that this works
for them?

I'm running Python 2.3.2 on Linux and PyMOL 0.95.

Thanks, Randy

Dear PyMOLers,

A couple of users of my scripts had contacted me about problems with my
draw_symops_cctbx.py and all_axes_new.py scripts. I've (I think) solved
those problems and added a new functionality requested by one of them.

The main problem was getting anything using cctbx to run properly from
python scripts run within PyMOL. The solution was to make sure that
PyMOL and cctbx were using the same python version. In order to do this,
it is necessary to install cctbx and PyMOL from sources rather than
installing the pre-built binaries.  A secondary problem seemed to stem
=66rom a slight change in cctbx itself.

The new feature of the draw_symops_cctbx.py script is that you can
now add an extension parameter to draw axes that are longer than the
default. Hence:

  draw_symops object, extension=3D.5

and the axes will be longer by 50% of the default *at each end*, i.e.
double in length.  This could be useful when trying to look at
symmetry-related molecules lying outside the unit cell boundaries.

I had previously noted that there were some missing axes or cell edges
(drawn with my draw_cell.py script) depending on the cell parameters,
and I mentioned to Mike that one could avoid this by modifying one cell
angle by a tiny amount (e.g. 90.001 instead of 90.).  I think I've
tracked this down correctly to a bug in the CGO drawing routine.  I've
just written to Warren about, but in the meantime I've added a
workaround within the two scripts that takes care of it.

Anyone interested in using these script should get the new versions of

  draw_symops_cctbx.py
  all_axes_new.py
  draw_cell.py

=66rom my web site.

Cheers,
Rob
--=20
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

PyMOLer's,

Lots of good feedback on the sequence viewer has been coming in -- thank you
everyone, and please keep it up.  I've got about a week's work of changes to
make, but will continue to push out new releases as they are ready.

I did want to draw your attention to the fact that up until the most recent
beta, THR was being risrepresented using 'R' for arginine -- oops!  Please
update your 0.96 beta versions to 10 if you're going to make use of this new
feature in order to view correct sequences.

I've also greatly increased the performance of the sequence viewer with
large structures.  You can further increase performance by using Selection
Mode->Atoms under the Mouse menu.  It is now reasonable to use the sequence
viewer on very large systems consisting of 50,000 atoms or more.

Cheers,
Warren

--
mailto:wa...@de...
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154 
Fax   (650)-593-4020
 

The sequence viewer is a brilliant addition to pymol and I'm already 
finding it quite useful after playing around with it a bit. However, 
I've noticed a possible bug, although I don't know what's causing it. 
When viewing the pdb file 1fe6 (a coiled coil protein) and using the 
sequence viewer, the sequence RLT it displayed as RLR (residues 14-16) 
despite the graphics correctly showing a threonine residue. You can see 
a screenshot here http://www.cus.cam.ac.uk/~rbd22/Screenshot.png.
Any ideas?

Cheers

Roger