pymol-users Mailing List for PyMOL Molecular Graphics System

Michael,

	You can delete the bond and then add a dashed bond (distance) in
to replace it:

select atom1, ...
select atom2, ...

unbond atom1,atom2
distance bnd,atom1,atom2
hide labels,bnd

But if all you want to do is change the radius, there is the
stick_radius setting, which does that...

show sticks
set stick_radius, 0.1

etc.

Cheers,
Warren


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

-----Original Message-----
From: pym...@li...
[mailto:pym...@li...] On Behalf Of Michael
Tallhamer
Sent: Wednesday, May 28, 2003 10:32 AM
To: pym...@li...
Subject: [PyMOL] Changing lines to be dashed lines

PyMOLers

Is it possible to change the lines that represent bonds to dashed lines
like 
the ones used for distaces so I can change the radius and width
parameters.

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Hi Martin,
Visit Robert Campbell's repository of PyMOL scripts 
(http://adelie.biochem.queensu.ca/~rlc/work/pymol/)...where you'll find 
Python scripts  to import into PyMOL for drawing unit cell edges 
(draw_cell.py), symmetry axes (draw_symops.py), and lots of other stuff...

    Cameron



mkienetz wrote:

>Dear All,
>
>How do I show the unit cell using pymol?
>
>Martin
>
>Martin Kienetz
>429 MSB
>Department of Biochemistry
>University of Alberta
>Edmonton AB
>T6G 2H7
>(780) 492-2422
>
>
>
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Dear All,

How do I show the unit cell using pymol?

Martin

Martin Kienetz
429 MSB
Department of Biochemistry
University of Alberta
Edmonton AB
T6G 2H7
(780) 492-2422

[sorry to send this to both lists, but I think it may be applicable...]

Dear O & PyMOLers,

Have any of you experienced difficulty with stereo on RedHat 9??

With PyMOL, trying to switch to stereo view results in the "Error: 
Selected stereo mode is not available.", and in O the error is this:
"GLUT: Fatal Error in lin_ono_9.0.0: visual with necessary capabilities 
not found."  I suspect the root of both problems is the same.

I checked the shared library dependencies of O (which seem okay from the 
output of "ldd /path-to-o/lin_ono*"), and verified that the glut-3.7-13 
  package was installed (rpm -q glut-3.7-13), as well as the following 
two Mesa-related packages:

XFree86-Mesa-libGLU-4.3.0-2
XFree86-Mesa-libGL-4.3.0-2

Stereo mode for both of these programs worked fine in a previous 
installation in which I was running red hat 8. With the current systems, 
I did a fresh install of rh9 (shrike) on two machines:

(1) a Dell XEON machine with an NVidia Quadro4 700 XGL graphics card, 
using the NVIDIA Kernel Module 1.0-4363 (with a ViewSonic flatpanel 
monitor -- so I don't expect to actually do true Quad-buffered stereo 
displays or anything like that, mainly just testing)

(2) a PC with a ViewSonic P225f CRT monitor (this is the system I would 
actually like to use for stereo), powered by an ATI Radeon 8500LE 
graphics card.

If anyone has encountered similar difficulties or has any helpful hints, 
I'd greatly appreciate hearin bout it!

	Cameron


-- 
--------------------------------------------------
  Cameron Mura
  Urey Hall, Rm. 4234
  Department of Chemistry & Biochemistry
  University of California, San Diego
  9500 Gilman Dr. Dept. 0365
  La Jolla, CA 92093-0365
  Email: cm...@mc...
  Phone: 858.534.0956
  Fax:   858.534.7042
--------------------------------------------------

PyMOLers

Is it possible to change the lines that represent bonds to dashed lines like 
the ones used for distaces so I can change the radius and width parameters.

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PyMOLer's,=20

Okay, with apologies to Per Kraulis, I have implemented Bjorn's request.

There is now a "plane2color"-like feature in PyMOL.=20

For example figures, see http://pymol.sf.net/ms1.jpg and
http://pymol.sf.net/ms2.jpg which were both just created using PyMOL
alone, without any reliance on Molscript, though I wouldn=92t have
believed it myself if you showed them to me this morning!

The new command is:

   set cartoon_highlight_color, color-name

as in=20

   set cartoon_highlight_color, grey70

If you can compile PyMOL source code from the CVS repository, then you
can access this feature right away.  Otherwise, look for it in the
upcoming 0.88 release.

Sorry for all the extra traffic on this thread today, but it isn't often
that we get a new feature request from a major PyMOL sponsor that can
actually be met that same day.

Cheers,
Warren

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

-----Original Message-----
From: Warren L. DeLano [mailto:wa...@de...]=20
Sent: Tuesday, May 27, 2003 1:17 PM
To: 'Warren L. DeLano'; 'Bj=F6rn Kauppi';
'pym...@li...'
Subject: RE: [PyMOL] plane2colour

Whoops, clarification.  I misinterpreted the question...

ray_interior_color meets a different need.  So far, there isn't any
plane2color-like feature in PyMOL.  Sorry for the confusion.

Cheers,
Warren

-----Original Message-----
From: pym...@li...
[mailto:pym...@li...] On Behalf Of Warren L.
DeLano
Sent: Tuesday, May 27, 2003 9:19 AM
To: 'Bj=F6rn Kauppi'; pym...@li...
Subject: RE: [PyMOL] plane2colour

Bjorn,

Good news, I just recently added opaque, colored, "insides" of cartoons,
surfaces, and spheres to the upcoming release. =20

In version 0.88 and beyond, "set interior_color, color-name" will
achieve this effect.

Cheers,
Warren

--
mailto:wa...@de...
Warren L. DeLano
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154=20
Fax   (650)-593-4020
-----Original Message-----
From: pym...@li...
[mailto:pym...@li...] On Behalf Of Bj=F6rn
Kauppi
Sent: Tuesday, May 27, 2003 6:49 AM
To: pym...@li...
Subject: [PyMOL] plane2colour

Hi,

Is it an equivalent in PyMOL to the plane2colour command in Molscript?
i.e. controlling the colour of the "inside" of an cartoon-drawn helix?
Or can I get a similar effect with PyMOL somehow?


Bj=F6rn

Jason,

	The "mpng" command in recent versions of PyMOL takes two
arguments, first and last, which control which frames are rendered.  You
can have your script set these appropriately based on where the job is
running.

Cheers,
Warren


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

-----Original Message-----
From: pym...@li...
[mailto:pym...@li...] On Behalf Of Jason
Thomas Maynes
Sent: Tuesday, May 27, 2003 9:57 AM
To: pym...@li...
Subject: [PyMOL] mpng command

Hello:

Does anybody know if you can specify certain movie frames to render and
write out (ie. to batch render movie frames on different computers)
other
than just dicing up one movie into four or five different scripts and
piecing them together.

Thanks in advance.

Cheers,
JTM

"We can be sure that if a detailed understanding of the molecular basis
of
chemo-therapeutic activity were to be obtained, the advance of medicine
would be greatly accelerated."

Linus Pauling, Nobel Laureate 1954

"...everything that living things do can be understood in terms of the
jigglings and wigglings of atoms."

Richard Feynman

*************************
Jason Thomas Maynes
PhD/MD Program
Department of Biochemistry
Faculty of Medicine
University of Alberta
ja...@bi...
*************************



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Whoops, clarification.  I misinterpreted the question...

ray_interior_color meets a different need.  So far, there isn't any
plane2color-like feature in PyMOL.  Sorry for the confusion.

Cheers,
Warren

-----Original Message-----
From: pym...@li...
[mailto:pym...@li...] On Behalf Of Warren L.
DeLano
Sent: Tuesday, May 27, 2003 9:19 AM
To: 'Bj=F6rn Kauppi'; pym...@li...
Subject: RE: [PyMOL] plane2colour

Bjorn,

Good news, I just recently added opaque, colored, "insides" of cartoons,
surfaces, and spheres to the upcoming release. =20

In version 0.88 and beyond, "set interior_color, color-name" will
achieve this effect.

Cheers,
Warren

--
mailto:wa...@de...
Warren L. DeLano
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154=20
Fax   (650)-593-4020
-----Original Message-----
From: pym...@li...
[mailto:pym...@li...] On Behalf Of Bj=F6rn
Kauppi
Sent: Tuesday, May 27, 2003 6:49 AM
To: pym...@li...
Subject: [PyMOL] plane2colour

Hi,

Is it an equivalent in PyMOL to the plane2colour command in Molscript?
i.e. controlling the colour of the "inside" of an cartoon-drawn helix?
Or can I get a similar effect with PyMOL somehow?


Bj=F6rn

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you
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Hello:

Does anybody know if you can specify certain movie frames to render and
write out (ie. to batch render movie frames on different computers) other
than just dicing up one movie into four or five different scripts and
piecing them together.

Thanks in advance.

Cheers,
JTM

"We can be sure that if a detailed understanding of the molecular basis of
chemo-therapeutic activity were to be obtained, the advance of medicine
would be greatly accelerated."

Linus Pauling, Nobel Laureate 1954

"...everything that living things do can be understood in terms of the
jigglings and wigglings of atoms."

Richard Feynman

*************************
Jason Thomas Maynes
PhD/MD Program
Department of Biochemistry
Faculty of Medicine
University of Alberta
ja...@bi...
*************************

Bjorn,

Good news, I just recently added opaque, colored, "insides" of cartoons,
surfaces, and spheres to the upcoming release. =20

In version 0.88 and beyond, "set interior_color, color-name" will
achieve this effect.

Cheers,
Warren



--
mailto:wa...@de...
Warren L. DeLano
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154=20
Fax   (650)-593-4020
-----Original Message-----
From: pym...@li...
[mailto:pym...@li...] On Behalf Of Bj=F6rn
Kauppi
Sent: Tuesday, May 27, 2003 6:49 AM
To: pym...@li...
Subject: [PyMOL] plane2colour

Hi,

Is it an equivalent in PyMOL to the plane2colour command in Molscript?
i.e. controlling the colour of the "inside" of an cartoon-drawn helix?
Or can I get a similar effect with PyMOL somehow?


Bj=F6rn

************************************************************************
***
This e-mail may contain confidential information proprietary to Karo Bio
AB
and Karo Bio USA, Inc. and is meant for the intended addressee(s) only.
Any
unauthorized review, use, disclosure or distribution is prohibited. If
you
have received this message in error, please advise the sender and delete
the e-mail and any attachments from your files.
************************************************************************
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Hi,

Is it an equivalent in PyMOL to the plane2colour command in Molscript? i=2Ee=2E c=
ontrolling the colour of the "inside" of an cartoon-drawn helix? Or can I get a s=
imilar effect with PyMOL somehow?


Bj=F6rn

***************************************************************************
This e-mail may contain confidential information proprietary to Karo Bio AB
and Karo Bio USA, Inc=2E and is meant for the intended addressee(s)  Any
unauthorized review, use, disclosure or distribution is prohibited=2E If you
have received this message in error, please advise the sender and delete
the e-mail and any attachments from your files=2E
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Hi Folks,

Some of you may have been using my color_b.py script for colouring by
the value of the B-factor.  Thanks to the stimulus of one user, I've
updated it to have a variety of colouring gradients.  You can now select
=66rom the following options:

  Gradients:
    'bwr'   blue-white-red (like grasp electrostatic colouring)
    'rwb'   red-white-blue
    'bgr'   blue-green-red (also known as 'rainbow')
    'rgb'   red-green-blue (also known as 'reverserainbow')
    'bmr'   blue-magenta-red
    'rmb'   red-magenta-blue
    'gray'  dark-to-light gray-scale=20
    'reversegray' light-to-dark gray-scale
 =20
For each of these gradients you can provide a saturation and value (as
in the "s" and "v" in the "HSV" colour scale).  So you can make the
colours pastel or highly saturated and dark as you so desire!  For the
gray-scale gradients, "sat" sets the minimum intensity and "value" sets
the maximum intensity.

Now, rather than specifying ramp=3D1 or ramp=3D0 to select the type
of "binning" of the data, I changed the option to mode=3D'ramp' or
mode=3D'hist' to select binning by equal numbers of atoms in each colour
(ramp) or equal spacing of the b-values in each colour (hist).

I've also written a couple of new scripts:

1) data2bfactor.py, which reads a data file and alters the B-factor
for each residue (or atom) of the requested molecule with the values
in the data file. Obviously one might use this in conjuction with the
color_b.py script to colour your molecule by the value in the data. :)

(Caution, this is somewhat crude and due to the use of the "alter"
function in PyMOL is very slow, especially for altering individual
atomic B-factors -- I hope to improve it, but it works for me for now).

There are two functions in this script, data2b_res and data2b_atom
for reading data per residue or per atom respectively.  They expect
to read a data file of the form:

CHAIN RESI RESN data

or

CHAIN RESI RESN NAME data

(where CHAIN,RESI,RESN,NAME mean the same as they do in PyMOL selection
commands). Blank lines or comment lines in the data file preceded with
a '#' are ignored. After doing "run data2bfactor.py" you can call the
functions with:

  data2b_res('mol','file.data')  or data2b_atom('mol','file.data')

where you'll obviously need to fill in the correct values for 'mol'=20
and 'file.data'.

2) stride_ss.py, which takes the output from the "stride" secondary
structure calculation and apply it to a molecule within PyMOL.
Obviously you'll need a copy of stride, which I got with my copy of VMD
(http://www.ks.uiuc.edu/Research/vmd/). Of course I only have VMD in
order to get stride, not because of its graphical abilities. :)

Please note, for those of you that may have bookmarked (or have a link
to) my web site at Johns Hopkins, I left there 5 months ago. Please
refer to my current web site for my PyMOL stuff:

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


I hope these are helpful to somebody!

Cheers,
Robert
--=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

Hi Cameron,

I did run into a similar problem on RH9. Error message I got was 
different but it also came from a glut library. I was able to get around 
the problem by downgrading glut to the version that came with RH8.0 (you 
just force install glut and, if you need to, glut-devel). RedHat knows 
about the problems related to glut libs but I don't think they 
understand yet what's causing them...

Cheers,
-Viktor


Cameron Mura wrote:
> Hi,
> I'm wondering if anyone's experienced problems with PyMOL compatibility 
> with an NVidia graphics card? I ran PyMOL on a RedHat 8.0 system without 
> problems, but recently changed to rh9.0(shrike), and I get the following 
> lines of error when I try to run PyMOL from the prompt (and pymol 
> doesn't start):
> 
> """
> CHEMCCA35:cmura[42] pymol
> Traceback (most recent call last):
>  File 
> "/usr/lib/python2.2/site-packages/pymol/modules/pymol/__init__.py", line 
> 93, in ?
>    import pymol
>  File 
> "/usr/lib/python2.2/site-packages/pymol/modules/pymol/__init__.py", line 
> 236, in ?
>    import _cmd
> ImportError: /usr/lib/libglut.so.3: undefined symbol: 
> glXBindChannelToWindowSGIX
> """
> 
> Some system info.: Red Hat 9.0 (Shrike; 2.4.20-13.9smp kernel) with an 
> NVidia Quadro4 700 XGL graphics card. NVidia driver info. is:
> NVRM version: NVIDIA Linux x86 nvidia.o Kernel Module  1.0-4363  Sat Apr 
> 19 17:46:46 PDT 2003
> GCC version:  gcc version 3.2.2 20030222 (Red Hat Linux 3.2.2-5)
> 
>  From the last line of the error, I suspect the problem has something to 
> do with incompatibility between my rh9 installation and python 
> interpreter as utilized by PyMOL? But I don't know enough to fix it....
> Has anyone else seen (and fixed?) this problem??
> 

-- 
Viktor Hornak
SUNY at Stony Brook

PyMOLers,

I can confirm that there are problems with RedHat9.0 -- which was
shipped with by RedHat with malfunctioning C libraries that will cause
PyMOL to hang and occasionally even crash the system.  

My recommendation is to wait for RedHat 9.1 or try SUSE 8.2.

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

-----Original Message-----
From: pym...@li...
[mailto:pym...@li...] On Behalf Of Cameron
Mura
Sent: Wednesday, May 21, 2003 12:50 PM
To: pym...@li...
Subject: [PyMOL] PyMOL compatibility w/ NVidia card on rh9 system

Hi,
I'm wondering if anyone's experienced problems with PyMOL compatibility 
with an NVidia graphics card? I ran PyMOL on a RedHat 8.0 system without

problems, but recently changed to rh9.0(shrike), and I get the following

lines of error when I try to run PyMOL from the prompt (and pymol 
doesn't start):

"""
CHEMCCA35:cmura[42] pymol
Traceback (most recent call last):
  File 
"/usr/lib/python2.2/site-packages/pymol/modules/pymol/__init__.py", line

93, in ?
    import pymol
  File 
"/usr/lib/python2.2/site-packages/pymol/modules/pymol/__init__.py", line

236, in ?
    import _cmd
ImportError: /usr/lib/libglut.so.3: undefined symbol: 
glXBindChannelToWindowSGIX
"""

Some system info.: Red Hat 9.0 (Shrike; 2.4.20-13.9smp kernel) with an 
NVidia Quadro4 700 XGL graphics card. NVidia driver info. is:
NVRM version: NVIDIA Linux x86 nvidia.o Kernel Module  1.0-4363  Sat Apr

19 17:46:46 PDT 2003
GCC version:  gcc version 3.2.2 20030222 (Red Hat Linux 3.2.2-5)

 From the last line of the error, I suspect the problem has something to

do with incompatibility between my rh9 installation and python 
interpreter as utilized by PyMOL? But I don't know enough to fix it....
Has anyone else seen (and fixed?) this problem??

Thanks a lot,

    Cameron



PS. How does one search through the pymol users list mail archive at 
http://sourceforge.net/mailarchive/forum.php??
   

-- 
--------------------------------------------------
 Cameron Mura
 Urey Hall, Rm. 4234
 Department of Chemistry & Biochemistry
 University of California, San Diego
 9500 Gilman Dr. Dept. 0365
 La Jolla, CA 92093-0365
 Email: cm...@mc...
 http://mccammon.ucsd.edu/~cmura
 Phone: 858.534.0956
 Fax:   858.534.7042
--------------------------------------------------




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This SF.net email is sponsored by: ObjectStore.
If flattening out C++ or Java code to make your application fit in a
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Now part of Progress Software. http://www.objectstore.net/sourceforge
_______________________________________________
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Hi,
I'm wondering if anyone's experienced problems with PyMOL compatibility 
with an NVidia graphics card? I ran PyMOL on a RedHat 8.0 system without 
problems, but recently changed to rh9.0(shrike), and I get the following 
lines of error when I try to run PyMOL from the prompt (and pymol 
doesn't start):

"""
CHEMCCA35:cmura[42] pymol
Traceback (most recent call last):
  File 
"/usr/lib/python2.2/site-packages/pymol/modules/pymol/__init__.py", line 
93, in ?
    import pymol
  File 
"/usr/lib/python2.2/site-packages/pymol/modules/pymol/__init__.py", line 
236, in ?
    import _cmd
ImportError: /usr/lib/libglut.so.3: undefined symbol: 
glXBindChannelToWindowSGIX
"""

Some system info.: Red Hat 9.0 (Shrike; 2.4.20-13.9smp kernel) with an 
NVidia Quadro4 700 XGL graphics card. NVidia driver info. is:
NVRM version: NVIDIA Linux x86 nvidia.o Kernel Module  1.0-4363  Sat Apr 
19 17:46:46 PDT 2003
GCC version:  gcc version 3.2.2 20030222 (Red Hat Linux 3.2.2-5)

 From the last line of the error, I suspect the problem has something to 
do with incompatibility between my rh9 installation and python 
interpreter as utilized by PyMOL? But I don't know enough to fix it....
Has anyone else seen (and fixed?) this problem??

Thanks a lot,

    Cameron



PS. How does one search through the pymol users list mail archive at 
http://sourceforge.net/mailarchive/forum.php??
   

-- 
--------------------------------------------------
 Cameron Mura
 Urey Hall, Rm. 4234
 Department of Chemistry & Biochemistry
 University of California, San Diego
 9500 Gilman Dr. Dept. 0365
 La Jolla, CA 92093-0365
 Email: cm...@mc...
 http://mccammon.ucsd.edu/~cmura
 Phone: 858.534.0956
 Fax:   858.534.7042
--------------------------------------------------

Bartholomeus,

Your question seems to be essentially the same as one asked on the ccp4bb 
last year.  Here is the answer to that question.


>Re: [ccp4bb]: Waters!
>
>--------------------------------------------------------------------------------
>
>To: ra...@po...
>Subject: Re: [ccp4bb]: Waters!
>From: "Gerard \"DVD\" Kleywegt" <ge...@xr...>
>Date: Wed, 7 Aug 2002 21:45:17 +0200 (CEST)
>cc: Gerard Kleywegt <ge...@xr...>, CCP4 Bulletin Board 
><CC...@dl...>
>In-Reply-To: 
><Pin...@po...>
>Sender: own...@dl...
>
>--------------------------------------------------------------------------------
>
>***  For details on how to be removed from this list visit the  ***
>***          CCP4 home page http://www.ccp4.ac.uk         ***
>
> > is there a program that will take a protein structure with waters and
> > give a list of the waters that are buried/ or strip of the waters on the
> > surface....
>
>maybe unexpected, but MAMA actually does this. make a
>quick and dirty mask around your molecule, expand a
>couple of times, contract a couple of times (to fill
>cavities etc) - then use the ATom_fit command; see
>http://xray.bmc.uu.se/usf/mama_man.html#S22
>
>--dvd
>
>******************************************************************
>                         Gerard J.  Kleywegt
>     [Research Fellow of the Royal  Swedish Academy of Sciences]
>Dept. of Cell & Molecular Biology  University of Uppsala
>                 Biomedical Centre  Box 596
>                 SE-751 24 Uppsala  SWEDEN
>
>     http://xray.bmc.uu.se/gerard/  mailto:ge...@xr...
>******************************************************************
>    The opinions in this message are fictional.  Any similarity
>    to actual opinions, living or dead, is purely coincidental.
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At 09:01 AM 19/05/2003, Bartholomeus Kuettner wrote:
>Dear PyMol community,
>
>During analyzing the water structure of a protein I was wondering if PyMol
>is capable to select buried water molecules. Since the surface waters occupy
>clefts it would be nice to see if there is a regular distribution inside of
>the protein as well.
>
>So is it possible to make a selection of buried water molecules?
>
>I imagine something in a way like 'water without distance to
>surface-object'. But so far I didn't have yet such a deep dive into the
>sophisticated selection capabilities of PyMol and would be lost here. The
>problem I see arising would be that the surface object is present (as
>residues) even in protein's interior and make a correct selection
>impossible.
>
>Greetings,
>Bartholomeus
>
>
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----------------------------------------------------------------------
Anthony Duff
Postdoctoral Fellow
School of Molecular and Microbial Biosciences
Biochemistry Building, G08
University of Sydney, NSW 2006 Australia
Phone. 61-2-9351-7817   Fax. 61-2-9351-4726
----------------------------------------------------------------------

Bartholemeus,

	No, there isn't any way to do this directly with the selection
language.  The closest you can get is to simply select the waters in
proximity to protein atoms.  

select close_waters, hoh/ within 3.1 of not hoh/

You could then use some external tool to calculate the SASA of these
waters to determine whether or not they are buried.

However, try the following script -- it may get close to what you want.
Note however that the van der Waals "overlap" command isn't yet
validated or documented.

# begin "buried.pml"

load $PYMOL_PATH/test/dat/1tii.pdb

hide
show sph,hoh/
show surface
set surface_color,white

/wats = map(lambda x:"%s`%d"%x,cmd.index("hoh/"))

/over = map(lambda x: \
  (cmd.overlap(x,"not hoh/",adjust=5.0),x), wats)

# least buried

color green,hoh/

/for a in filter(lambda x:x[0]>25, over): \
   cmd.color("cyan",a[1])

/for a in filter(lambda x:x[0]>50, over): \
   cmd.color("blue",a[1])

/for a in filter(lambda x:x[0]>75, over): \
   cmd.color("yellow",a[1])

# most buried

/for a in filter(lambda x:x[0]>100, over): \
   cmd.color("red",a[1])

# now show interior...

clip slab,10

# end of script

Cheers,
Warren

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

-----Original Message-----
From: pym...@li...
[mailto:pym...@li...] On Behalf Of
Bartholomeus Kuettner
Sent: Sunday, May 18, 2003 3:02 PM
To: pym...@li...
Subject: [PyMOL] select buried water molecules

Dear PyMol community,

During analyzing the water structure of a protein I was wondering if
PyMol
is capable to select buried water molecules. Since the surface waters
occupy
clefts it would be nice to see if there is a regular distribution inside
of
the protein as well.

So is it possible to make a selection of buried water molecules?

I imagine something in a way like 'water without distance to
surface-object'. But so far I didn't have yet such a deep dive into the
sophisticated selection capabilities of PyMol and would be lost here.
The
problem I see arising would be that the surface object is present (as
residues) even in protein's interior and make a correct selection
impossible.

Greetings,
Bartholomeus


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The safe answer is "no".

In truth, it is possible to get some information through the Wizard
mechanism, but the approach is complex, undocumented, and likely to
change.   

you want to use PyMOL as a front-end for PyOpenGL, the development work
to support this hasn't yet been done.  Sorry.

Cheers,
Warren

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

-----Original Message-----
From: pym...@li...
[mailto:pym...@li...] On Behalf Of Mahesh N
Sent: Sunday, May 18, 2003 8:57 PM
To: pymol user
Subject: [PyMOL] Callsbacks to mouse event

Hello All,
Is it possible to attach (python) callbacks to the mouse events occuring
in PyMol's rendering area?
Thanks!
--Mahesh N




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Yibin,

show sticks, (not name c,n,o)
show cartoon
set cartoon_smooth_loops, 0

   and perhaps

set cartoon_flat_sheets, 0

Cheers,
Warren

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

-----Original Message-----
From: pym...@li...
[mailto:pym...@li...] On Behalf Of yibin xu
Sent: Monday, May 19, 2003 11:08 PM
To: 'PyMOL list'
Subject: [PyMOL] how to show sticks for the side-chains of selected
residues



Dear All,

I want to show sticks for only side-chains (CA and beyond CA) of
selected residues in the cartoon mode. Is there an easy way to do that (
my way is to use SELECT followed by showing sc but mc atoms are still
displayed)? 
Thank you very much in advance.
Regards
yibin  



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If flattening out C++ or Java code to make your application fit in a
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Dear All,

I want to show sticks for only side-chains (CA and beyond CA) of
selected residues in the cartoon mode. Is there an easy way to do that (
my way is to use SELECT followed by showing sc but mc atoms are still
displayed)? 
Thank you very much in advance.
Regards
yibin  

Hello All
Is there a way to get an arvhive of the current snapshot of the mailing
list to the local machine?

Thanks!
--Mahesh N

Hello All,
Is it possible to attach (python) callbacks to the mouse events occuring
in PyMol's rendering area?
Thanks!
--Mahesh N

Thanks Warren!
Your suggestion worked.
Cheers!
--Mahesh N

Dear PyMol community,

During analyzing the water structure of a protein I was wondering if PyMol
is capable to select buried water molecules. Since the surface waters occupy
clefts it would be nice to see if there is a regular distribution inside of
the protein as well.

So is it possible to make a selection of buried water molecules?

I imagine something in a way like 'water without distance to
surface-object'. But so far I didn't have yet such a deep dive into the
sophisticated selection capabilities of PyMol and would be lost here. The
problem I see arising would be that the surface object is present (as
residues) even in protein's interior and make a correct selection
impossible.

Greetings,
Bartholomeus

Hi Robert,

	Actually, PDB atom ordering is deep inside the C core. I just
glanced at the code...it should be possible to add this capability, but
it is not a trivial task.  There's currently no way to force PyMOL to do
this, and it may or may not make it into the next version.

	For the time being, I can only suggest a workaround, which
requires overwriting the B-factor field:

alter all,b=ID/100.0
save test.pdb

Now you can reorder the output PDB file based on the B-factor field.  It
should be possible to write a short Python script which does this, while
at the same time renumbering the PDB.

For example:

f=open("test.pdb")
l = f.readlines()
f.close()

l = filter(lambda x:x[0:6] in ('HETATM','ATOM  '),l)
l = map(lambda x:(float(x[60:66]),x),l)
l.sort()
l = map(lambda x:x[1],l)
c=1
ll = []
for a in l:
   a = a[0:6] + "%5d"%c + a[11:]
   c = c + 1
   ll.append(a)

g=open("reorder.pdb","w")
g.write(string.join(ll,''))
g.close()
   
Cheers,
Warren

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

-----Original Message-----
From: pym...@li...
[mailto:pym...@li...] On Behalf Of Robert
Havlin
Sent: Saturday, May 17, 2003 10:26 AM
To: pym...@li...
Subject: [PyMOL] Atom Ordering when Saving

I was curious how I might prevent Pymol from re-ordering the atoms when 
saving to a pdb file.
I am using a .pml script to output a large number of peptide files for 
use in gaussian, but I need to preserve the atom
order in the output file.

I am not a python expert, but it seems like it should be in 
exporting.py..  But it is not obvious where the atom reordering is done.

Thanks,
Bob



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This SF.net email is sponsored by: If flattening out C++ or Java
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_______________________________________________
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