pymol-users — Collaborative support and tips for PyMOL users

[PyMOL] Re: mice for OSX PyMOL

[Bronwyn C. <br...@bi...>]

Whoops, I replied instead of sending to the list. Sorry Luca. Here's 
what I put anyway.
>
> And I've got myself a Kensington mouse with 5 buttons (one of them also 
> a wheel).  It's good too, although if I'd been paying for it myself I'd 
> have got something less fancy.
>
> As a welcome side effect, my wrist, upon which I've been having to wear 
> a brace for some time (since shortly after getting my first Apple 
> optical mouse in fact) while mousing, has improved considerably and I'm 
> no longer using the brace.  Maybe I should sue Apple?  Just kidding.
>
> Bronwyn
>
>
>> I use a basic Logitech 2 button + wheel mouse, and it seems to work 
>> just fine...
>> -Luca
>>
>> On Friday, September 6, 2002, at 04:29 PM, wg...@ch... 
>> wrote:
>>
>>> I've been using the commands and a lobotomized 1-button mouse.  It 
>>> would ge a great question for the pymol users email list.
>>>
>>> Anybody know of an improvement mouse-wise for OS X?
>>
> Bronwyn Carlisle
> Biochemistry Department
> University of Otago
> Dunedin
> New Zealand
>
> Tel 64 3 479 7704
>

RE: [PyMOL] Re: mice for OSX PyMOL

[Christopher Y. <chr...@ut...>]

No problems w/ Kensington Orbit mice under OS X w/ PyMol...


At 6:33 PM -0400 9/9/02, Luca Jovine wrote:
>I use a basic Logitech 2 button + wheel mouse, and it seems to work 
>just fine...
>-Luca
>
>On Friday, September 6, 2002, at 04:29 PM, wg...@ch... wrote:
>
>>I've been using the commands and a lobotomized 1-button mouse.  It 
>>would ge a great question for the pymol users email list.
>>
>>Anybody know of an improvement mouse-wise for OS X?
>
>--------------------------------------------------------
>Luca Jovine, Ph.D.
>Department of Molecular, Cell & Developmental Biology
>Mount Sinai School of Medicine
>Annenberg Building, Room 25-18
>One Gustave L. Levy Place, New York, NY 10029-6574, USA
>Voice: +1.212.241-8620  FAX: +1.509.356-2832
>E-Mail: luc...@ma...
>W3: http://www.mssm.edu/students/jovinl02
>--------------------------------------------------------
>

-- 
Christopher M. Yip, Ph.D., P.Eng.
Associate Professor
Department of Chemical Engineering and Applied Chemistry
Institute of Biomaterials and Biomedical Engineering
Department of Biochemistry
University of Toronto
407 Rosebrugh Building, 4 Taddle Creek Rd.
Toronto, Ontario CANADA M5S 3G9
Office:(416) 978-7853; Lab:(416) 946-5022; Fax: (416) 978-4317;
e-mail: chr...@ut...
WWW: http://bigten.ibme.utoronto.ca

RE: [PyMOL] Re: mice for OSX PyMOL

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

I use a basic Logitech 2 button + wheel mouse, and it seems to work just 
fine...
-Luca

On Friday, September 6, 2002, at 04:29 PM, wg...@ch... 
wrote:

> I've been using the commands and a lobotomized 1-button mouse.  It would 
> ge a great question for the pymol users email list.
>
> Anybody know of an improvement mouse-wise for OS X?

--------------------------------------------------------
Luca Jovine, Ph.D.
Department of Molecular, Cell & Developmental Biology
Mount Sinai School of Medicine
Annenberg Building, Room 25-18
One Gustave L. Levy Place, New York, NY 10029-6574, USA
Voice: +1.212.241-8620  FAX: +1.509.356-2832
E-Mail: luc...@ma...
W3: http://www.mssm.edu/students/jovinl02
--------------------------------------------------------

RE: [PyMOL] Re: Amber

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

Michael,

	None of the official releases have Amber trajectory support (although =
the mac 0.84 beta may have an early version of this code).  I'm planning =
on another release near the end of September.

If you can build from the CVS repository, then you can use the code =
today:

(1) make sure that your trajectory and topology files have the same =
prefix and end in .top and .trj respectively.  Also make sure that your =
topology exactly corresponds to the trajectory file (you may need to =
create a new topology file if you've deleted some atoms from the =
trajectory).

(2) Now load them:

load parm.top
load_traj parm.trj

help load_traj

has some additional options, such as start, stop, average, interval, =
selection...

So long as trajectories are generated from the same topology, you can =
concatentate them as follows:

load_traj part1.trj,parm
load_tram part2.trj,parm
load_traj part3.trj,parm

For now, you'll probably want to preprocess your trajectory using ptraj =
in order to center, average, and perhaps to remove waters.  And you'll =
need to create a new topology file reflecting any atom deletions.  Tom =
Cheatham and I are talking about trying to fold a copy of ptraj into =
PyMOL, but don't have any definite plans yet.

Cheers,
Warren

--
mailto:wa...@su...
Warren L. DeLano, Ph.D.
Informatics Manager
Sunesis Pharmaceuticals, Inc.
341 Oyster Point Blvd.
S. San Francisco, CA 94080
(650)-266-3606  FAX:(650)-266-3501

[PyMOL] Re: PyMOL-users digest, Vol 1 #158 - 2 msgs

[Michael F. <mf...@cc...>]

I know there has been some work done on using AMBER trajectories with PyMol.
Any pointers???



Mike Ford

pym...@li... wrote:

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>
> Today's Topics:
>
>    1. PyMOL input for the Mac and movie question (Scott Classen)
>    2. RE: PyMOL input for the Mac and movie question (DeLano, Warren)
>
> --__--__--
>
> Message: 1
> Date: Mon, 9 Sep 2002 10:46:05 -0700
> From: Scott Classen <cl...@uc...>
> To: pym...@li...
> Subject: [PyMOL] PyMOL input for the Mac and movie question
>
> Mac PyMOL users
> A lab mate has a Microsoft 3 button optical mouse so I tried it out on
> my G3 powerbook  and it works very well with PyMOL. Yeah!!! I guess I'll
> have to but a mouse.
>
> OK I am now trying to make a movie and I have a question
> I start the movie out like this:
>
> mset 1 x72
> mdo 1: turn x,5; turn y,5
> mdo 2: turn x,5; turn y,5
> mdo 3: turn x,5; turn y,5
> mdo 4: turn x,5; turn y,5
> mdo 5: turn x,5; turn y,5
> etc
> etc
>
> So I've made a 72 frame movie with 5 degree rotations about the x and y
> axes. If I'm thinking about this properly the molecule should be in the
> exact same orientation at the end of the movie (i.e. 72x5=360degrees)
> however this is not the case. Why?
>
> Warren,
>         could you make available the script you used to make the lambda
> demo movie that came with PyMOL? This would help greatly with my
> understanding of how to do more complicated motions in PyMOL.
>
> Thanks,
> Scott
>
> ==============================================
>    Scott Classen
>    cl...@uc...
>    University of California, Berkeley
>    Department of Molecular & Cell Biology
>    229 Stanley Hall #3206
>    Berkeley, CA 94720-3206
>    LAB 510.643.9491
>    FAX 510.643.9290
> ==============================================
>
> --__--__--
>
> Message: 2
> Subject: RE: [PyMOL] PyMOL input for the Mac and movie question
> Date: Mon, 9 Sep 2002 10:57:10 -0700
> From: "DeLano, Warren" <wa...@su...>
> To: "Scott Classen" <cl...@uc...>,
>         <pym...@li...>
>
> Scott,
>
> > From: Scott Classen [mailto:cl...@uc...]
>
> > OK I am now trying to make a movie and I have a question
> > I start the movie out like this:
> >=20
> > mset 1 x72
> > mdo 1: turn x,5; turn y,5
> > mdo 2: turn x,5; turn y,5
> > mdo 3: turn x,5; turn y,5
> > mdo 4: turn x,5; turn y,5
> > mdo 5: turn x,5; turn y,5
> > etc
> > etc
> >=20
>
> > So I've made a 72 frame movie with 5 degree rotations about=20
> > the x and y=20
> > axes. If I'm thinking about this properly the molecule should=20
> > be in the=20
> > exact same orientation at the end of the movie (i.e. =
> 72x5=3D360degrees)=20
> > however this is not the case. Why?
>
> No it won't because you're not rotating 360 degress.  Instead, you're =
> splitting 720 degrees of rotation about two axes which are constantly =
> changing (relative to original orientation).
>
> Try this instead:
>
> mset 1 x72
> movie.nutate 1,72,20
>
> >=20
> > Warren,
> >       could you make available the script you used to make the lambda=20
> > demo movie that came with PyMOL? This would help greatly with my=20
> > understanding of how to do more complicated motions in PyMOL.
> >=20
>
> On the mac version (only?) I think it can be found in =
> examples/devel/D01lambda.py (or something similar).
>
> Cheers,
> Warren
>
> --__--__--
>
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>
> End of PyMOL-users Digest

RE: [PyMOL] PyMOL input for the Mac and movie question

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

Scott,

> From: Scott Classen [mailto:cl...@uc...]

> OK I am now trying to make a movie and I have a question
> I start the movie out like this:
>=20
> mset 1 x72
> mdo 1: turn x,5; turn y,5
> mdo 2: turn x,5; turn y,5
> mdo 3: turn x,5; turn y,5
> mdo 4: turn x,5; turn y,5
> mdo 5: turn x,5; turn y,5
> etc
> etc
>=20

> So I've made a 72 frame movie with 5 degree rotations about=20
> the x and y=20
> axes. If I'm thinking about this properly the molecule should=20
> be in the=20
> exact same orientation at the end of the movie (i.e. =
72x5=3D360degrees)=20
> however this is not the case. Why?

No it won't because you're not rotating 360 degress.  Instead, you're =
splitting 720 degrees of rotation about two axes which are constantly =
changing (relative to original orientation).

Try this instead:

mset 1 x72
movie.nutate 1,72,20

>=20
> Warren,
> 	could you make available the script you used to make the lambda=20
> demo movie that came with PyMOL? This would help greatly with my=20
> understanding of how to do more complicated motions in PyMOL.
>=20

On the mac version (only?) I think it can be found in =
examples/devel/D01lambda.py (or something similar).

Cheers,
Warren

[PyMOL] PyMOL input for the Mac and movie question

[Scott C. <cl...@uc...>]

Mac PyMOL users
A lab mate has a Microsoft 3 button optical mouse so I tried it out on 
my G3 powerbook  and it works very well with PyMOL. Yeah!!! I guess I'll 
have to but a mouse.


OK I am now trying to make a movie and I have a question
I start the movie out like this:

mset 1 x72
mdo 1: turn x,5; turn y,5
mdo 2: turn x,5; turn y,5
mdo 3: turn x,5; turn y,5
mdo 4: turn x,5; turn y,5
mdo 5: turn x,5; turn y,5
etc
etc

So I've made a 72 frame movie with 5 degree rotations about the x and y 
axes. If I'm thinking about this properly the molecule should be in the 
exact same orientation at the end of the movie (i.e. 72x5=360degrees) 
however this is not the case. Why?

Warren,
	could you make available the script you used to make the lambda 
demo movie that came with PyMOL? This would help greatly with my 
understanding of how to do more complicated motions in PyMOL.

Thanks,
Scott



==============================================
   Scott Classen
   cl...@uc...
   University of California, Berkeley
   Department of Molecular & Cell Biology
   229 Stanley Hall #3206
   Berkeley, CA 94720-3206
   LAB 510.643.9491
   FAX 510.643.9290
==============================================

[PyMOL] Accessing pymol OpenGL functionality from C/SDL

[Gib B. <bo...@ih...>]

Hi,

I'm not a chemist, but I love the molecular imagery that pymol creates. 
I am developing a program that generates a wide variety of graphical
effects, and I'd really like to be able to add molecular fly-throughs to
the menu.  My code is based on SDL, and I'm using OpenGL for all display
functions.  The end use will be in rather non-scientific settings (e.g.
dance clubs), but I'm very keen to incorporate scientific imagery of all
kinds.

I'm wondering if (with a bit of surgery) I'd be able to get access to
the lower-level functionality of pymol, by which I mean the file I/O and
rendering functions.  I will not want to use the GUI at all.  SDL would
create the surface(s), and handle the buffer swapping.  My goal is to be
able to send a request to the pymol API asking for a frustum view to be
rendered on the provided surface.

Am I dreaming?

Gib

[PyMOL] Re: PyMOL input

[<wg...@ch...>]

I've been using the commands and a lobotomized 1-button mouse.  It would 
ge a great question for the pymol users email list.

Anybody know of an improvement mouse-wise for OS X?


On Friday, September 6, 2002, at 12:31 PM, Scott Classen wrote:

> Dr. Scott
> 	I just installed the OSX version of PyMOL and I think it will be 
> very useful if I can figure out how to zoom, pan, rotate like I can in 
> O. Warren recommends a 3 button mouse. So what do Mac users do? What do 
> you do? I have been able to zoom in and out using the move z,100 comand 
> but his is a bit awkward.
> Thanks,
> Scott
>
> ==============================================
>   Scott Classen
>   cl...@uc...
>   University of California, Berkeley
>   Department of Molecular & Cell Biology
>   229 Stanley Hall #3206
>   Berkeley, CA 94720-3206
>   LAB 510.643.9491
>   FAX 510.643.9290
> ==============================================
>
>
>
William G. Scott

Associate Professor
Department of Chemistry and Biochemistry
and The Center for the Molecular Biology of RNA
Sinsheimer Laboratories
University of California at Santa Cruz
Santa Cruz, California 95064
USA

phone:  +1-831-459-5367 (office)
                +1-831-459-5292 (lab)
fax:         +1-831-4593139  (fax)

-----BEGIN GEEK CODE BLOCK-----
Version: 3.12
GS dpu s:+ a C--- U*--- P+ L+ E--- W-- N o-- K- w--
O- M+ V- PS+++ PE-- Y+ PGP-- t- 5- X R* tv-- b+++ DI++ D----
G-- e++++ h---- r+++ y++++
------END GEEK CODE BLOCK------

Re: [PyMOL] Reading CCP4 maps

[Quyen H. <ho...@mc...>]

I would like to express my appreciation for all the responses to my
question, they were exactly what I was looking for!

Thank you!

Regards,
Quyen

_______________________________
Quyen Hoang
McMaster University
Department of Biochemistry
Health Science Centre Room 4H31
1200 Main Street West
Hamilton, Ontario. L8S 4L8
CANADA
Phone: (905)525-9140 ext: 22457
*********Bad to the Bone********

Re: [PyMOL] Reading CCP4 maps

[Gareth S. <ga...@eb...>]

One other thing - 

PyMOL has a flag which determines whether the density values will be 
normalised - if this flag is not set, then

	isomesh mesh_name, map_name, 1

will contour the map at 1-sigma; to contour at an absolute value, you must 
do
	
	set normalize_ccp4_maps=0

BEFORE loading the map.  If the flag is set, the program will print some
information about the calculated mean and std deviation when you load a
map.  Commonly-used settings like this can be put in your ~/.pymolrc file
(at least on a UNIX system), so that they are executed whenever PyMOL
starts up.

Gareth



-------------------------------------------------------------------------------
 Gareth Stockwell
 EMBL - European Bioinformatics Institute
 Wellcome Trust Genome Campus
 Hinxton
 Cambridge CB10 1SD                                         ga...@eb...
 Tel 01223 492548                               http://www.ebi.ac.uk/~gareth

Re: [PyMOL] Reading CCP4 maps

[Nigel M. <a_...@at...>]

You can also type

help load

into either window for similar info.

Nigel
----- Original Message -----
From: "Robert Campbell" <rl...@k2...>
To: <pym...@li...>
Sent: Thursday, September 05, 2002 12:47 PM
Subject: Re: [PyMOL] Reading CCP4 maps


> Quyen,
>
> * Quyen Hoang <ho...@mc...> [2002-09-05 15:32] wrote:
> > I would like to read CCP4 electron-density maps into PyMol, but I don't
> > know how (explore maps loaded fine). Would someone please give me a
quick
> > summary of the procedure.
> > Thank you!
>
> simply doing:
>
>   load mapfile.ccp4, map_object_name
>
> will load the map, but if the filename doesn't end in '.ccp4', then you'll
> need to specify that it is CCP4 format with something like:
>
>   load mapfile.ccp4_map, map_object_name, 1, ccp4
>
> Then you'll want to display it with a similar sort of isomesh command
> that you would have used for the xplor map.
>
>   isomesh mesh_object_name, map_object_name, contour level, selection,
radius
>
> The on-line manual describes this pretty clearly (in fact, probably
> better than I have!):
>
>   http://pymol.sourceforge.net/html/S0400xtal.html
>
> Cheers,
> Robert
> --
> Robert L. Campbell, Ph.D.               http://biophysics.med.jhmi.edu/rlc
> rl...@k2...                                    phone: 410-614-6313
> Research Specialist/X-ray Facility Manager
> HHMI/Dept. of Biophysics & Biophysical Chem., The Johns Hopkins University
>     PGP Fingerprint: 9B49 3D3F A489 05DC B35C  8E33 F238 A8F5 F635 C0E2
>
>
> -------------------------------------------------------
> This sf.net email is sponsored by: OSDN - Tired of that same old
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> PyM...@li...
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Re: [PyMOL] Reading CCP4 maps

[Robert C. <rl...@k2...>]

Quyen,

* Quyen Hoang <ho...@mc...> [2002-09-05 15:32] wrote:
> I would like to read CCP4 electron-density maps into PyMol, but I don't
> know how (explore maps loaded fine). Would someone please give me a quick
> summary of the procedure.
> Thank you!

simply doing:

  load mapfile.ccp4, map_object_name

will load the map, but if the filename doesn't end in '.ccp4', then you'll
need to specify that it is CCP4 format with something like:

  load mapfile.ccp4_map, map_object_name, 1, ccp4

Then you'll want to display it with a similar sort of isomesh command
that you would have used for the xplor map.

  isomesh mesh_object_name, map_object_name, contour level, selection, radius

The on-line manual describes this pretty clearly (in fact, probably
better than I have!):

  http://pymol.sourceforge.net/html/S0400xtal.html

Cheers,
Robert
-- 
Robert L. Campbell, Ph.D.               http://biophysics.med.jhmi.edu/rlc
rl...@k2...                                    phone: 410-614-6313
Research Specialist/X-ray Facility Manager
HHMI/Dept. of Biophysics & Biophysical Chem., The Johns Hopkins University
    PGP Fingerprint: 9B49 3D3F A489 05DC B35C  8E33 F238 A8F5 F635 C0E2

[PyMOL] electron density in plane

[David <sp...@xr...>]

Hi,

I would like to do the following: define a plane, e.g. the center of the
clipping volume/slab (which probably is already defined somewhere), and
colour it according to electron density, if possible transparent. 
So one would have to make an intersection of the clipping plane with the
electron density and define a 2D grid on that plane, which then is
coloured from black to something according to the electron density.

I checked some of the modules and it seems that the density is now
stored as a linear array, which is not a problem. However, the graphics
may be less trivial, it is basically a (flat) surface with different
colours.

Any pointers would be appreciated.

-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
sp...@xr...	sp...@gr...   http://zorn.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

[PyMOL] Reading CCP4 maps

[Quyen H. <ho...@mc...>]

Hi,
I would like to read CCP4 electron-density maps into PyMol, but I don't
know how (explore maps loaded fine). Would someone please give me a quick
summary of the procedure.
Thank you!

Regards,
Quyen

_______________________________
Quyen Hoang
McMaster University
Department of Biochemistry
Health Science Centre Room 4H31
1200 Main Street West
Hamilton, Ontario. L8S 4L8
CANADA
Phone: (905)525-9140 ext: 22457
*********Bad to the Bone********

[PyMOL] coloring objects

[Michael F. <mf...@cc...>]

I really like this program (trying to wean myself from InsightII), but I'm
still working a few things out:

When I color objects, they seem to get a colored, but it is 'hidden' by the
cpk coloring initially assigned.  I've tried several things, but no luck.



Mike Ford

pym...@li... wrote:

> Send PyMOL-users mailing list submissions to
>         pym...@li...
>
> To subscribe or unsubscribe via the World Wide Web, visit
>         https://lists.sourceforge.net/lists/listinfo/pymol-users
> or, via email, send a message with subject or body 'help' to
>         pym...@li...
>
> You can reach the person managing the list at
>         pym...@li...
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of PyMOL-users digest..."
>
> Today's Topics:
>
>    1. Question on clipping with surfaces (Timothy Moore)
>    2. Re: Question on clipping with surfaces (Warren L. DeLano 1)
>
> --__--__--
>
> Message: 1
> Date: Wed, 04 Sep 2002 14:56:42 +0100
> From: "Timothy Moore" <mr...@no...>
> To: <pym...@li...>
> Subject: [PyMOL] Question on clipping with surfaces
>
> Hello all,
>
> I don't know whether this has been covered before but I have some
> questions on clipping whilst using surfaces. Before I go on I will state
> that pymol produces the best surfaces for my purposes, of any program I
> have seen so far. However, (sorry there is always room to be better! ;)
> ) the ideal situation would be if the cut "surface" was represented as
> if the molecule was solid. ie: you didn't see inside the molecule
> itself, but the cut plane. Is there any way to do this (e.g. via povray
> rendering)? I appreciate it is probably not exactly easy though.
>
> Alternatively, it would be good if it was possible to make the inside
> surface of a molecule appear completely black without resorting to
> ambient=0.
>
> Any ideas?
>
> Tim
>
> --__--__--
>
> Message: 2
> Date: Wed, 4 Sep 2002 07:45:09 -0700 (PDT)
> From: "Warren L. DeLano 1" <wa...@su...>
> To: Timothy Moore <mr...@no...>
> cc:  <pym...@li...>
> Subject: Re: [PyMOL] Question on clipping with surfaces
>
> On Wed, 4 Sep 2002, Timothy Moore wrote:
>
> > I don't know whether this has been covered before but I have some
> > questions on clipping whilst using surfaces. Before I go on I will state
> > that pymol produces the best surfaces for my purposes, of any program I
> > have seen so far. However, (sorry there is always room to be better! ;)
> > ) the ideal situation would be if the cut "surface" was represented as
> > if the molecule was solid. ie: you didn't see inside the molecule
> > itself, but the cut plane. Is there any way to do this (e.g. via povray
> > rendering)? I appreciate it is probably not exactly easy though.
> >
> > Alternatively, it would be good if it was possible to make the inside
> > surface of a molecule appear completely black without resorting to
> > ambient=0.
>
> Tim,
>
>    What you're asking for is mathematically non-trivial.  In fact, I
> haven't even solved this problem for spheres yet in the raytracer.
>
>    As far as I can tell, setting ambient to zero alone doesn't quite do
> the job, since some triangles still get lit by the light source.
>
>    The best combination I can find is:
>
> set ambient=0
> set direct=0.7
> set reflect=0.0
> set backface_cull=0
>
>    While gives no shadows an only a few artifacts.
>
>    As an alternative, you might just consider showing the inside of the
> surface directly...that will create less visual artifacts, and so long as
> ambient and direct are sufficiently low, it will look reasonable in "ray".
>
> util.ray_shadows("heavy")
> set two_sided_lighting=1
> set backface_cull=0
>
> Cheers,
> Warren
>
> --__--__--
>
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>
> End of PyMOL-users Digest

[PyMOL] measuring angles and distances

[Michael F. <mf...@cc...>]

How do I measure angles and distances in pymol???


Michael Ford



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> Today's Topics:
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>    1. Question on clipping with surfaces (Timothy Moore)
>    2. Re: Question on clipping with surfaces (Warren L. DeLano 1)
>
> --__--__--
>
> Message: 1
> Date: Wed, 04 Sep 2002 14:56:42 +0100
> From: "Timothy Moore" <mr...@no...>
> To: <pym...@li...>
> Subject: [PyMOL] Question on clipping with surfaces
>
> Hello all,
>
> I don't know whether this has been covered before but I have some
> questions on clipping whilst using surfaces. Before I go on I will state
> that pymol produces the best surfaces for my purposes, of any program I
> have seen so far. However, (sorry there is always room to be better! ;)
> ) the ideal situation would be if the cut "surface" was represented as
> if the molecule was solid. ie: you didn't see inside the molecule
> itself, but the cut plane. Is there any way to do this (e.g. via povray
> rendering)? I appreciate it is probably not exactly easy though.
>
> Alternatively, it would be good if it was possible to make the inside
> surface of a molecule appear completely black without resorting to
> ambient=0.
>
> Any ideas?
>
> Tim
>
> --__--__--
>
> Message: 2
> Date: Wed, 4 Sep 2002 07:45:09 -0700 (PDT)
> From: "Warren L. DeLano 1" <wa...@su...>
> To: Timothy Moore <mr...@no...>
> cc:  <pym...@li...>
> Subject: Re: [PyMOL] Question on clipping with surfaces
>
> On Wed, 4 Sep 2002, Timothy Moore wrote:
>
> > I don't know whether this has been covered before but I have some
> > questions on clipping whilst using surfaces. Before I go on I will state
> > that pymol produces the best surfaces for my purposes, of any program I
> > have seen so far. However, (sorry there is always room to be better! ;)
> > ) the ideal situation would be if the cut "surface" was represented as
> > if the molecule was solid. ie: you didn't see inside the molecule
> > itself, but the cut plane. Is there any way to do this (e.g. via povray
> > rendering)? I appreciate it is probably not exactly easy though.
> >
> > Alternatively, it would be good if it was possible to make the inside
> > surface of a molecule appear completely black without resorting to
> > ambient=0.
>
> Tim,
>
>    What you're asking for is mathematically non-trivial.  In fact, I
> haven't even solved this problem for spheres yet in the raytracer.
>
>    As far as I can tell, setting ambient to zero alone doesn't quite do
> the job, since some triangles still get lit by the light source.
>
>    The best combination I can find is:
>
> set ambient=0
> set direct=0.7
> set reflect=0.0
> set backface_cull=0
>
>    While gives no shadows an only a few artifacts.
>
>    As an alternative, you might just consider showing the inside of the
> surface directly...that will create less visual artifacts, and so long as
> ambient and direct are sufficiently low, it will look reasonable in "ray".
>
> util.ray_shadows("heavy")
> set two_sided_lighting=1
> set backface_cull=0
>
> Cheers,
> Warren
>
> --__--__--
>
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> End of PyMOL-users Digest

Re: [PyMOL] Question on clipping with surfaces

[Warren L. D. 1 <wa...@su...>]

On Wed, 4 Sep 2002, Timothy Moore wrote:

> I don't know whether this has been covered before but I have some
> questions on clipping whilst using surfaces. Before I go on I will state
> that pymol produces the best surfaces for my purposes, of any program I
> have seen so far. However, (sorry there is always room to be better! ;)
> ) the ideal situation would be if the cut "surface" was represented as
> if the molecule was solid. ie: you didn't see inside the molecule
> itself, but the cut plane. Is there any way to do this (e.g. via povray
> rendering)? I appreciate it is probably not exactly easy though.
>
> Alternatively, it would be good if it was possible to make the inside
> surface of a molecule appear completely black without resorting to
> ambient=0.

Tim,

   What you're asking for is mathematically non-trivial.  In fact, I
haven't even solved this problem for spheres yet in the raytracer.

   As far as I can tell, setting ambient to zero alone doesn't quite do
the job, since some triangles still get lit by the light source.

   The best combination I can find is:

set ambient=0
set direct=0.7
set reflect=0.0
set backface_cull=0

   While gives no shadows an only a few artifacts.

   As an alternative, you might just consider showing the inside of the
surface directly...that will create less visual artifacts, and so long as
ambient and direct are sufficiently low, it will look reasonable in "ray".

util.ray_shadows("heavy")
set two_sided_lighting=1
set backface_cull=0

Cheers,
Warren

[PyMOL] Question on clipping with surfaces

[Timothy M. <mr...@no...>]

Hello all,

I don't know whether this has been covered before but I have some
questions on clipping whilst using surfaces. Before I go on I will state
that pymol produces the best surfaces for my purposes, of any program I
have seen so far. However, (sorry there is always room to be better! ;)
) the ideal situation would be if the cut "surface" was represented as
if the molecule was solid. ie: you didn't see inside the molecule
itself, but the cut plane. Is there any way to do this (e.g. via povray
rendering)? I appreciate it is probably not exactly easy though.

Alternatively, it would be good if it was possible to make the inside
surface of a molecule appear completely black without resorting to
ambient=0.

Any ideas?

Tim

Re: [PyMOL] OS X pymol version 0.84beta is excellent. Thank you!!!

[<wg...@ch...>]

I've put a screen-shot here if anyone wants to have a look.  
http://chemistry.ucsc.edu/~wgscott/xtal/page6.html
Hopefully this will generate a little free publicity...


On Monday, September 2, 2002, at 08:02 PM, Bronwyn Carlisle wrote:

> I second that motion.  Very nice.
>
> Thank-you
>
> Bronwyn
>
> On Tuesday, September 3, 2002, at 02:49  PM, wg...@ch... 
> wrote:
>
>> I just noticed the OS X pymol native update, downloaded and installed 
>> it and it is great.  It also makes me think that one day I might even 
>> install OS 10.2....(there was no reason to if pymol didn't work).
>>
>> Nice job Warren!
>>
>> Thanks.
>>
>> Bill Scott
>>
William G. Scott

Associate Professor
Department of Chemistry and Biochemistry
and The Center for the Molecular Biology of RNA
Sinsheimer Laboratories
University of California at Santa Cruz
Santa Cruz, California 95064
USA

phone:  +1-831-459-5367 (office)
                +1-831-459-5292 (lab)
fax:         +1-831-4593139  (fax)

-----BEGIN GEEK CODE BLOCK-----
Version: 3.12
GS dpu s:+ a C--- U*--- P+ L+ E--- W-- N o-- K- w--
O- M+ V- PS+++ PE-- Y+ PGP-- t- 5- X R* tv-- b+++ DI++ D----
G-- e++++ h---- r+++ y++++
------END GEEK CODE BLOCK------

>> -------------------------------------------------------
>> This sf.net email is sponsored by: OSDN - Tired of that same old
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>>
> Bronwyn Carlisle
> Biochemistry Department
> University of Otago
> Dunedin
> New Zealand
>
> Tel 64 3 479 7704
>
>

Re: [PyMOL] OS X pymol version 0.84beta is excellent. Thank you!!!

[Christopher Y. <chr...@ut...>]

At 7:49 PM -0700 9/2/02, wg...@ch... wrote:
>I just noticed the OS X pymol native update, downloaded and 
>installed it and it is great.  It also makes me think that one day I 
>might even install OS 10.2....(there was no reason to if pymol 
>didn't work).
>
>Nice job Warren!
>
>Thanks.
>
>
>Bill Scott
>
>William G. Scott
>


I'll echo both of Bill's comments - I too just installed the beta 
version of PyMol and it looks great - I have Jaguar but was holding 
off until everything I wanted to run under 10.2 worked - and it would 
appear that "O" has also got a fix in place as of today for 10.2's 
minor conniptions re: the terminal windows...

Just installed that too

Chris
-- 
Christopher M. Yip, Ph.D., P.Eng.
Associate Professor
Department of Chemical Engineering and Applied Chemistry
Institute of Biomaterials and Biomedical Engineering
Department of Biochemistry
University of Toronto
407 Rosebrugh Building, 4 Taddle Creek Rd.
Toronto, Ontario CANADA M5S 3G9
Office:(416) 978-7853; Lab:(416) 946-5022; Fax: (416) 978-4317;
e-mail: chr...@ut...
WWW: http://bigten.ibme.utoronto.ca

[PyMOL] OS X pymol version 0.84beta is excellent. Thank you!!!

[<wg...@ch...>]

I just noticed the OS X pymol native update, downloaded and installed it 
and it is great.  It also makes me think that one day I might even 
install OS 10.2....(there was no reason to if pymol didn't work).

Nice job Warren!

Thanks.


Bill Scott

William G. Scott

Associate Professor
Department of Chemistry and Biochemistry
and The Center for the Molecular Biology of RNA
Sinsheimer Laboratories
University of California at Santa Cruz
Santa Cruz, California 95064
USA

phone:  +1-831-459-5367 (office)
                +1-831-459-5292 (lab)
fax:         +1-831-4593139  (fax)

-----BEGIN GEEK CODE BLOCK-----
Version: 3.12
GS dpu s:+ a C--- U*--- P+ L+ E--- W-- N o-- K- w--
O- M+ V- PS+++ PE-- Y+ PGP-- t- 5- X R* tv-- b+++ DI++ D----
G-- e++++ h---- r+++ y++++
------END GEEK CODE BLOCK------

[PyMOL] New Mac OSX Beta Release

[Warren L. D. 1 <wa...@su...>]

On Mon, 2 Sep 2002 NKS...@lb... wrote:

> An appropriate U.S. Labor Day announcement as we remember the hard work
> Warren has put into PyMOL.

Thanks! and there still quite a lot to do...

...such as pushing out a new native Mac OSX beta release:

Version 0.84beta is a follow-on to the limited test release from early
summer.  It is still not a complete version of PyMOL, but it is getting
better.

And, this version seems to work fine on MacOS 10.2

http://pymol.sf.net

Enjoy,
Warren

[PyMOL] iPyMOL announcement

[<NKS...@lb...>]

An appropriate U.S. Labor Day announcement as we remember the hard work 
Warren has put into PyMOL. 

Good luck with iPyMOL.

Nick Sauter
Lawrence Berkeley National Laboratory

[PyMOL] INCENTIVIZE ?!

[Luke R. <lr...@ms...>]

Warren,

   You have clearly been working too hard - incentivize?  And all CAPS,
too.

   I hope I'm not alone in trying to _disincent_ you from using such a
word, the horror of which was totally unanticipated by me.

Happy Labor Day!  

Luke