pymol-users Mailing List for PyMOL Molecular Graphics System

Molecular (a discrete approximation to the Connolly surface).
 
--
mailto:wa...@de...
Warren L. DeLano, Ph.D. 
Principal
DeLano Scientific LLC
Voice (650)-346-1154 
Fax   (650)-593-4020

-----Original Message-----
From: pym...@li...
[mailto:pym...@li...] On Behalf Of Dennis
Wolan
Sent: Tuesday, April 29, 2003 2:42 PM
To: pym...@li...
Subject: [PyMOL] surface

Dear all,

This has probably been asked a thousand times, but is the default
surface representation a molecular surface or a solvent accessible
surface? 

Thanks in advance,

Dennis

(sorry, bad day continues)

fixed type in the sample usage:

# first, load the function from a .py file

run turn_y_light.py

# now use it...

turn y,3
turn_y_light(3)
ray
png image1.png

turn y,-6
turn_y_light(-6)
ray
png image2.png

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

-----Original Message-----
From: pym...@li...
[mailto:pym...@li...] On Behalf Of Warren L.
DeLano
Sent: Wednesday, April 30, 2003 1:54 PM
To: 'Anthony Duff'; pym...@li...
Cc: f.H...@ch...
Subject: RE: [PyMOL] RE: Stereo pictures, light vector and shadows

Yep, I blew it -- neglected to check my work.  Scratch all of my
previous emails on the subject.

The following function (turn_y_light.py) will correctly rotate the light
in order to offset the effect of "turn y,#"

def turn_y_light(rot):
   # assuming "rot" has angle in degrees
   rot_rad = math.pi*rot/180.0 
   (X0,Y0,Z0)=cmd.get_setting_tuple("light")[1]
   X1= X0*math.cos(rot_rad) + Z0*math.sin(rot_rad)
   Y1= Y0
   Z1= Z0*math.cos(rot_rad) - X0*math.sin(rot_rad)
   cmd.set("light",[X1,Y1,Z1])

sample usage:

# first, load the function from a .py file

run turn_y_light.py

# now use it...

turn y,3
turn_y_list(3)
ray
png image1.png

turn y,-6
turn_y_light(-6)
ray
png image2.png

Sorry for the confusion!  

Warren

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

-----Original Message-----
From: pym...@li...
[mailto:pym...@li...] On Behalf Of Anthony
Duff
Sent: Tuesday, April 29, 2003 9:08 PM
To: pym...@li...
Subject: Re: [PyMOL] RE: Stereo pictures, light vector and shadows


Warren's script is not quite right.  The value -0.902 is not correct.
Apparently, my picture, with a stick peptide casting a shadow on the
inner 
surface of a deep crevice, is particularly demanding.

I have done the vector calculations.  See the attached excel worksheet
for 
light vectors for any desired stereo angle.

I am using the script below.  It produces perfect shadows and
reflections.


turn y, 3
set light=[-0.43709,-0.34800,-0.82937]
ray 1120,818
png image.l.png

turn y, -6
set light=[-0.34800,-0.34800,-0.87051]
ray 1120,818
png image.r.png



Anthony



At 05:10 AM 24/04/2003, Warren L. DeLano wrote:


>In the script I just posted, I used unit vectors to specify the light
>direction and simply rotated that vector by 6 degrees.  The first
vector
>is merely [-0.4,-0.4,-1.0] normalized.  The second is that same vector
>rotated 6 degrees about the Y axis.
>
>I then loaded the output into Illustrator and was able to view both
>cross-eye and wall-eye stereo pairs with clean shadows.
>
>
> >
> > Try using this sequence to create your stereo pair:
> >
> > set light=[-0.348,-0.348,-0.870]
> > ray
> > png image1.png
> > turn y,6
> > set light=[-0.437,-0.348,-0.902]
> > ray
> > png image2.png
> > turn y,-6
> >
> > Cheers,
> > Warren

----------------------------------------------------------------------
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
----------------------------------------------------------------------



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Yep, I blew it -- neglected to check my work.  Scratch all of my
previous emails on the subject.

The following function (turn_y_light.py) will correctly rotate the light
in order to offset the effect of "turn y,#"

def turn_y_light(rot):
   # assuming "rot" has angle in degrees
   rot_rad = math.pi*rot/180.0 
   (X0,Y0,Z0)=cmd.get_setting_tuple("light")[1]
   X1= X0*math.cos(rot_rad) + Z0*math.sin(rot_rad)
   Y1= Y0
   Z1= Z0*math.cos(rot_rad) - X0*math.sin(rot_rad)
   cmd.set("light",[X1,Y1,Z1])

sample usage:

# first, load the function from a .py file

run turn_y_light.py

# now use it...

turn y,3
turn_y_list(3)
ray
png image1.png

turn y,-6
turn_y_light(-6)
ray
png image2.png

Sorry for the confusion!  

Warren

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

-----Original Message-----
From: pym...@li...
[mailto:pym...@li...] On Behalf Of Anthony
Duff
Sent: Tuesday, April 29, 2003 9:08 PM
To: pym...@li...
Subject: Re: [PyMOL] RE: Stereo pictures, light vector and shadows


Warren's script is not quite right.  The value -0.902 is not correct.
Apparently, my picture, with a stick peptide casting a shadow on the
inner 
surface of a deep crevice, is particularly demanding.

I have done the vector calculations.  See the attached excel worksheet
for 
light vectors for any desired stereo angle.

I am using the script below.  It produces perfect shadows and
reflections.


turn y, 3
set light=[-0.43709,-0.34800,-0.82937]
ray 1120,818
png image.l.png

turn y, -6
set light=[-0.34800,-0.34800,-0.87051]
ray 1120,818
png image.r.png



Anthony



At 05:10 AM 24/04/2003, Warren L. DeLano wrote:


>In the script I just posted, I used unit vectors to specify the light
>direction and simply rotated that vector by 6 degrees.  The first
vector
>is merely [-0.4,-0.4,-1.0] normalized.  The second is that same vector
>rotated 6 degrees about the Y axis.
>
>I then loaded the output into Illustrator and was able to view both
>cross-eye and wall-eye stereo pairs with clean shadows.
>
>
> >
> > Try using this sequence to create your stereo pair:
> >
> > set light=[-0.348,-0.348,-0.870]
> > ray
> > png image1.png
> > turn y,6
> > set light=[-0.437,-0.348,-0.902]
> > ray
> > png image2.png
> > turn y,-6
> >
> > Cheers,
> > Warren

----------------------------------------------------------------------
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
----------------------------------------------------------------------

At 10:50 AM -0700 4/30/03, wg...@ch... wrote:
>Coincidently that was the exact same program that hosed my python 
>installation too.
>
>>I had set up my computer to run the python based AutoDock Tools
>>interface to the docking program AutoDock. The installer for this
>>program puts its own copy of python as a subdirectory in the main
>>application directory and adds some environment variables to the
>>.cshrc file. Apparently, some variable created here affected other
>>python based apps. When I commented these out and opened a new xterm
>>and ran pymol, everything worked normally.
>
>Moreover, my attempts to re-engineer the AutoDock installation ended 
>in a complete morass.  This is a great reason for installation 
>software to at least allow you the option of using your already 
>installed system python.

Here's what I told my students. It seemed like a reasonable solution.

_________

It appears that the problem was introduced by the installation of 
ADT. The ADT installer puts some lines in your .cshrc file that 
prevents pymol from working properly.  So here is a solution that 
worked for me.

Take out the ADT lines and put them into a separate text file--say 
call it "ADTenv.csh". If you open a new xterm, pymol should not work 
properly.

If you want to run ADT, open a new xterm and "source ADTenv.csh" (no 
quotes). Then run "adt" (no quotes) from this window.
_________

Although I didn't try it, I assume that you can't run pymol from that 
xterm once you've run the ADTenv.csh script.

TG
-- 
_________________
Terry M. Gray, Ph.D., Computer Support Scientist
Chemistry Department, Colorado State University
Fort Collins, Colorado  80523
gr...@la...  http://www.chm.colostate.edu/~grayt/
phone: 970-491-7003 fax: 970-491-1801

Coincidently that was the exact same program that hosed my python 
installation too.

> I had set up my computer to run the python based AutoDock Tools
> interface to the docking program AutoDock. The installer for this
> program puts its own copy of python as a subdirectory in the main
> application directory and adds some environment variables to the
> .cshrc file. Apparently, some variable created here affected other
> python based apps. When I commented these out and opened a new xterm
> and ran pymol, everything worked normally.

Moreover, my attempts to re-engineer the AutoDock installation ended in 
a complete morass.  This is a great reason for installation software to 
at least allow you the option of using your already installed system 
python.

You can also color by secondary structure by using the following
commands:

color purple
color orange, ss s
color mred2, ss h

The first command colors everything purple, including loops.  The second
colors all beta strands orange, and the third colors all helices mred2.

Tony

________________________________________________________________________
Camille wrote:

    Hello Pymol community,
            I'm experiencing a problem when colouring a pdb by secondary
    structure. The colour bleeds from the ends of helices and sheets
    into loop.
    
    for example, if I were to....
    
    color orange, a/49:52/
    color purple, a/53:55/
    color mred2, a/56:59/
    
    
    where a/49:52/ is beta strand and a/53:55/ is loop and a/56:59/  is
    beta strand, I get bleed from the ends of the strand into the loop.
    
    
    Is there any way around this to get the colors to only apply to the
    defined secondary structure elements (I read in an ss_pml with
    "alter... yada yada yada....") as in molscript?
    
    I apologise if this question has been dealt with before (I have
    tried to find previous messages). I imagine that this would be
    important to many who would like to use pymol to make figures for
    publication.
    
    Many thanks,
    
            Camille

Warren's script is not quite right.  The value -0.902 is not correct.
Apparently, my picture, with a stick peptide casting a shadow on the inner 
surface of a deep crevice, is particularly demanding.

I have done the vector calculations.  See the attached excel worksheet for 
light vectors for any desired stereo angle.

I am using the script below.  It produces perfect shadows and reflections.


turn y, 3
set light=[-0.43709,-0.34800,-0.82937]
ray 1120,818
png image.l.png

turn y, -6
set light=[-0.34800,-0.34800,-0.87051]
ray 1120,818
png image.r.png



Anthony



At 05:10 AM 24/04/2003, Warren L. DeLano wrote:


>In the script I just posted, I used unit vectors to specify the light
>direction and simply rotated that vector by 6 degrees.  The first vector
>is merely [-0.4,-0.4,-1.0] normalized.  The second is that same vector
>rotated 6 degrees about the Y axis.
>
>I then loaded the output into Illustrator and was able to view both
>cross-eye and wall-eye stereo pairs with clean shadows.
>
>
> >
> > Try using this sequence to create your stereo pair:
> >
> > set light=[-0.348,-0.348,-0.870]
> > ray
> > png image1.png
> > turn y,6
> > set light=[-0.437,-0.348,-0.902]
> > ray
> > png image2.png
> > turn y,-6
> >
> > Cheers,
> > Warren

----------------------------------------------------------------------
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
----------------------------------------------------------------------

> Hi,
>
> Anybody know what this message is caused by?
>
> ____________
>
> [chem05:~] grayt% pymol
> Traceback (most recent call last):
>    File "/sw/lib/pymol/modules/pymol/__init__.py", line 59, in ?
>      import threading
>    File "/sw/lib/python2.2/threading.py", line 4, in ?
>      import time
> ImportError: No module named time



I got the same error the other day when I installed a program that 
carried with it an obsolete (i think 2.0) version of python that took 
over as the system virus.

Steve Gates might have done something similar with the recent updates.

Do a

which python

and it should report /sw/bin/python

If it doesn't, it might be simplest to force a python rebuild in fink 
with

fink rebuild python

If that doesn't work either let me (or the maintainer) know...

Bill



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)
url:          http://chemistry.ucsc.edu/scott_w.html

>>
>>Anybody know what this message is caused by?
>
>Yep :) I have seen this a couple times before, do you have a 
>'sw/lib/python2.2/lib-dynload/time.so' if you don't do a 'fink 
>rebuild python22' even if it is there still do a 'fink rebuild 
>python22' a rebuilding of python always seems to fix it.
>
>Matt



Matt,

Thanks for the tip. I had rebuilt python22 and pymol to no avail, but 
I did "solve" the problem.

I had set up my computer to run the python based AutoDock Tools 
interface to the docking program AutoDock. The installer for this 
program puts its own copy of python as a subdirectory in the main 
application directory and adds some environment variables to the 
.cshrc file. Apparently, some variable created here affected other 
python based apps. When I commented these out and opened a new xterm 
and ran pymol, everything worked normally.

Sorry I didn't give you all the relevant info. I thought I had 
successfully run pymol after installing ADT, but I apparently did not.

Ideally, I can get ADT to use the fink python, but I don't know if I 
want to take the time to sort out what all is going on. I guess I can 
run a special setup script if I want to run ADT and then open a new 
xterm if I want to run pymol.

TG

-- 
_________________
Terry M. Gray, Ph.D., Computer Support Scientist
Chemistry Department, Colorado State University
Fort Collins, Colorado  80523
gr...@la...  http://www.chm.colostate.edu/~grayt/
phone: 970-491-7003 fax: 970-491-1801

On Wednesday, Apr 30, 2003, at 05:38 Australia/Sydney, Terry M. Gray 
wrote:

> Hi,
>
> Anybody know what this message is caused by?

Yep :) I have seen this a couple times before, do you have a 
'sw/lib/python2.2/lib-dynload/time.so' if you don't do a 'fink rebuild 
python22' even if it is there still do a 'fink rebuild python22' a 
rebuilding of python always seems to fix it.

Matt

>
> ____________
>
> [chem05:~] grayt% pymol
> Traceback (most recent call last):
>   File "/sw/lib/pymol/modules/pymol/__init__.py", line 59, in ?
>     import threading
>   File "/sw/lib/python2.2/threading.py", line 4, in ?
>     import time
> ImportError: No module named time
> ______________

Dear all,
 
This has probably been asked a thousand times, but is the default
surface representation a molecular surface or a solvent accessible
surface? 
 
Thanks in advance,
 
Dennis

Hi,

Anybody know what this message is caused by?

____________

[chem05:~] grayt% pymol
Traceback (most recent call last):
   File "/sw/lib/pymol/modules/pymol/__init__.py", line 59, in ?
     import threading
   File "/sw/lib/python2.2/threading.py", line 4, in ?
     import time
ImportError: No module named time
______________

It worked fine the other day. The only thing I've done on my system 
is to add the new iTunes/QT/iPod stuff. Other X programs seem to work 
fine.

TG

-- 
_________________
Terry M. Gray, Ph.D., Computer Support Scientist
Chemistry Department, Colorado State University
Fort Collins, Colorado  80523
gr...@la...  http://www.chm.colostate.edu/~grayt/
phone: 970-491-7003 fax: 970-491-1801

Hello,

* ca...@mr... <ca...@mr...> [2003-04-29 14:08] wrote:
> 
> Hello Pymol community,
> 	I'm experiencing a problem when colouring a pdb by secondary 
> structure. The colour bleeds from the ends of helices and sheets into 
> loop.
> 
> for example, if I were to....
> 
> color orange, a/49:52/
> color purple, a/53:55/
> color mred2, a/56:59/
> 
> 
> where a/49:52/ is beta strand and a/53:55/ is loop and a/56:59/  is 
> beta strand, I get bleed from the ends of the strand into the loop.

Try setting cartoon_discrete_colors to 'on' (or 1).

  set cartoon_discrete_colors, 1

or from the the "Cartoon" menu of the external GUI find "Discrete
Colors" as the last item in the menu.

Hope this helps,
Robert
-- 
Robert L. Campbell, Ph.D.                         <rl...@po...>
Senior Research Associate                            phone: 613-533-6821
Dept. of Biochemistry, Queen's University,             fax: 613-633-2497
Kingston, ON K7L 3N6  Canada       http://adelie.biochem.queensu.ca/~rlc
    PGP Fingerprint: 9B49 3D3F A489 05DC B35C  8E33 F238 A8F5 F635 C0E2

Hello Pymol community,
	I'm experiencing a problem when colouring a pdb by secondary 
structure. The colour bleeds from the ends of helices and sheets into 
loop.

for example, if I were to....

color orange, a/49:52/
color purple, a/53:55/
color mred2, a/56:59/


where a/49:52/ is beta strand and a/53:55/ is loop and a/56:59/  is 
beta strand, I get bleed from the ends of the strand into the loop.


Is there any way around this to get the colors to only apply to the 
defined secondary structure elements (I read in an ss_pml with 
"alter... yada yada yada....") as in molscript?

I apologise if this question has been dealt with before (I have tried 
to find previous messages). I imagine that this would be important to 
many who would like to use pymol to make figures for publication.

Many thanks,

	Camille

Dharmenda,
 
I added that capability last week, it'll be in the next release.
 
Warren
 
 
--
mailto:wa...@de...
Warren L. DeLano, Ph.D. 
Principal
DeLano Scientific LLC
Voice (650)-346-1154 
Fax   (650)-593-4020
 
-----Original Message-----
From: pym...@li...
[mailto:pym...@li...] On Behalf Of dharmendra
Sent: Sunday, April 27, 2003 1:35 AM
To: pym...@li...
Subject: [PyMOL] how to position the rendering
 
Hello,
  I want my pymol rendering area to be placed in the bottom left corner.
Can i specify the co-ordinates for the pymol,so that it will be
positioned in the keft bottom corner.
 
thanks
dharmendra

Hello,
  I want my pymol rendering area to be placed in the bottom left corner.
Can i specify the co-ordinates for the pymol,so that it will be =
positioned in the keft bottom corner.

thanks
dharmendra

Warren,

can you give me more details regarding one of your old posts (see 
below). We got ATI FireGL X1/256MB with stereo jack but I cannot get it 
to work in stereo under Linux. I got drivers from ATI's web page 
(fglrx-glc22-4.2.0-2.9.6.i586.rpm) and they work more or less fine in a 
regular mono regime (RH8.0) but I couldn't find anything about how to 
enable stereo (from withing XF86Config). I wrote to ATI technical 
support and got a reply that their current drivers _do not_ support 
stereo and I should wait for the next release.

Any help appreciated,
-Viktor

One other non-related note for those upgrading to RedHat 9 (from RH8.0): 
  Pymol stopped working after an upgrade because of glut:

ImportError: /usr/lib/libglut.so.3: undefined symbol: XGetExtensionVersion

I asked about it in redhat list and they (a guy from redhat) think it's 
only related to systems with proprietary nvidia drivers. Because I got 
the same error message on a system without nvidia drivers I don't think 
that's the case. I found an 'easy' fix: just downgrade glut to the 
version from RedHat 8.0: however I don't really know if this may break 
something else...


-------- Original Message --------
Subject: RE: [PyMOL] 3D on linux
Date: Wed, 29 Jan 2003 11:33:22 -0800
From: DeLano, Warren <wa...@su...>
To: Naveen Michaud-Agrawal <nmi...@jh...>, 
<pym...@li...>

We've had great results with the FireGL series, and the OpenGL 
performance of the FireGL X1 is excellent 
(http://www.spec.org/gpc/opc.data/vp7/summary.html).

However, the trick with these cards is to allow ATI's binary driver 
compatibility to dictate your choice of Linux distribution and version. 
  This is fine for new dedicated 3D workstations (read SGI 
replacements), but not so good for existing linux setups.

Stereo support is trouble-free.
-- 
Viktor Hornak
SUNY at Stony Brook

Here's still another URL. Although the list of
colors
is not extensive, you can see colors:

<a
href="CMYK-safe" rel="nofollow">http://www.usgs.gov/visual-id/palette.html">CMYK-safe
RGB colors</a>

Dave Fahrney
Professor of Biochemistry
Colorado State University
 
> Message: 6
> From: <ca...@mr...>
> Date: Wed, 23 Apr 2003 10:30:42 +0000
> To: pym...@li...
> Subject: [PyMOL] RGB2CMYK
> 
> Hi,
>         can anyone direct me to a url with RGB colours (in the format below)
> and their CMYK equivalents? At the moment I'm messing around with the
> following kind of thing....
> 
> set_color cyan2=[0.7, 1.0, 1.0]
> 
>         I need to use a cyan color in a figure but unfortunately this becomes
> very dark when the resulting ray traced image file is viewed in CMYK
> mode in illustrator. Greens, especially, seem to suffer in conversion.
> Help!
> 
> cheers,
>         Camille
> 
> MRC-LMB
> Cambridge University
> UK
>

Hi all,

I have a quite strange problem using pymol and dont have even a clou what
might cause the behaviour.

While coloring the chains of a molecule (for example: load
pdb1a22.ent; color red, chain "A") the X-server and with it my complete computer crashes reproducible.
The same happens if I choose another molecule, like for example
pdb1cho.ent.

I first thought of configuration problems but one of my collegues
had similar problems trying to select more than 15 atoms at once.
He wrote a workaround, selecting the atoms of a chain manually and it worked.


I would like to ask if this problem is already known and if anyone
could give me a hint where to look for a
solution. Since the complete system crashes I am not very fond of
experiments.

Best regards
Vera



--
Vera Grimm				E-mail: ver...@un...
Department of Biochemistry		Tel. +49 221 470 6437
Zuelpicherstr. 47, Cologne		Fax. +49 221 470 6431

Scott,

PyMOL's lighting model is merely a direction, not a point.  The default
direction vector isn't even normalized to unit length.

In the script I just posted, I used unit vectors to specify the light
direction and simply rotated that vector by 6 degrees.  The first vector
is merely [-0.4,-0.4,-1.0] normalized.  The second is that same vector
rotated 6 degrees about the Y axis.

I then loaded the output into Illustrator and was able to view both
cross-eye and wall-eye stereo pairs with clean shadows.

I hope that helps.

Cheers,
Warren

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

-----Original Message-----
From: Scott Classen [mailto:cl...@uc...] 
Sent: Wednesday, April 23, 2003 12:07 PM
To: pym...@li...
Cc: wa...@de...
Subject: Stereo pictures, light vector and shadows

Warren,
	Could you explain the values for the set light command? It
appears the 
default values are [-0.40000,-0.40000,-1.00000]
how do the values below correspond to a 6 degree rotation of the light 
source?
Thanks,
Scott


On Wednesday, April 23, 2003, at 08:59  AM, Warren L. DeLano wrote:

> Yow, good point!  I'm surprise none of us realized this before : )
You
> need to change the direction of the light 6 degrees as well.
>
> Try using this sequence to create your stereo pair:
>
> set light=[-0.348,-0.348,-0.870]
> ray
> png image1.png
> turn y,6
> set light=[-0.437,-0.348,-0.902]
> ray
> png image2.png
> turn y,-6
>
> Cheers,
> Warren




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

Warren,
	Could you explain the values for the set light command? It appears the 
default values are [-0.40000,-0.40000,-1.00000]
how do the values below correspond to a 6 degree rotation of the light 
source?
Thanks,
Scott


On Wednesday, April 23, 2003, at 08:59  AM, Warren L. DeLano wrote:

> Yow, good point!  I'm surprise none of us realized this before : )  You
> need to change the direction of the light 6 degrees as well.
>
> Try using this sequence to create your stereo pair:
>
> set light=[-0.348,-0.348,-0.870]
> ray
> png image1.png
> turn y,6
> set light=[-0.437,-0.348,-0.902]
> ray
> png image2.png
> turn y,-6
>
> Cheers,
> Warren




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

Yow, good point!  I'm surprise none of us realized this before : )  You
need to change the direction of the light 6 degrees as well.

Try using this sequence to create your stereo pair:

set light=[-0.348,-0.348,-0.870]
ray
png image1.png
turn y,6
set light=[-0.437,-0.348,-0.902]
ray
png image2.png
turn y,-6

Cheers,
Warren

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

-----Original Message-----
From: pym...@li...
[mailto:pym...@li...] On Behalf Of Anthony
Duff
Sent: Tuesday, April 22, 2003 9:03 PM
To: pym...@li...
Subject: Re: [PyMOL] Stereo pictures, light vector and shadows




I make stereo pictures by making two pictures, with the command "turn y,
6" 
in between.

Now that I am looking into a crevice, I have discovered a problem with
this 
simple method.  When the view is rotated, the light vector moves with
the 
view.  This results in the two pictures having different shadows, thus 
ruining the stereo picture.  I don't want to give up on having shadows.

Has anybody solved this problem?

I am attempting to solve the problem by specifying the light setting
(set 
light = [-0.4, -0.4, -1.0]).
What are the definitions of the light parameters?


Anthony

----------------------------------------------------------------------
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
----------------------------------------------------------------------



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Camille,

This capability exists in the development version, but isn't ready for
prime-time yet.  Look for it in the next release.  

In the meantime, you might try using raster3d to render your grasp
surface, via its "ungrasp" tool. 

http://www.bmsc.washington.edu/raster3d/html/r3d_filters.html#grasp

Or you can load the converted grasp surface into PyMOL as a ".r3d" file
and render it there.  

Warren

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

-----Original Message-----
From: pym...@li...
[mailto:pym...@li...] On Behalf Of
ca...@mr...
Sent: Wednesday, April 23, 2003 3:01 AM
To: pym...@li...
Subject: [PyMOL] surface charge?

Hi Warren,
	I'm using PyMol to make the figures in a paper I am currently
writing. 
I know that pymol can generate surfaces at the moment but not charge. 
Is there any way to colour a surface by charge in pymol using charges 
calculated in grasp? ...or can I import a grasp surface? I heard that 
this sort of thing was in the pipe-line, do you have a rough estimate 
of when it will be available?


Camille

p.s. I'm working on os x with npymol.



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Camille,

Gil Prive posted a set of CMYK colors before:

http://sourceforge.net/mailarchive/message.php?msg_id=2299470

My only comment was that you don't need to add a preceeding underscore
to his color names -- you can simply redefine the ones which already
exist.

set_color _green= [0.00 , 0.53 , 0.22]

can be

set_color green=[0.00,0.53,0.22] 

etc.

One thing you can do with existing images is use Photoshop's
Image->Mode->Convert To Profile option to adjust how the conversion is
performed (at least I think that is what it does).  I'm not sure
Illustrator allow you to control RGB to CMYK conversions as well as
Photoshop.

The thing to understand is that CMYK is a subset of RGB color space.
Many RGB colors simply don't exist in it.  Bright green is one of them.
RGB to CMYK is lossy, nonlinear, and dependent on the assumptions which
are made about the ink colors, blending, and about the paper stock.

Warren

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

-----Original Message-----
From: pym...@li...
[mailto:pym...@li...] On Behalf Of
ca...@mr...
Sent: Wednesday, April 23, 2003 3:31 AM
To: pym...@li...
Subject: [PyMOL] RGB2CMYK

Hi,
	can anyone direct me to a url with RGB colours (in the format
below) 
and their CMYK equivalents? At the moment I'm messing around with the 
following kind of thing....

set_color cyan2=[0.7, 1.0, 1.0]

	I need to use a cyan color in a figure but unfortunately this
becomes 
very dark when the resulting ray traced image file is viewed in CMYK 
mode in illustrator. Greens, especially, seem to suffer in conversion. 
Help!

cheers,
	Camille

MRC-LMB
Cambridge University
UK



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On Wednesday, April 23, 2003, at 06:30 AM, <ca...@mr...> 
wrote:

> can anyone direct me to a url with RGB colours (in the format below) 
> and their CMYK equivalents? At the moment I'm messing around with the 
> following kind of thing....

Hi Camille,

One free utility I found very useful for this kind of things is 
ColorWrite (http://www.adaptiveview.com/cw); it's a Java application, 
so you can run it under OS X, Linux, Solaris and Windows.
Good luck,

Luca

--------------------------------------------------------
Luca Jovine, Ph.D.
Brookdale 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
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