pymol-users Mailing List for PyMOL Molecular Graphics System

Greetings Henning,

The visible disks & colors in the Mutagenesis Wizard indicate pairwise
overlap of atomic van der Waals radii.  The intent is to provide a
qualitative feedback regarding contacts and bumps.

Short green lines or small green disks are shown when atoms are almost in
contact or slightly overlapping.  Large red disks indicate signficant van
der Waals overlap.  Everything else lies between those extremes.

Cheers,
Warren

--
DeLano Scientific LLC
Subscriber Support Services
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> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf 
> Of Henning Stehr
> Sent: Tuesday, April 29, 2008 7:39 AM
> To: PyM...@li...
> Cc: Din...@ed...
> Subject: [PyMOL] Color codes in mutagenesis wizard?
> 
> Hi,
> 
> I was asked the following question and couldn't find the 
> answer, can anyone help?
> 
> "When I mutate a buried small amino acid side-chain to a 
> larger one, it correctly reveals some clashes around that new 
> side-chain. I suppose the disk shaped clusters mean clashes. 
> Can someone please confirm this? I was wondering what the 
> colour of the disk shapes mean (red, green - do they refer to 
> atom type?), and does the variable size of the disk mean anything?"
> 
> Cheers,
> Henning
> 
> -------------------------------------------------------
> Henning Stehr (Dipl. Ing.)
> Structural Proteomics Group
> Max-Planck-Institute for Molecular Genetics Ihnestrasse 63-73
> 14195 Berlin, Germany
> -------------------------------------------------------
> 
> --------------------------------------------------------------
> -----------
> This SF.net email is sponsored by the 2008 JavaOne(SM) 
> Conference Don't miss this year's exciting event. There's 
> still time to save $100. 
> Use priority code J8TL2D2. 
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> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users

Scott,

Ways of launching PyMOL from the commmand-line on Mac OS X.

Option A:

In current MacPyMOL builds (I think 1.0 as well), inside the .app bundle
there is a ./setup.sh script which, when run from inside that working
diretory, writes a "../pymol" command which can be used to reliably launch
MacPyMOL or PyMOLX11Hybrid from the command line.  You can then copy or move
this script into your path.

Option B:

Use the built-in "alias" command within whatever shell you prefer.

tcsh: put in your ".cshrc"

alias pymol /Applications/MacPyMOL.app/Contents/MacOS/MacPyMOL

bash: put in your ".profile"

alias pymol=/Applications/MacPyMOL.app/Contents/MacOS/MacPyMOL

Cheers,
Warren

--
DeLano Scientific LLC
Subscriber Support Services
mailto:de...@de...
 

> -----Original Message-----
> From: Scott Shandler [mailto:sha...@ma...] 
> Sent: Tuesday, April 29, 2008 7:30 AM
> To: DeLano Scientific
> Subject: Re: [PyMOL] PyMOL + Leopard + symlink
> 
> Hello again Warren,
> 
> Thanks for your quick response, I thought there was something 
> funky with my machine.  The intent of the symlink is to make 
> it simpler to open the X11 version on a mac.  I use 
> terminal/x11 environment regularly and the symlink is just a 
> short command to open the program.  Maybe I could wrap the 
> actual call in a shell script or something, possibly I could 
> just use the application name (MacPyMOL) after adding it to my path.
> 

Hi,

I was asked the following question and couldn't find the answer, can
anyone help?

"When I mutate a buried small amino acid side-chain to a larger one,
it correctly reveals some clashes around that new side-chain. I
suppose the disk shaped clusters mean clashes. Can someone please
confirm this? I was wondering what the colour of the disk shapes mean
(red, green - do they refer to atom type?), and does the variable size
of the disk mean anything?"

Cheers,
Henning

-------------------------------------------------------
Henning Stehr (Dipl. Ing.)
Structural Proteomics Group
Max-Planck-Institute for Molecular Genetics
Ihnestrasse 63-73
14195 Berlin, Germany
-------------------------------------------------------

Scott,

There is something weird about launching applications via symlinks on Mac OS
X which I have never been able to understand, but I suspect it has to do
with how Mac OS X distinguishes application bundles from ordinary unix
executables.  However, on top of all that operating system magic, MacPyMOL
is itself set up to autoconfigure based on the name of the associated
bundle.  

What is the intent behind using the symlink?  Perhaps there is another way
of meeting your need...

Cheers,
Warren


--
DeLano Scientific LLC
Subscriber Support Services
mailto:de...@de...
 

> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf 
> Of Scott Shandler
> Sent: Monday, April 28, 2008 11:03 AM
> To: pym...@li...
> Subject: [PyMOL] PyMOL + Leopard + symlink
> 
> Hello all,
> 
> I am having a strange issue with PyMOLX11Hybrid application.  
> I have noticed that with PyMOL 1.1beta3 if you create a 
> symlink to the renamed X11 binary 
> (/Applications/PyMOLX11Hybrid.app/Contents/MacOS/
> MacPyMOL, via command 1 below) you are able to open pymol via 
> the command line, however I am unable to type in the main molecular  
> display window.   Also, probably related, the MacPyMOL application  
> does not appear to be running when using the symlink, just that the   
> X11 environment loads if needed.
> 
> However, if you run the program directly (i.e. /Applications/ 
> PyMOLX11Hybrid.app/Contents/MacOS/MacPyMOL, via command 2 
> below), you are able type in the main window and the MacPyMOL 
> application is running as well.
> 
> Seems like launching the program in 'different' (??) ways 
> results in different application functionality.  Is there 
> some sort of command line arg for MacPyMOL to enable the 
> proper environment settings?
> 
> Thanks in advance,
> 
> -Scott
> 
> 
> symlink:
> 
> ln -s 
> /Applications/PyMOLX11Hybrid.app/Contents/MacOS/MacPyMOL 
> /usr/ local/bin/pymol
> 
> Command 1:  (not able able type in the main window, MacPyMOL 
> does not appear to be running either, /usr/local/bin is in my path):
> ~/pymol
> 
> Command 2: (everything works as expected) 
> /Applications/PyMOLX11Hybrid.app/Contents/MacOS/MacPyMOL
> 
> ____________________________________________
> Scott Shandler, M.B.A
> Ph.D. Candidate Biochemistry & Molecular Biophysics 
> University of Pennsylvania sha...@ma...
> 
> 
> 
> 
> --------------------------------------------------------------
> -----------
> This SF.net email is sponsored by the 2008 JavaOne(SM) 
> Conference Don't miss this year's exciting event. There's 
> still time to save $100. 
> Use priority code J8TL2D2. 
> http://ad.doubleclick.net/clk;198757673;13503038;p?http://java
.sun.com/javaone
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users

Hello all,

I am having a strange issue with PyMOLX11Hybrid application.  I have  
noticed that with PyMOL 1.1beta3 if you create a symlink to the  
renamed X11 binary (/Applications/PyMOLX11Hybrid.app/Contents/MacOS/ 
MacPyMOL, via command 1 below) you are able to open pymol via the  
command line, however I am unable to type in the main molecular  
display window.   Also, probably related, the MacPyMOL application  
does not appear to be running when using the symlink, just that the   
X11 environment loads if needed.

However, if you run the program directly (i.e. /Applications/ 
PyMOLX11Hybrid.app/Contents/MacOS/MacPyMOL, via command 2 below), you  
are able type in the main window and the MacPyMOL application is  
running as well.

Seems like launching the program in 'different' (??) ways results in  
different application functionality.  Is there some sort of command  
line arg for MacPyMOL to enable the proper environment settings?

Thanks in advance,

-Scott


symlink:

ln -s /Applications/PyMOLX11Hybrid.app/Contents/MacOS/MacPyMOL /usr/ 
local/bin/pymol

Command 1:  (not able able type in the main window, MacPyMOL does not  
appear to be running either, /usr/local/bin is in my path):
~/pymol

Command 2: (everything works as expected)
/Applications/PyMOLX11Hybrid.app/Contents/MacOS/MacPyMOL

____________________________________________
Scott Shandler, M.B.A
Ph.D. Candidate Biochemistry & Molecular Biophysics
University of Pennsylvania
sha...@ma...

Dear Juliana --

> does anyone know how to set transparency to a small portions of a  
> molecule: for example, in a 150-aa molecule, set the first 10  
> residues to be transparent?

I don't know if what you are asking is possible, but here is how I'd do:

create short_part, i. 1:10
set transparency, 0.6
set transparency, 0.5, short_part

you then have 2 different transparency settings for your molecule,  
and for the residues 1 to 10, respectively.

HTH
Kind regards.

Leo
------------------------------------------------------------
Chavas Leonard, Ph.D.
Research Associate
------------------------------------------------------------
Faculty of Life Sciences
The University of Manchester
The Michael Smith Building
Oxford Road
Manchester Lancashire
M13 9PT
------------------------------------------------------------
Tel: +44(0)161-275-1586
e-mail: Leo...@ma...

Hi All-

does anyone know how to set transparency to a small portions of a
molecule: for example, in a 150-aa molecule, set the first 10 residues
to be transparent?

thanks a lot!

cheers,
juliana 

PyMOLers,

Just wanted to let you know that the source code for the ImmerseViz extension 
has been released.  Check out the ImmerseViz PyMOLWiki page

	http://www.pymolwiki.org/index.php/ImmersiveViz

as it points to all the necessary places (code/developers/information).  This 
is a really cool idea, with lots of potential for cool extensions.

-- Jason

-- 

Jason Vertrees (javertre@{utmb,cs.dartmouth}.edu)
Doctoral Candidate
Biophysical, Structural & Computational Biology Program
University of Texas Medical Branch 
Galveston, Texas

http://www.best.utmb.edu/
http://www.pymolwiki.org/

Matt,
 
A key PyMOL concept for Tkinter developer to grasp is that Tkinter runs in a
separate thread from PyMOL.  Thus, direct calls to Tkinter from a PyMOL
thread will fail erratically, as observed below. 
 
Fortunately, PyMOL is built so that it can receive API calls asychronously
from any thread.  Therefore, you can develop using Tkinter from the its own
thread, and then message PyMOL from there.  The only hard part is launching
your GUI, which is something you cannot do from a PyMOL script or program
directly.  Instead, you add a new item in the Plugin menu or a whole new
menu for your GUI as part of your initialization.
 
The plugin approach is the safe way to add new functionality using Tkinter.
See modules/pmg_tk/startup/__init__.py for example code to get you started.

 
Cheers,
Warren
 
--
DeLano Scientific LLC
Subscriber Support Services
mailto:de...@de...
 


  _____  

From: pym...@li...
[mailto:pym...@li...] On Behalf Of Matthew
O'Meara
Sent: Friday, April 25, 2008 12:46 PM
To: PyM...@li...
Subject: [PyMOL] access to tkinter root for new Toplevel?


Hi All,

I would like to write a Wizard that spawns a separate window.  Right now I'm
just calling Tkinter.Toplevel() with no arguments but it dies with
non-deterministic tkinter errors.  I think the issue is I need to pass the
Tkinter.Tk() instance into the Toplevel command.  

1) Is there a way I can get access to the main Tkinter.Tk() instance from
within my Wizard?


I've made a simple version of what I would like that shows the behavior I'm
seeing.  To run, copy this into a file called testWizard.py and place into
the wizard directory.  Since I installed from Distutils on linux, my wizard
directory is /usr/local/lib/python2.5/site-packages/pymol/wizard/.  Then
fire up pymol and type into the command line 'wizard testWizard'.  If you
version is <1.0 try deleting '_self=cmd' and '_self'.   For me it crashes
about every third or so time, usually with different errors. 


from pymol.wizard import Wizard
from pymol import cmd
import pymol
import Tkinter


class TestWizard(Wizard):

    def __init__(self,_self=cmd):
        Wizard.__init__(self, _self)

        self.res_table = Tkinter.Tk()  # <- pass app.root in here????

        for i in range( 1000 ): Tkinter.Button(self.res_table,
text=str(i)).pack()


Thanks in advance!
Matt

Hi All,

I would like to write a Wizard that spawns a separate window.  Right now I'm
just calling Tkinter.Toplevel() with no arguments but it dies with
non-deterministic tkinter errors.  I think the issue is I need to pass the
Tkinter.Tk() instance into the Toplevel command.

1) Is there a way I can get access to the main Tkinter.Tk() instance from
within my Wizard?


I've made a simple version of what I would like that shows the behavior I'm
seeing.  To run, copy this into a file called testWizard.py and place into
the wizard directory.  Since I installed from Distutils on linux, my wizard
directory is /usr/local/lib/python2.5/site-packages/pymol/wizard/.  Then
fire up pymol and type into the command line 'wizard testWizard'.  If you
version is <1.0 try deleting '_self=cmd' and '_self'.   For me it crashes
about every third or so time, usually with different errors.


from pymol.wizard import Wizard
from pymol import cmd
import pymol
import Tkinter


class TestWizard(Wizard):

    def __init__(self,_self=cmd):
        Wizard.__init__(self, _self)

        self.res_table = Tkinter.Tk()  # <- pass app.root in here????

        for i in range( 1000 ): Tkinter.Button(self.res_table,
text=str(i)).pack()


Thanks in advance!
Matt

Hi Warren,

I got all that covered already. I think I have a way of doing what I want. I just define the help on the first scene and predisplay it upon loading. That should do the trick. 

Cheers,

	Carsten


> -----Original Message-----
> From: DeLano Scientific [mailto:de...@de...]
> Sent: Friday, April 25, 2008 3:28 PM
> To: Schubert, Carsten [PRDUS]; pym...@li...
> Subject: RE: [PyMOL] Embeding commands in PyMol session?
> 
> 
> Hi Carsten,
> 
> The best way to share PyMOL content with novice users is via 
> pre-defined
> scenes stored in a session file.  Users can then simply open 
> the session
> file and use Page Down to iterate through the scenes.  Each 
> scene can be
> annotated with text, for example:
> 
> scene 001, store, The target structure (press the Page Down key).
> ...
> scene 002, store, Surface of the binding site.
> ...
> scene 003, store, Our lead compound ABC-12346.
> ...
> 
> NOTE: For multi-line annotations, you need to use the Python 
> form of the
> command:
> 
> cmd.scene("003","store","My first line of text\nMy second 
> line of text")
> 
> Cheers,
> Warren
> 
> --
> DeLano Scientific LLC
> Subscriber Support Services
> mailto:de...@de...
>  
> 
> > -----Original Message-----
> > From: pym...@li... 
> > [mailto:pym...@li...] On Behalf 
> > Of Schubert, Carsten [PRDUS]
> > Sent: Friday, April 25, 2008 6:38 AM
> > To: pym...@li...
> > Subject: [PyMOL] Embeding commands in PyMol session?
> > 
> > Hi,
> > 
> > is it possible to embed commands or scripts into a pymol 
> > session? I am routinely creating PyMol sessions for users who 
> > for the most part have no clue how to use PyMol. So I'd like 
> > to include a dialog or message, which gets displayed after 
> > the session has loaded and clues the user in how to start or 
> > at least what he is looking at.
> > 
> > Cheers,
> > 
> > 	Carsten
> > 
> > --------------------------------------------------------------
> > -----------
> > This SF.net email is sponsored by the 2008 JavaOne(SM) 
> > Conference Don't miss this year's exciting event. There's 
> > still time to save $100. 
> > Use priority code J8TL2D2. 
> > http://ad.doubleclick.net/clk;198757673;13503038;p?http://java
> .sun.com/javaone
> > _______________________________________________
> > PyMOL-users mailing list
> > PyM...@li...
> > https://lists.sourceforge.net/lists/listinfo/pymol-users
> 
> 
> 

Hi Carsten,

The best way to share PyMOL content with novice users is via pre-defined
scenes stored in a session file.  Users can then simply open the session
file and use Page Down to iterate through the scenes.  Each scene can be
annotated with text, for example:

scene 001, store, The target structure (press the Page Down key).
...
scene 002, store, Surface of the binding site.
...
scene 003, store, Our lead compound ABC-12346.
...

NOTE: For multi-line annotations, you need to use the Python form of the
command:

cmd.scene("003","store","My first line of text\nMy second line of text")

Cheers,
Warren

--
DeLano Scientific LLC
Subscriber Support Services
mailto:de...@de...
 

> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf 
> Of Schubert, Carsten [PRDUS]
> Sent: Friday, April 25, 2008 6:38 AM
> To: pym...@li...
> Subject: [PyMOL] Embeding commands in PyMol session?
> 
> Hi,
> 
> is it possible to embed commands or scripts into a pymol 
> session? I am routinely creating PyMol sessions for users who 
> for the most part have no clue how to use PyMol. So I'd like 
> to include a dialog or message, which gets displayed after 
> the session has loaded and clues the user in how to start or 
> at least what he is looking at.
> 
> Cheers,
> 
> 	Carsten
> 
> --------------------------------------------------------------
> -----------
> This SF.net email is sponsored by the 2008 JavaOne(SM) 
> Conference Don't miss this year's exciting event. There's 
> still time to save $100. 
> Use priority code J8TL2D2. 
> http://ad.doubleclick.net/clk;198757673;13503038;p?http://java
.sun.com/javaone
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users

Hi,

is it possible to embed commands or scripts into a pymol session? I am routinely creating PyMol sessions for users who for the most part have no clue how to use PyMol. So I'd like to include a dialog or message, which gets displayed after the session has loaded and clues the user in how to start or at least what he is looking at.

Cheers,

	Carsten

Ben,

Here are two answers:

A) If you absolutely need to pipe commands into PyMOL, then you should use
the -K option to keep PyMOL from automatically quitting once standard input
has been exhausted:

echo '...;quit' | pymol -pKcq

Note that the '-i' and '-x' options are superfluous with '-c'.

B) However, a cleaner approach would be to run the Python script as the
first argument to PyMOL followed by a -d statement.

pymol -cq BuildHelix.py -d 'BuildMe("AAAAAAAAA")'

Cheers,
Warren

--
DeLano Scientific LLC
Subscriber Support Services
mailto:de...@de...
 

> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf 
> Of Benjamin Hall
> Sent: Thursday, April 24, 2008 8:35 AM
> To: pym...@li...
> Subject: [PyMOL] Problem Saving Molecules from batch mode
> 
> Hi
> 
> I'm writing a short script to use pymol to generate "ideal" 
> alpha helices out of arbitrary sequences. I use a short 
> script, BuildHelix.py:
> 
> from pymol import cmd, stored
> 
> def BuildMe(sequence):
>     cmd.set("secondary_structure",1.00)
>     for aa in sequence: cmd._alt(string.lower(aa))
>     cmd.save(sequence+".pdb")
> 
> cmd.extend( "BuildMe", BuildMe )
> 
> I can then run this from the gui prompt, or in interactive 
> mode without the gui without issue, as follows:
> 
> run BuildHelix.py
> BuildMe("AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA")
> quit
> 
> However, as I want to use this in an automated way, I have 
> been trying this command:
> 
> echo 'run
> BuildHelix.py\nBuildMe("AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA")\nq
uit\n)' | pymol -xpic
> 
> This works intermittently, roughly 1 in 3 or 4 times. Adding 
> cmd.sync() lines to either the script or the command doesn't 
> change the results. 
> However, if I use the command "quit()" (rather than "quit"), 
> pymol crashes with an error in threading.py and the file is 
> correctly written out. The error given is
> 
> PyMOL>quit()
> Traceback (most recent call last):
>   File "/var/lib/python-support/python2.5/pymol/parser.py", 
> line 456, in parse
>     exec(layer.com2+"\n",self.pymol_names,self.pymol_names)
>   File "<string>", line 1, in <module>
>   File "site.py", line 256, in __call__
>     raise SystemExit(code)
> SystemExit: None
> Exception in thread Thread-1:
> Traceback (most recent call last):
>   File "threading.py", line 460, in __bootstrap
>     self.run()
>   File "threading.py", line 440, in run
>     self.__target(*self.__args, **self.__kwargs)
>   File "/var/lib/python-support/python2.5/pymol/parser.py", 
> line 500, in stdin_reader
>     l = sys.stdin.readline()
> ValueError: I/O operation on closed file
> 
> I'm running version 1.0re1, though I have also tested with 0.98.
> 
> Any advice would be much appreciated. Thanks in advance
> 
> Ben Hall
> 
> --------------------------------------------------------------
> -----------
> This SF.net email is sponsored by the 2008 JavaOne(SM) 
> Conference Don't miss this year's exciting event. There's 
> still time to save $100. 
> Use priority code J8TL2D2. 
> http://ad.doubleclick.net/clk;198757673;13503038;p?http://java
.sun.com/javaone
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users

Matrin,

set retain_order

before loading the input PDB file.

Depending on the application, you may also wish to 

set pdb_retain_ids

Cheers,
Warren

--
DeLano Scientific LLC
Subscriber Support Services
mailto:de...@de...
 

> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf 
> Of Martin Höfling
> Sent: Thursday, April 24, 2008 11:13 AM
> To: pym...@li...
> Subject: [PyMOL] Keeping PDB ordering
> 
> Hi all,
> 
> is there a simple way to prevent reordering of atoms and 
> insertion of additional TER records by pymol? I have a 
> protein embedded in a bilayer with tip4p water, where this 
> occurs when I delete parts and export the rest of the System.
> 
> Best wishes
> 	Martin
> 
> --------------------------------------------------------------
> -----------
> This SF.net email is sponsored by the 2008 JavaOne(SM) 
> Conference Don't miss this year's exciting event. There's 
> still time to save $100. 
> Use priority code J8TL2D2. 
> http://ad.doubleclick.net/clk;198757673;13503038;p?http://java
.sun.com/javaone
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users

Hi all,

is there a simple way to prevent reordering of atoms and insertion of 
additional TER records by pymol? I have a protein embedded in a bilayer with 
tip4p water, where this occurs when I delete parts and export the rest of the 
System.

Best wishes
	Martin

Woops, sorry. See, that's why it's so much better to put things on the
user list :)

Tsjerk

On Thu, Apr 24, 2008 at 6:23 PM, DeLano Scientific <de...@de...> wrote:
> > Pymol (at least up to 0.99rc6) has a problem with multiple
>  > transparencies in ray-tracing.
>
>  That's news to me.  Combination of multiple transparent surfaces is indeed
>  broken in the OpenGL viewer up into 1.x.  However, the ray tracer has been
>  able to do this almost since the beginning.
>
>  The thing is, with PyMOL, you get to choose whether or not you see multiple
>  transparent layers.  Given the geometric intricacy of molecular surfaces, it
>  is often preferable to only see the front-most transparent surface, so that
>  is the default behavior:
>
>  set transparency_mode, 2
>
>  If, instead, you want to render all transparent layers:
>
>  set transparency_mode, 1
>
>  If you want increased contrast when rendering:
>
>  set ray_transparency_contrast, 1.5
>
>  If you want to factor in surface normals:
>
>  set ray_transparency_oblique, 1.1
>
>  If you don't want transparent surfaces casting a shadow:
>
>  set ray_transparency_shadow, 0
>
>  If you don't want any shadows at all:
>
>  set ray_shadow, 0
>
>  Cheers,
>  Warren
>
>
>
>  > If you really need it, you can
>  > export the scene to povray, which will allow you to build
>  > complex scenes with multiple transparent objects. This may be
>  > the same issue as losing the shaded face between two boxes.
>  > There it may help to define each plane uniquely, rather than
>  > placing two boxes with the faces coinciding. Or you can try
>  > to add a little bit of space between the boxes. But I should
>  > add that I haven't tried these things yet.
>  >
>  > By the way, I also bounce this mail the pymol user list, so
>  > that others may add their comments and/or can learn from it.
>  >
>  > Best,
>  >
>  > Tsjerk
>  >
>  > On Thu, Apr 24, 2008 at 3:41 PM, Dean Waldow
>  > <wa...@ch...> wrote:
>  > > Tsjerk,
>  > >
>  > >  Thanks, perhaps that might related to other things I have
>  > noticed....
>  > >
>  > >  I have noticed some oddities (which I think I can work
>  > around) when I
>  > > place multiple boxes next to each other and then do a ray. Have you
>  > > seen anything like these and not that I expect you to have the
>  > > answers... :) I thought I would mention them in case you
>  > have seen them. I'm using .99r6 I think.
>  > >
>  > >  1) Looking through one of the middle boxes molecules in
>  > there get a 'snow'
>  > > look if the color settings are 1 but when I most the color
>  > settings a
>  > > little lower than 1 that seems to got away.
>  > >  2) One other obj (spheroid) which I had set at transparent
>  > disappears
>  > > when viewed through a transparent box after issuing the ray command.
>  > >  3) Also when I issue the ray command, I can't see the shadowed
>  > > boundary between boxes like I can before before the ray command.
>  > >
>  > >  Thanks again. I really appreciate the tips!
>  > >
>  > >  Dean
>  > >
>  > >
>  > >
>  > >  On Apr 24, 2008, at 2:21 AM, Tsjerk Wassenaar wrote:
>  > >
>  > >
>  > > > Hi Dean,
>  > > >
>  > > > Good that it works. I suspect the only real difference is
>  > the use of
>  > > > ALPHA, which sets the transparency. Do mind the position of the
>  > > > ALPHA keyword and it's value, as these are important.
>  > > >
>  > > > Best,
>  > > >
>  > > > Tsjerk
>  > > >
>  > > > On Wed, Apr 23, 2008 at 8:08 PM, Dean Waldow
>  > <wa...@ch...> wrote:
>  > > >
>  > > > >  Hi Tsjerk,
>  > > > >
>  > > > > It works Great!  Thanks so much. I'll have to study
>  > your code to
>  > > > > see
>  > > where I
>  > > > > was going wrong.
>  > > > >
>  > > > > Dean
>  > > > >
>  > > > >
>  > > > > On Apr 23, 2008, at 10:39 AM, Tsjerk Wassenaar wrote:
>  > > > >
>  > > > >
>  > > > > Hi Dean,
>  > > > >
>  > > > > Funny, really. Last week I was just playing around a bit with
>  > > > > creating boxes in pymol, e.g. to create a bounding box, and I
>  > > > > wanted to have it transparent. So here's a script, giving you a
>  > > > > function 'rect', which takes two tuples, specifying the
>  > far edges of the box:
>  > > > >
>  > > > > rect( [x0,y0,z0], [x1,y1,z1],name="box",rgbt=[1,1,0,0.5])
>  > > > >
>  > > > > The rgbt argument specifies the color and transparency.
>  > Feel free
>  > > > > to go through the code to see how things are done (although you
>  > > > > won't hear me say it's perfect). In case you have any
>  > suggestions,
>  > > > > also feel free to contact me, either on or off list.
>  > > > >
>  > > > > I hope it helps. Cheers,
>  > > > >
>  > > > > Tsjerk
>  > > > >
>  > > > > On Wed, Apr 23, 2008 at 5:22 PM, Dean Waldow
>  > <wa...@ch...>
>  > > wrote:
>  > > > >  Hi Folks,
>  > > > >
>  > > > > I am very new to pymol and have been learning a lot about using
>  > > (mac)pymol.
>  > > > > However, I seem to be unable to make a box which is transparent
>  > > > > and has color. I have been able to make a box with the
>  > *.py script
>  > > > > below but
>  > > when I
>  > > > > do the ray tracing to get a nice image the box turns to grey /
>  > > > > black. I
>  > > have
>  > > > > also been able to to make prolate and oblate spheriods
>  > using ideas
>  > > > > from
>  > > the
>  > > > > pymol wiki.
>  > > > >
>  > > > > My eventual goal is to have about three slabs or boxes with
>  > > > > spheroids at
>  > > the
>  > > > > interface of these slabs and my pdb results from a monte carlo
>  > > simulation
>  > > > > where the spheriods highlight the changes in shape of my
>  > > > > copolymers at
>  > > the
>  > > > > interface.
>  > > > >
>  > > > > Has anyone succeeded in making colored transparent
>  > boxes? Or might
>  > > > > there
>  > > be
>  > > > > another strategy?
>  > > > >
>  > > > > Thanks,
>  > > > >
>  > > > > Dean Waldow
>  > > > >
>  > > > > Here is the script (modified from one that makes a
>  > bounding box I
>  > > believe)
>  > > > > that makes my current solid box which turns grey with I
>  > issue the
>  > > > > ray
>  > > > > command:
>  > > > >
>  > > > >
>  > > > > from pymol.cgo import *
>  > > > > from pymol import cmd
>  > > > > #
>  > > > > # SEGMENT     1
>  > > > > box = [
>  > > > >   LINEWIDTH, 1.0,
>  > > > >   BEGIN, VERTEX,
>  > > > >   COLOR, 0.0, 0.0, 0.0,
>  > > > >
>  > > > > # Face 1
>  > > > >   VERTEX,   55.000,   55.000,   55.000,
>  > > > >   VERTEX,   55.000,    5.000,   55.000,
>  > > > >   VERTEX,   55.000,    5.000,    5.000,
>  > > > >
>  > > > >   VERTEX,   55.000,    5.000,    5.000,
>  > > > >   VERTEX,   55.000,   55.000,    5.000,
>  > > > >   VERTEX,   55.000,   55.000,   55.000,
>  > > > >
>  > > > > # Face 2
>  > > > >   VERTEX,    5.000,   55.000,   55.000,
>  > > > >   VERTEX,    5.000,    5.000,   55.000,
>  > > > >   VERTEX,    5.000,    5.000,    5.000,
>  > > > >
>  > > > >   VERTEX,    5.000,    5.000,    5.000,
>  > > > >   VERTEX,    5.000,   55.000,    5.000,
>  > > > >   VERTEX,    5.000,   55.000,   55.000,
>  > > > >
>  > > > > # Face 3
>  > > > >   VERTEX,   55.000,   55.000,   55.000,
>  > > > >   VERTEX,    5.000,   55.000,   55.000,
>  > > > >   VERTEX,    5.000,   55.000,    5.000,
>  > > > >
>  > > > >   VERTEX,    5.000,   55.000,    5.000,
>  > > > >   VERTEX,   55.000,   55.000,    5.000,
>  > > > >   VERTEX,   55.000,   55.000,   55.000,
>  > > > >
>  > > > > # Face 4
>  > > > >   VERTEX,   55.000,    5.000,   55.000,
>  > > > >   VERTEX,    5.000,    5.000,   55.000,
>  > > > >   VERTEX,    5.000,    5.000,    5.000,
>  > > > >
>  > > > >   VERTEX,    5.000,    5.000,    5.000,
>  > > > >   VERTEX,   55.000,    5.000,    5.000,
>  > > > >   VERTEX,   55.000,    5.000,   55.000,
>  > > > >
>  > > > > # Face 5
>  > > > >   VERTEX,   55.000,   55.000,   55.000,
>  > > > >   VERTEX,    5.000,   55.000,   55.000,
>  > > > >   VERTEX,    5.000,    5.000,   55.000,
>  > > > >
>  > > > >   VERTEX,    5.000,    5.000,   55.000,
>  > > > >   VERTEX,   55.000,    5.000,   55.000,
>  > > > >   VERTEX,   55.000,   55.000,   55.000,
>  > > > >
>  > > > > # Face 6
>  > > > >   VERTEX,   55.000,   55.000,    5.000,
>  > > > >   VERTEX,    5.000,   55.000,    5.000,
>  > > > >   VERTEX,    5.000,    5.000,    5.000,
>  > > > >
>  > > > >   VERTEX,    5.000,    5.000,    5.000,
>  > > > >   VERTEX,   55.000,    5.000,    5.000,
>  > > > >   VERTEX,   55.000,   55.000,    5.000,
>  > > > >
>  > > > >   END
>  > > > >   ]
>  > > > >
>  > > > > obj = box
>  > > > >
>  > > > > cmd.load_cgo(obj,'segment',   1)
>  > > > >
>  > > > >
>  > > > >
>  > > > > --
>  > > > >
>  > > > >
>  > ------------------------------------------------------------------
>  > > > > ------
>  > > > >
>  > > > > Dean Waldow, Professor               (253) 535-7533
>  > > > >
>  > > > > Department of Chemistry              (253) 536-5055 (FAX)
>  > > > >
>  > > > > Pacific Lutheran University          wa...@ch...
>  > > > >
>  > > > > Tacoma, WA  98447   USA
>  > http://www.chem.plu.edu/waldow/
>  > > > >
>  > > > >
>  > ------------------------------------------------------------------
>  > > > > ------
>  > > > >
>  > > > > ---> CIRRUS and the Chemistry homepage:
>  > <" rel="nofollow">http://www.chem.plu.edu/>
>  > > > > ---> <----
>  > > > >
>  > > > >
>  > ------------------------------------------------------------------
>  > > > > ------
>  > > > >
>  > > > >
>  > > > >
>  > > > >
>  > > > >
>  > >
>  > ----------------------------------------------------------------------
>  > > ---
>  > > > >  This SF.net email is sponsored by the 2008 JavaOne(SM)
>  > Conference
>  > > > > Don't miss this year's exciting event. There's still
>  > time to save $100.
>  > > > >  Use priority code J8TL2D2.
>  > > > >
>  > > > >
>  > >
>  > http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com
>  > > /javaone
>  > > > > _______________________________________________
>  > > > >  PyMOL-users mailing list
>  > > > >  PyM...@li...
>  > > > > https://lists.sourceforge.net/lists/listinfo/pymol-users
>  > > > >
>  > > > >
>  > > > >
>  > > > >
>  > > > >
>  > > > >
>  > > > > --
>  > > > > Tsjerk A. Wassenaar, Ph.D.
>  > > > > Junior UD (post-doc)
>  > > > > Biomolecular NMR, Bijvoet Center
>  > > > > Utrecht University
>  > > > > Padualaan 8
>  > > > > 3584 CH Utrecht
>  > > > > The Netherlands
>  > > > > P: +31-30-2539931
>  > > > > F: +31-30-2537623<rect.py>
>  > > > >
>  > > > > --
>  > > > >
>  > > > >
>  > > > >
>  > ------------------------------------------------------------------
>  > > > > ------
>  > > > >
>  > > > > Dean Waldow, Professor               (253) 535-7533
>  > > > >
>  > > > > Department of Chemistry              (253) 536-5055 (FAX)
>  > > > >
>  > > > > Pacific Lutheran University          wa...@ch...
>  > > > >
>  > > > > Tacoma, WA  98447   USA
>  > http://www.chem.plu.edu/waldow/
>  > > > >
>  > > > >
>  > ------------------------------------------------------------------
>  > > > > ------
>  > > > >
>  > > > > ---> CIRRUS and the Chemistry homepage:
>  > <" rel="nofollow">http://www.chem.plu.edu/>
>  > > > > ---> <----
>  > > > >
>  > > > >
>  > ------------------------------------------------------------------
>  > > > > ------
>  > > > >
>  > > > >
>  > > > >
>  > > > >
>  > > > >
>  > > >
>  > > >
>  > > >
>  > > > --
>  > > > Tsjerk A. Wassenaar, Ph.D.
>  > > > Junior UD (post-doc)
>  > > > Biomolecular NMR, Bijvoet Center
>  > > > Utrecht University
>  > > > Padualaan 8
>  > > > 3584 CH Utrecht
>  > > > The Netherlands
>  > > > P: +31-30-2539931
>  > > > F: +31-30-2537623
>  > > >
>  > >
>  > >
>  >
>  >
>  >
>  > --
>  > Tsjerk A. Wassenaar, Ph.D.
>  > Junior UD (post-doc)
>  > Biomolecular NMR, Bijvoet Center
>  > Utrecht University
>  > Padualaan 8
>  > 3584 CH Utrecht
>  > The Netherlands
>  > P: +31-30-2539931
>  > F: +31-30-2537623
>  >
>  > --------------------------------------------------------------
>
>
> > -----------
>  > This SF.net email is sponsored by the 2008 JavaOne(SM)
>  > Conference Don't miss this year's exciting event. There's
>  > still time to save $100.
>  > Use priority code J8TL2D2.
>  > http://ad.doubleclick.net/clk;198757673;13503038;p?http://java
>  .sun.com/javaone
>  > _______________________________________________
>  > PyMOL-users mailing list
>  > PyM...@li...
>  > https://lists.sourceforge.net/lists/listinfo/pymol-users
>
>



-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

> Pymol (at least up to 0.99rc6) has a problem with multiple 
> transparencies in ray-tracing. 

That's news to me.  Combination of multiple transparent surfaces is indeed
broken in the OpenGL viewer up into 1.x.  However, the ray tracer has been
able to do this almost since the beginning.

The thing is, with PyMOL, you get to choose whether or not you see multiple
transparent layers.  Given the geometric intricacy of molecular surfaces, it
is often preferable to only see the front-most transparent surface, so that
is the default behavior:

set transparency_mode, 2

If, instead, you want to render all transparent layers:

set transparency_mode, 1

If you want increased contrast when rendering:

set ray_transparency_contrast, 1.5

If you want to factor in surface normals:

set ray_transparency_oblique, 1.1

If you don't want transparent surfaces casting a shadow:

set ray_transparency_shadow, 0

If you don't want any shadows at all:

set ray_shadow, 0

Cheers,
Warren
 
> If you really need it, you can 
> export the scene to povray, which will allow you to build 
> complex scenes with multiple transparent objects. This may be 
> the same issue as losing the shaded face between two boxes. 
> There it may help to define each plane uniquely, rather than 
> placing two boxes with the faces coinciding. Or you can try 
> to add a little bit of space between the boxes. But I should 
> add that I haven't tried these things yet.
> 
> By the way, I also bounce this mail the pymol user list, so 
> that others may add their comments and/or can learn from it.
> 
> Best,
> 
> Tsjerk
> 
> On Thu, Apr 24, 2008 at 3:41 PM, Dean Waldow 
> <wa...@ch...> wrote:
> > Tsjerk,
> >
> >  Thanks, perhaps that might related to other things I have 
> noticed....
> >
> >  I have noticed some oddities (which I think I can work 
> around) when I 
> > place multiple boxes next to each other and then do a ray. Have you 
> > seen anything like these and not that I expect you to have the 
> > answers... :) I thought I would mention them in case you 
> have seen them. I'm using .99r6 I think.
> >
> >  1) Looking through one of the middle boxes molecules in 
> there get a 'snow'
> > look if the color settings are 1 but when I most the color 
> settings a 
> > little lower than 1 that seems to got away.
> >  2) One other obj (spheroid) which I had set at transparent 
> disappears 
> > when viewed through a transparent box after issuing the ray command.
> >  3) Also when I issue the ray command, I can't see the shadowed 
> > boundary between boxes like I can before before the ray command.
> >
> >  Thanks again. I really appreciate the tips!
> >
> >  Dean
> >
> >
> >
> >  On Apr 24, 2008, at 2:21 AM, Tsjerk Wassenaar wrote:
> >
> >
> > > Hi Dean,
> > >
> > > Good that it works. I suspect the only real difference is 
> the use of 
> > > ALPHA, which sets the transparency. Do mind the position of the 
> > > ALPHA keyword and it's value, as these are important.
> > >
> > > Best,
> > >
> > > Tsjerk
> > >
> > > On Wed, Apr 23, 2008 at 8:08 PM, Dean Waldow 
> <wa...@ch...> wrote:
> > >
> > > >  Hi Tsjerk,
> > > >
> > > > It works Great!  Thanks so much. I'll have to study 
> your code to 
> > > > see
> > where I
> > > > was going wrong.
> > > >
> > > > Dean
> > > >
> > > >
> > > > On Apr 23, 2008, at 10:39 AM, Tsjerk Wassenaar wrote:
> > > >
> > > >
> > > > Hi Dean,
> > > >
> > > > Funny, really. Last week I was just playing around a bit with 
> > > > creating boxes in pymol, e.g. to create a bounding box, and I 
> > > > wanted to have it transparent. So here's a script, giving you a 
> > > > function 'rect', which takes two tuples, specifying the 
> far edges of the box:
> > > >
> > > > rect( [x0,y0,z0], [x1,y1,z1],name="box",rgbt=[1,1,0,0.5])
> > > >
> > > > The rgbt argument specifies the color and transparency. 
> Feel free 
> > > > to go through the code to see how things are done (although you 
> > > > won't hear me say it's perfect). In case you have any 
> suggestions, 
> > > > also feel free to contact me, either on or off list.
> > > >
> > > > I hope it helps. Cheers,
> > > >
> > > > Tsjerk
> > > >
> > > > On Wed, Apr 23, 2008 at 5:22 PM, Dean Waldow 
> <wa...@ch...>
> > wrote:
> > > >  Hi Folks,
> > > >
> > > > I am very new to pymol and have been learning a lot about using
> > (mac)pymol.
> > > > However, I seem to be unable to make a box which is transparent 
> > > > and has color. I have been able to make a box with the 
> *.py script 
> > > > below but
> > when I
> > > > do the ray tracing to get a nice image the box turns to grey / 
> > > > black. I
> > have
> > > > also been able to to make prolate and oblate spheriods 
> using ideas 
> > > > from
> > the
> > > > pymol wiki.
> > > >
> > > > My eventual goal is to have about three slabs or boxes with 
> > > > spheroids at
> > the
> > > > interface of these slabs and my pdb results from a monte carlo
> > simulation
> > > > where the spheriods highlight the changes in shape of my 
> > > > copolymers at
> > the
> > > > interface.
> > > >
> > > > Has anyone succeeded in making colored transparent 
> boxes? Or might 
> > > > there
> > be
> > > > another strategy?
> > > >
> > > > Thanks,
> > > >
> > > > Dean Waldow
> > > >
> > > > Here is the script (modified from one that makes a 
> bounding box I
> > believe)
> > > > that makes my current solid box which turns grey with I 
> issue the 
> > > > ray
> > > > command:
> > > >
> > > >
> > > > from pymol.cgo import *
> > > > from pymol import cmd
> > > > #
> > > > # SEGMENT     1
> > > > box = [
> > > >   LINEWIDTH, 1.0,
> > > >   BEGIN, VERTEX,
> > > >   COLOR, 0.0, 0.0, 0.0,
> > > >
> > > > # Face 1
> > > >   VERTEX,   55.000,   55.000,   55.000,
> > > >   VERTEX,   55.000,    5.000,   55.000,
> > > >   VERTEX,   55.000,    5.000,    5.000,
> > > >
> > > >   VERTEX,   55.000,    5.000,    5.000,
> > > >   VERTEX,   55.000,   55.000,    5.000,
> > > >   VERTEX,   55.000,   55.000,   55.000,
> > > >
> > > > # Face 2
> > > >   VERTEX,    5.000,   55.000,   55.000,
> > > >   VERTEX,    5.000,    5.000,   55.000,
> > > >   VERTEX,    5.000,    5.000,    5.000,
> > > >
> > > >   VERTEX,    5.000,    5.000,    5.000,
> > > >   VERTEX,    5.000,   55.000,    5.000,
> > > >   VERTEX,    5.000,   55.000,   55.000,
> > > >
> > > > # Face 3
> > > >   VERTEX,   55.000,   55.000,   55.000,
> > > >   VERTEX,    5.000,   55.000,   55.000,
> > > >   VERTEX,    5.000,   55.000,    5.000,
> > > >
> > > >   VERTEX,    5.000,   55.000,    5.000,
> > > >   VERTEX,   55.000,   55.000,    5.000,
> > > >   VERTEX,   55.000,   55.000,   55.000,
> > > >
> > > > # Face 4
> > > >   VERTEX,   55.000,    5.000,   55.000,
> > > >   VERTEX,    5.000,    5.000,   55.000,
> > > >   VERTEX,    5.000,    5.000,    5.000,
> > > >
> > > >   VERTEX,    5.000,    5.000,    5.000,
> > > >   VERTEX,   55.000,    5.000,    5.000,
> > > >   VERTEX,   55.000,    5.000,   55.000,
> > > >
> > > > # Face 5
> > > >   VERTEX,   55.000,   55.000,   55.000,
> > > >   VERTEX,    5.000,   55.000,   55.000,
> > > >   VERTEX,    5.000,    5.000,   55.000,
> > > >
> > > >   VERTEX,    5.000,    5.000,   55.000,
> > > >   VERTEX,   55.000,    5.000,   55.000,
> > > >   VERTEX,   55.000,   55.000,   55.000,
> > > >
> > > > # Face 6
> > > >   VERTEX,   55.000,   55.000,    5.000,
> > > >   VERTEX,    5.000,   55.000,    5.000,
> > > >   VERTEX,    5.000,    5.000,    5.000,
> > > >
> > > >   VERTEX,    5.000,    5.000,    5.000,
> > > >   VERTEX,   55.000,    5.000,    5.000,
> > > >   VERTEX,   55.000,   55.000,    5.000,
> > > >
> > > >   END
> > > >   ]
> > > >
> > > > obj = box
> > > >
> > > > cmd.load_cgo(obj,'segment',   1)
> > > >
> > > >
> > > >
> > > > --
> > > >
> > > > 
> ------------------------------------------------------------------
> > > > ------
> > > >
> > > > Dean Waldow, Professor               (253) 535-7533
> > > >
> > > > Department of Chemistry              (253) 536-5055 (FAX)
> > > >
> > > > Pacific Lutheran University          wa...@ch...
> > > >
> > > > Tacoma, WA  98447   USA              
> http://www.chem.plu.edu/waldow/
> > > >
> > > > 
> ------------------------------------------------------------------
> > > > ------
> > > >
> > > > ---> CIRRUS and the Chemistry homepage: 
> <" rel="nofollow">http://www.chem.plu.edu/> 
> > > > ---> <----
> > > >
> > > > 
> ------------------------------------------------------------------
> > > > ------
> > > >
> > > >
> > > >
> > > >
> > > >
> > 
> ----------------------------------------------------------------------
> > ---
> > > >  This SF.net email is sponsored by the 2008 JavaOne(SM) 
> Conference  
> > > > Don't miss this year's exciting event. There's still 
> time to save $100.
> > > >  Use priority code J8TL2D2.
> > > >
> > > >
> > 
> http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com
> > /javaone
> > > > _______________________________________________
> > > >  PyMOL-users mailing list
> > > >  PyM...@li...  
> > > > https://lists.sourceforge.net/lists/listinfo/pymol-users
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > --
> > > > Tsjerk A. Wassenaar, Ph.D.
> > > > Junior UD (post-doc)
> > > > Biomolecular NMR, Bijvoet Center
> > > > Utrecht University
> > > > Padualaan 8
> > > > 3584 CH Utrecht
> > > > The Netherlands
> > > > P: +31-30-2539931
> > > > F: +31-30-2537623<rect.py>
> > > >
> > > > --
> > > >
> > > >
> > > > 
> ------------------------------------------------------------------
> > > > ------
> > > >
> > > > Dean Waldow, Professor               (253) 535-7533
> > > >
> > > > Department of Chemistry              (253) 536-5055 (FAX)
> > > >
> > > > Pacific Lutheran University          wa...@ch...
> > > >
> > > > Tacoma, WA  98447   USA              
> http://www.chem.plu.edu/waldow/
> > > >
> > > > 
> ------------------------------------------------------------------
> > > > ------
> > > >
> > > > ---> CIRRUS and the Chemistry homepage: 
> <" rel="nofollow">http://www.chem.plu.edu/> 
> > > > ---> <----
> > > >
> > > > 
> ------------------------------------------------------------------
> > > > ------
> > > >
> > > >
> > > >
> > > >
> > > >
> > >
> > >
> > >
> > > --
> > > Tsjerk A. Wassenaar, Ph.D.
> > > Junior UD (post-doc)
> > > Biomolecular NMR, Bijvoet Center
> > > Utrecht University
> > > Padualaan 8
> > > 3584 CH Utrecht
> > > The Netherlands
> > > P: +31-30-2539931
> > > F: +31-30-2537623
> > >
> >
> >
> 
> 
> 
> --
> Tsjerk A. Wassenaar, Ph.D.
> Junior UD (post-doc)
> Biomolecular NMR, Bijvoet Center
> Utrecht University
> Padualaan 8
> 3584 CH Utrecht
> The Netherlands
> P: +31-30-2539931
> F: +31-30-2537623
> 
> --------------------------------------------------------------
> -----------
> This SF.net email is sponsored by the 2008 JavaOne(SM) 
> Conference Don't miss this year's exciting event. There's 
> still time to save $100. 
> Use priority code J8TL2D2. 
> http://ad.doubleclick.net/clk;198757673;13503038;p?http://java
.sun.com/javaone
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users

Hi Tsjerk,

> The first issue I haven't encountered yet. I can't really say where
> that's coming from. As for the second issue, that is a known glitch.
> Pymol (at least up to 0.99rc6) has a problem with multiple
> transparencies in ray-tracing. If you really need it, you can export
> the scene to povray, which will allow you to build complex scenes with
> multiple transparent objects. This may be the same issue as losing the
> shaded face between two boxes. There it may help to define each plane
> uniquely, rather than placing two boxes with the faces coinciding. Or
> you can try to add a little bit of space between the boxes. But I
> should add that I haven't tried these things yet.

I should get the current open source code and compile it (which I  
think it possible or purchase a compiled version - I have to look  
into these things) to see if any of these issues go away. I'll have  
to learn about povray to try that suggestion.  I have tried putting  
spaces between the 'slabs' so to speak and there was no difference. I  
even put a very thin slab of a nearly opaque layer at the interface  
with the same result. As you suggest, I suspect it may be related to  
the one partially transparent object disappearing when viewed through  
the partially transparent  slab or box.

> By the way, I also bounce this mail the pymol user list, so that
> others may add their comments and/or can learn from it.

Sure... sorry I didn't notice.

Thanks again,

Dean

> Best,
>
> Tsjerk
>
> On Thu, Apr 24, 2008 at 3:41 PM, Dean Waldow <wa...@ch...>  
> wrote:
>> Tsjerk,
>>
>>  Thanks, perhaps that might related to other things I have  
>> noticed....
>>
>>  I have noticed some oddities (which I think I can work around)  
>> when I place
>> multiple boxes next to each other and then do a ray. Have you seen  
>> anything
>> like these and not that I expect you to have the answers... :) I  
>> thought I
>> would mention them in case you have seen them. I'm using .99r6 I  
>> think.
>>
>>  1) Looking through one of the middle boxes molecules in there get  
>> a 'snow'
>> look if the color settings are 1 but when I most the color  
>> settings a little
>> lower than 1 that seems to got away.
>>  2) One other obj (spheroid) which I had set at transparent  
>> disappears when
>> viewed through a transparent box after issuing the ray command.
>>  3) Also when I issue the ray command, I can't see the shadowed  
>> boundary
>> between boxes like I can before before the ray command.
>>
>>  Thanks again. I really appreciate the tips!
>>
>>  Dean
>>
>>
>>
>>  On Apr 24, 2008, at 2:21 AM, Tsjerk Wassenaar wrote:
>>
>>
>>> Hi Dean,
>>>
>>> Good that it works. I suspect the only real difference is the use of
>>> ALPHA, which sets the transparency. Do mind the position of the  
>>> ALPHA
>>> keyword and it's value, as these are important.
>>>
>>> Best,
>>>
>>> Tsjerk
>>>
>>> On Wed, Apr 23, 2008 at 8:08 PM, Dean Waldow  
>>> <wa...@ch...> wrote:
>>>
>>>>  Hi Tsjerk,
>>>>
>>>> It works Great!  Thanks so much. I'll have to study your code to  
>>>> see
>> where I
>>>> was going wrong.
>>>>
>>>> Dean
>>>>
>>>>
>>>> On Apr 23, 2008, at 10:39 AM, Tsjerk Wassenaar wrote:
>>>>
>>>>
>>>> Hi Dean,
>>>>
>>>> Funny, really. Last week I was just playing around a bit with  
>>>> creating
>>>> boxes in pymol, e.g. to create a bounding box, and I wanted to  
>>>> have it
>>>> transparent. So here's a script, giving you a function 'rect',  
>>>> which
>>>> takes two tuples, specifying the far edges of the box:
>>>>
>>>> rect( [x0,y0,z0], [x1,y1,z1],name="box",rgbt=[1,1,0,0.5])
>>>>
>>>> The rgbt argument specifies the color and transparency. Feel  
>>>> free to
>>>> go through the code to see how things are done (although you won't
>>>> hear me say it's perfect). In case you have any suggestions,  
>>>> also feel
>>>> free to contact me, either on or off list.
>>>>
>>>> I hope it helps. Cheers,
>>>>
>>>> Tsjerk
>>>>
>>>> On Wed, Apr 23, 2008 at 5:22 PM, Dean Waldow <wa...@ch...>
>> wrote:
>>>>  Hi Folks,
>>>>
>>>> I am very new to pymol and have been learning a lot about using
>> (mac)pymol.
>>>> However, I seem to be unable to make a box which is transparent  
>>>> and has
>>>> color. I have been able to make a box with the *.py script below  
>>>> but
>> when I
>>>> do the ray tracing to get a nice image the box turns to grey /  
>>>> black. I
>> have
>>>> also been able to to make prolate and oblate spheriods using  
>>>> ideas from
>> the
>>>> pymol wiki.
>>>>
>>>> My eventual goal is to have about three slabs or boxes with  
>>>> spheroids at
>> the
>>>> interface of these slabs and my pdb results from a monte carlo
>> simulation
>>>> where the spheriods highlight the changes in shape of my  
>>>> copolymers at
>> the
>>>> interface.
>>>>
>>>> Has anyone succeeded in making colored transparent boxes? Or  
>>>> might there
>> be
>>>> another strategy?
>>>>
>>>> Thanks,
>>>>
>>>> Dean Waldow
>>>>
>>>> Here is the script (modified from one that makes a bounding box I
>> believe)
>>>> that makes my current solid box which turns grey with I issue  
>>>> the ray
>>>> command:
>>>>
>>>>
>>>> from pymol.cgo import *
>>>> from pymol import cmd
>>>> #
>>>> # SEGMENT     1
>>>> box = [
>>>>   LINEWIDTH, 1.0,
>>>>   BEGIN, VERTEX,
>>>>   COLOR, 0.0, 0.0, 0.0,
>>>>
>>>> # Face 1
>>>>   VERTEX,   55.000,   55.000,   55.000,
>>>>   VERTEX,   55.000,    5.000,   55.000,
>>>>   VERTEX,   55.000,    5.000,    5.000,
>>>>
>>>>   VERTEX,   55.000,    5.000,    5.000,
>>>>   VERTEX,   55.000,   55.000,    5.000,
>>>>   VERTEX,   55.000,   55.000,   55.000,
>>>>
>>>> # Face 2
>>>>   VERTEX,    5.000,   55.000,   55.000,
>>>>   VERTEX,    5.000,    5.000,   55.000,
>>>>   VERTEX,    5.000,    5.000,    5.000,
>>>>
>>>>   VERTEX,    5.000,    5.000,    5.000,
>>>>   VERTEX,    5.000,   55.000,    5.000,
>>>>   VERTEX,    5.000,   55.000,   55.000,
>>>>
>>>> # Face 3
>>>>   VERTEX,   55.000,   55.000,   55.000,
>>>>   VERTEX,    5.000,   55.000,   55.000,
>>>>   VERTEX,    5.000,   55.000,    5.000,
>>>>
>>>>   VERTEX,    5.000,   55.000,    5.000,
>>>>   VERTEX,   55.000,   55.000,    5.000,
>>>>   VERTEX,   55.000,   55.000,   55.000,
>>>>
>>>> # Face 4
>>>>   VERTEX,   55.000,    5.000,   55.000,
>>>>   VERTEX,    5.000,    5.000,   55.000,
>>>>   VERTEX,    5.000,    5.000,    5.000,
>>>>
>>>>   VERTEX,    5.000,    5.000,    5.000,
>>>>   VERTEX,   55.000,    5.000,    5.000,
>>>>   VERTEX,   55.000,    5.000,   55.000,
>>>>
>>>> # Face 5
>>>>   VERTEX,   55.000,   55.000,   55.000,
>>>>   VERTEX,    5.000,   55.000,   55.000,
>>>>   VERTEX,    5.000,    5.000,   55.000,
>>>>
>>>>   VERTEX,    5.000,    5.000,   55.000,
>>>>   VERTEX,   55.000,    5.000,   55.000,
>>>>   VERTEX,   55.000,   55.000,   55.000,
>>>>
>>>> # Face 6
>>>>   VERTEX,   55.000,   55.000,    5.000,
>>>>   VERTEX,    5.000,   55.000,    5.000,
>>>>   VERTEX,    5.000,    5.000,    5.000,
>>>>
>>>>   VERTEX,    5.000,    5.000,    5.000,
>>>>   VERTEX,   55.000,    5.000,    5.000,
>>>>   VERTEX,   55.000,   55.000,    5.000,
>>>>
>>>>   END
>>>>   ]
>>>>
>>>> obj = box
>>>>
>>>> cmd.load_cgo(obj,'segment',   1)
>>>>
>>>>
>>>>
>>>> --
>>>>
>>>> ------------------------------------------------------------------- 
>>>> -----
>>>>
>>>> Dean Waldow, Professor               (253) 535-7533
>>>>
>>>> Department of Chemistry              (253) 536-5055 (FAX)
>>>>
>>>> Pacific Lutheran University          wa...@ch...
>>>>
>>>> Tacoma, WA  98447   USA              http://www.chem.plu.edu/ 
>>>> waldow/
>>>>
>>>> ------------------------------------------------------------------- 
>>>> -----
>>>>
>>>> ---> CIRRUS and the Chemistry homepage: <http://www.chem.plu.edu/ 
>>>> > <----
>>>>
>>>> ------------------------------------------------------------------- 
>>>> -----
>>>>
>>>>
>>>>
>>>>
>>>>
>> --------------------------------------------------------------------- 
>> ----
>>>>  This SF.net email is sponsored by the 2008 JavaOne(SM) Conference
>>>>  Don't miss this year's exciting event. There's still time to  
>>>> save $100.
>>>>  Use priority code J8TL2D2.
>>>>
>>>>
>> http://ad.doubleclick.net/clk;198757673;13503038;p?http:// 
>> java.sun.com/javaone
>>>> _______________________________________________
>>>>  PyMOL-users mailing list
>>>>  PyM...@li...
>>>>  https://lists.sourceforge.net/lists/listinfo/pymol-users
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> Tsjerk A. Wassenaar, Ph.D.
>>>> Junior UD (post-doc)
>>>> Biomolecular NMR, Bijvoet Center
>>>> Utrecht University
>>>> Padualaan 8
>>>> 3584 CH Utrecht
>>>> The Netherlands
>>>> P: +31-30-2539931
>>>> F: +31-30-2537623<rect.py>
>>>>
>>>> --
>>>>
>>>>
>>>> ------------------------------------------------------------------- 
>>>> -----
>>>>
>>>> Dean Waldow, Professor               (253) 535-7533
>>>>
>>>> Department of Chemistry              (253) 536-5055 (FAX)
>>>>
>>>> Pacific Lutheran University          wa...@ch...
>>>>
>>>> Tacoma, WA  98447   USA              http://www.chem.plu.edu/ 
>>>> waldow/
>>>>
>>>> ------------------------------------------------------------------- 
>>>> -----
>>>>
>>>> ---> CIRRUS and the Chemistry homepage: <http://www.chem.plu.edu/ 
>>>> > <----
>>>>
>>>> ------------------------------------------------------------------- 
>>>> -----
>>>>
>>>>
>>>>
>>>>
>>>>
>>>
>>>
>>>
>>> --
>>> Tsjerk A. Wassenaar, Ph.D.
>>> Junior UD (post-doc)
>>> Biomolecular NMR, Bijvoet Center
>>> Utrecht University
>>> Padualaan 8
>>> 3584 CH Utrecht
>>> The Netherlands
>>> P: +31-30-2539931
>>> F: +31-30-2537623
>>>
>>
>>
>
>
>
> -- 
> Tsjerk A. Wassenaar, Ph.D.
> Junior UD (post-doc)
> Biomolecular NMR, Bijvoet Center
> Utrecht University
> Padualaan 8
> 3584 CH Utrecht
> The Netherlands
> P: +31-30-2539931
> F: +31-30-2537623

-- 
------------------------------------------------------------------------
Dean Waldow, Professor               (253) 535-7533
Department of Chemistry              (253) 536-5055 (FAX)
Pacific Lutheran University          wa...@ch...
Tacoma, WA  98447   USA              http://www.chem.plu.edu/waldow/
------------------------------------------------------------------------
---> CIRRUS and the Chemistry homepage: <" rel="nofollow">http://www.chem.plu.edu/> <----
------------------------------------------------------------------------

Hi

I'm writing a short script to use pymol to generate "ideal" alpha 
helices out of arbitrary sequences. I use a short script, BuildHelix.py:

from pymol import cmd, stored

def BuildMe(sequence):
    cmd.set("secondary_structure",1.00)
    for aa in sequence: cmd._alt(string.lower(aa))
    cmd.save(sequence+".pdb")

cmd.extend( "BuildMe", BuildMe )

I can then run this from the gui prompt, or in interactive mode without 
the gui without issue, as follows:

run BuildHelix.py
BuildMe("AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA")
quit

However, as I want to use this in an automated way, I have been trying 
this command:

echo 'run 
BuildHelix.py\nBuildMe("AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA")\nquit\n)' | 
pymol -xpic

This works intermittently, roughly 1 in 3 or 4 times. Adding cmd.sync() 
lines to either the script or the command doesn't change the results. 
However, if I use the command "quit()" (rather than "quit"), pymol 
crashes with an error in threading.py and the file is correctly written 
out. The error given is

PyMOL>quit()
Traceback (most recent call last):
  File "/var/lib/python-support/python2.5/pymol/parser.py", line 456, in 
parse
    exec(layer.com2+"\n",self.pymol_names,self.pymol_names)
  File "<string>", line 1, in <module>
  File "site.py", line 256, in __call__
    raise SystemExit(code)
SystemExit: None
Exception in thread Thread-1:
Traceback (most recent call last):
  File "threading.py", line 460, in __bootstrap
    self.run()
  File "threading.py", line 440, in run
    self.__target(*self.__args, **self.__kwargs)
  File "/var/lib/python-support/python2.5/pymol/parser.py", line 500, in 
stdin_reader
    l = sys.stdin.readline()
ValueError: I/O operation on closed file

I'm running version 1.0re1, though I have also tested with 0.98.

Any advice would be much appreciated. Thanks in advance

Ben Hall

Hi Dean,

The first issue I haven't encountered yet. I can't really say where
that's coming from. As for the second issue, that is a known glitch.
Pymol (at least up to 0.99rc6) has a problem with multiple
transparencies in ray-tracing. If you really need it, you can export
the scene to povray, which will allow you to build complex scenes with
multiple transparent objects. This may be the same issue as losing the
shaded face between two boxes. There it may help to define each plane
uniquely, rather than placing two boxes with the faces coinciding. Or
you can try to add a little bit of space between the boxes. But I
should add that I haven't tried these things yet.

By the way, I also bounce this mail the pymol user list, so that
others may add their comments and/or can learn from it.

Best,

Tsjerk

On Thu, Apr 24, 2008 at 3:41 PM, Dean Waldow <wa...@ch...> wrote:
> Tsjerk,
>
>  Thanks, perhaps that might related to other things I have noticed....
>
>  I have noticed some oddities (which I think I can work around) when I place
> multiple boxes next to each other and then do a ray. Have you seen anything
> like these and not that I expect you to have the answers... :) I thought I
> would mention them in case you have seen them. I'm using .99r6 I think.
>
>  1) Looking through one of the middle boxes molecules in there get a 'snow'
> look if the color settings are 1 but when I most the color settings a little
> lower than 1 that seems to got away.
>  2) One other obj (spheroid) which I had set at transparent disappears when
> viewed through a transparent box after issuing the ray command.
>  3) Also when I issue the ray command, I can't see the shadowed boundary
> between boxes like I can before before the ray command.
>
>  Thanks again. I really appreciate the tips!
>
>  Dean
>
>
>
>  On Apr 24, 2008, at 2:21 AM, Tsjerk Wassenaar wrote:
>
>
> > Hi Dean,
> >
> > Good that it works. I suspect the only real difference is the use of
> > ALPHA, which sets the transparency. Do mind the position of the ALPHA
> > keyword and it's value, as these are important.
> >
> > Best,
> >
> > Tsjerk
> >
> > On Wed, Apr 23, 2008 at 8:08 PM, Dean Waldow <wa...@ch...> wrote:
> >
> > >  Hi Tsjerk,
> > >
> > > It works Great!  Thanks so much. I'll have to study your code to see
> where I
> > > was going wrong.
> > >
> > > Dean
> > >
> > >
> > > On Apr 23, 2008, at 10:39 AM, Tsjerk Wassenaar wrote:
> > >
> > >
> > > Hi Dean,
> > >
> > > Funny, really. Last week I was just playing around a bit with creating
> > > boxes in pymol, e.g. to create a bounding box, and I wanted to have it
> > > transparent. So here's a script, giving you a function 'rect', which
> > > takes two tuples, specifying the far edges of the box:
> > >
> > > rect( [x0,y0,z0], [x1,y1,z1],name="box",rgbt=[1,1,0,0.5])
> > >
> > > The rgbt argument specifies the color and transparency. Feel free to
> > > go through the code to see how things are done (although you won't
> > > hear me say it's perfect). In case you have any suggestions, also feel
> > > free to contact me, either on or off list.
> > >
> > > I hope it helps. Cheers,
> > >
> > > Tsjerk
> > >
> > > On Wed, Apr 23, 2008 at 5:22 PM, Dean Waldow <wa...@ch...>
> wrote:
> > >  Hi Folks,
> > >
> > > I am very new to pymol and have been learning a lot about using
> (mac)pymol.
> > > However, I seem to be unable to make a box which is transparent and has
> > > color. I have been able to make a box with the *.py script below but
> when I
> > > do the ray tracing to get a nice image the box turns to grey / black. I
> have
> > > also been able to to make prolate and oblate spheriods using ideas from
> the
> > > pymol wiki.
> > >
> > > My eventual goal is to have about three slabs or boxes with spheroids at
> the
> > > interface of these slabs and my pdb results from a monte carlo
> simulation
> > > where the spheriods highlight the changes in shape of my copolymers at
> the
> > > interface.
> > >
> > > Has anyone succeeded in making colored transparent boxes? Or might there
> be
> > > another strategy?
> > >
> > > Thanks,
> > >
> > > Dean Waldow
> > >
> > > Here is the script (modified from one that makes a bounding box I
> believe)
> > > that makes my current solid box which turns grey with I issue the ray
> > > command:
> > >
> > >
> > > from pymol.cgo import *
> > > from pymol import cmd
> > > #
> > > # SEGMENT     1
> > > box = [
> > >   LINEWIDTH, 1.0,
> > >   BEGIN, VERTEX,
> > >   COLOR, 0.0, 0.0, 0.0,
> > >
> > > # Face 1
> > >   VERTEX,   55.000,   55.000,   55.000,
> > >   VERTEX,   55.000,    5.000,   55.000,
> > >   VERTEX,   55.000,    5.000,    5.000,
> > >
> > >   VERTEX,   55.000,    5.000,    5.000,
> > >   VERTEX,   55.000,   55.000,    5.000,
> > >   VERTEX,   55.000,   55.000,   55.000,
> > >
> > > # Face 2
> > >   VERTEX,    5.000,   55.000,   55.000,
> > >   VERTEX,    5.000,    5.000,   55.000,
> > >   VERTEX,    5.000,    5.000,    5.000,
> > >
> > >   VERTEX,    5.000,    5.000,    5.000,
> > >   VERTEX,    5.000,   55.000,    5.000,
> > >   VERTEX,    5.000,   55.000,   55.000,
> > >
> > > # Face 3
> > >   VERTEX,   55.000,   55.000,   55.000,
> > >   VERTEX,    5.000,   55.000,   55.000,
> > >   VERTEX,    5.000,   55.000,    5.000,
> > >
> > >   VERTEX,    5.000,   55.000,    5.000,
> > >   VERTEX,   55.000,   55.000,    5.000,
> > >   VERTEX,   55.000,   55.000,   55.000,
> > >
> > > # Face 4
> > >   VERTEX,   55.000,    5.000,   55.000,
> > >   VERTEX,    5.000,    5.000,   55.000,
> > >   VERTEX,    5.000,    5.000,    5.000,
> > >
> > >   VERTEX,    5.000,    5.000,    5.000,
> > >   VERTEX,   55.000,    5.000,    5.000,
> > >   VERTEX,   55.000,    5.000,   55.000,
> > >
> > > # Face 5
> > >   VERTEX,   55.000,   55.000,   55.000,
> > >   VERTEX,    5.000,   55.000,   55.000,
> > >   VERTEX,    5.000,    5.000,   55.000,
> > >
> > >   VERTEX,    5.000,    5.000,   55.000,
> > >   VERTEX,   55.000,    5.000,   55.000,
> > >   VERTEX,   55.000,   55.000,   55.000,
> > >
> > > # Face 6
> > >   VERTEX,   55.000,   55.000,    5.000,
> > >   VERTEX,    5.000,   55.000,    5.000,
> > >   VERTEX,    5.000,    5.000,    5.000,
> > >
> > >   VERTEX,    5.000,    5.000,    5.000,
> > >   VERTEX,   55.000,    5.000,    5.000,
> > >   VERTEX,   55.000,   55.000,    5.000,
> > >
> > >   END
> > >   ]
> > >
> > > obj = box
> > >
> > > cmd.load_cgo(obj,'segment',   1)
> > >
> > >
> > >
> > > --
> > >
> > > ------------------------------------------------------------------------
> > >
> > > Dean Waldow, Professor               (253) 535-7533
> > >
> > > Department of Chemistry              (253) 536-5055 (FAX)
> > >
> > > Pacific Lutheran University          wa...@ch...
> > >
> > > Tacoma, WA  98447   USA              http://www.chem.plu.edu/waldow/
> > >
> > > ------------------------------------------------------------------------
> > >
> > > ---> CIRRUS and the Chemistry homepage: <" rel="nofollow">http://www.chem.plu.edu/> <----
> > >
> > > ------------------------------------------------------------------------
> > >
> > >
> > >
> > >
> > >
> -------------------------------------------------------------------------
> > >  This SF.net email is sponsored by the 2008 JavaOne(SM) Conference
> > >  Don't miss this year's exciting event. There's still time to save $100.
> > >  Use priority code J8TL2D2.
> > >
> > >
> http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone
> > > _______________________________________________
> > >  PyMOL-users mailing list
> > >  PyM...@li...
> > >  https://lists.sourceforge.net/lists/listinfo/pymol-users
> > >
> > >
> > >
> > >
> > >
> > >
> > > --
> > > Tsjerk A. Wassenaar, Ph.D.
> > > Junior UD (post-doc)
> > > Biomolecular NMR, Bijvoet Center
> > > Utrecht University
> > > Padualaan 8
> > > 3584 CH Utrecht
> > > The Netherlands
> > > P: +31-30-2539931
> > > F: +31-30-2537623<rect.py>
> > >
> > > --
> > >
> > >
> > > ------------------------------------------------------------------------
> > >
> > > Dean Waldow, Professor               (253) 535-7533
> > >
> > > Department of Chemistry              (253) 536-5055 (FAX)
> > >
> > > Pacific Lutheran University          wa...@ch...
> > >
> > > Tacoma, WA  98447   USA              http://www.chem.plu.edu/waldow/
> > >
> > > ------------------------------------------------------------------------
> > >
> > > ---> CIRRUS and the Chemistry homepage: <" rel="nofollow">http://www.chem.plu.edu/> <----
> > >
> > > ------------------------------------------------------------------------
> > >
> > >
> > >
> > >
> > >
> >
> >
> >
> > --
> > Tsjerk A. Wassenaar, Ph.D.
> > Junior UD (post-doc)
> > Biomolecular NMR, Bijvoet Center
> > Utrecht University
> > Padualaan 8
> > 3584 CH Utrecht
> > The Netherlands
> > P: +31-30-2539931
> > F: +31-30-2537623
> >
>
>



-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

Does anyone still have the software / scripts required to make SGI dials box
work with Pymol?
I found an old thred back in 2004 but all the links are dead.
Dials may not be necessary, but as I have some lying around doing nothing,
I¹d very much like to apply them to Pymol (especially as my SGI has no wheel
mouse).
Pparently SGI dials can be adapted to work on a PC, so if you find a dials
box it could come in handy.

Gary

The original pymol-users message can be found here:
http://sourceforge.net/mailarchive/message.php?msg_id=4ABE591494FF5246B38C0C
DA4CBFAFE80154BE4A%40exchange4.slac.stanford.edu







 Prof. Gary J. Hunter,
 Department of Physiology and Biochemistry,
 University of Malta, Msida, MSD 06, Malta.
 phone: +356 2340 2917
 phone: +356 21316655 (secretary),  Fax: +356 21310577

Hi Tsjerk,

It works Great!  Thanks so much. I'll have to study your code to see  
where I was going wrong.

Dean

On Apr 23, 2008, at 10:39 AM, Tsjerk Wassenaar wrote:

> Hi Dean,
>
> Funny, really. Last week I was just playing around a bit with creating
> boxes in pymol, e.g. to create a bounding box, and I wanted to have it
> transparent. So here's a script, giving you a function 'rect', which
> takes two tuples, specifying the far edges of the box:
>
> rect( [x0,y0,z0], [x1,y1,z1],name="box",rgbt=[1,1,0,0.5])
>
> The rgbt argument specifies the color and transparency. Feel free to
> go through the code to see how things are done (although you won't
> hear me say it's perfect). In case you have any suggestions, also feel
> free to contact me, either on or off list.
>
> I hope it helps. Cheers,
>
> Tsjerk
>
> On Wed, Apr 23, 2008 at 5:22 PM, Dean Waldow <wa...@ch...>  
> wrote:
>>  Hi Folks,
>>
>> I am very new to pymol and have been learning a lot about using  
>> (mac)pymol.
>> However, I seem to be unable to make a box which is transparent  
>> and has
>> color. I have been able to make a box with the *.py script below  
>> but when I
>> do the ray tracing to get a nice image the box turns to grey /  
>> black. I have
>> also been able to to make prolate and oblate spheriods using ideas  
>> from the
>> pymol wiki.
>>
>> My eventual goal is to have about three slabs or boxes with  
>> spheroids at the
>> interface of these slabs and my pdb results from a monte carlo  
>> simulation
>> where the spheriods highlight the changes in shape of my  
>> copolymers at the
>> interface.
>>
>> Has anyone succeeded in making colored transparent boxes? Or might  
>> there be
>> another strategy?
>>
>> Thanks,
>>
>> Dean Waldow
>>
>> Here is the script (modified from one that makes a bounding box I  
>> believe)
>> that makes my current solid box which turns grey with I issue the ray
>> command:
>>
>>
>> from pymol.cgo import *
>> from pymol import cmd
>> #
>> # SEGMENT     1
>> box = [
>>    LINEWIDTH, 1.0,
>>    BEGIN, VERTEX,
>>    COLOR, 0.0, 0.0, 0.0,
>>
>> # Face 1
>>    VERTEX,   55.000,   55.000,   55.000,
>>    VERTEX,   55.000,    5.000,   55.000,
>>    VERTEX,   55.000,    5.000,    5.000,
>>
>>    VERTEX,   55.000,    5.000,    5.000,
>>    VERTEX,   55.000,   55.000,    5.000,
>>    VERTEX,   55.000,   55.000,   55.000,
>>
>> # Face 2
>>    VERTEX,    5.000,   55.000,   55.000,
>>    VERTEX,    5.000,    5.000,   55.000,
>>    VERTEX,    5.000,    5.000,    5.000,
>>
>>    VERTEX,    5.000,    5.000,    5.000,
>>    VERTEX,    5.000,   55.000,    5.000,
>>    VERTEX,    5.000,   55.000,   55.000,
>>
>> # Face 3
>>    VERTEX,   55.000,   55.000,   55.000,
>>    VERTEX,    5.000,   55.000,   55.000,
>>    VERTEX,    5.000,   55.000,    5.000,
>>
>>    VERTEX,    5.000,   55.000,    5.000,
>>    VERTEX,   55.000,   55.000,    5.000,
>>    VERTEX,   55.000,   55.000,   55.000,
>>
>> # Face 4
>>    VERTEX,   55.000,    5.000,   55.000,
>>    VERTEX,    5.000,    5.000,   55.000,
>>    VERTEX,    5.000,    5.000,    5.000,
>>
>>    VERTEX,    5.000,    5.000,    5.000,
>>    VERTEX,   55.000,    5.000,    5.000,
>>    VERTEX,   55.000,    5.000,   55.000,
>>
>> # Face 5
>>    VERTEX,   55.000,   55.000,   55.000,
>>    VERTEX,    5.000,   55.000,   55.000,
>>    VERTEX,    5.000,    5.000,   55.000,
>>
>>    VERTEX,    5.000,    5.000,   55.000,
>>    VERTEX,   55.000,    5.000,   55.000,
>>    VERTEX,   55.000,   55.000,   55.000,
>>
>> # Face 6
>>    VERTEX,   55.000,   55.000,    5.000,
>>    VERTEX,    5.000,   55.000,    5.000,
>>    VERTEX,    5.000,    5.000,    5.000,
>>
>>    VERTEX,    5.000,    5.000,    5.000,
>>    VERTEX,   55.000,    5.000,    5.000,
>>    VERTEX,   55.000,   55.000,    5.000,
>>
>>    END
>>    ]
>>
>> obj = box
>>
>> cmd.load_cgo(obj,'segment',   1)
>>
>>
>>
>> --
>>
>> --------------------------------------------------------------------- 
>> ---
>>
>> Dean Waldow, Professor               (253) 535-7533
>>
>> Department of Chemistry              (253) 536-5055 (FAX)
>>
>> Pacific Lutheran University          wa...@ch...
>>
>> Tacoma, WA  98447   USA              http://www.chem.plu.edu/waldow/
>>
>> --------------------------------------------------------------------- 
>> ---
>>
>> ---> CIRRUS and the Chemistry homepage: <" rel="nofollow">http://www.chem.plu.edu/>  
>> <----
>>
>> --------------------------------------------------------------------- 
>> ---
>>
>>
>>
>>
>> --------------------------------------------------------------------- 
>> ----
>>  This SF.net email is sponsored by the 2008 JavaOne(SM) Conference
>>  Don't miss this year's exciting event. There's still time to save  
>> $100.
>>  Use priority code J8TL2D2.
>>
>> http://ad.doubleclick.net/clk;198757673;13503038;p?http:// 
>> java.sun.com/javaone
>> _______________________________________________
>>  PyMOL-users mailing list
>>  PyM...@li...
>>  https://lists.sourceforge.net/lists/listinfo/pymol-users
>>
>>
>
>
>
> -- 
> Tsjerk A. Wassenaar, Ph.D.
> Junior UD (post-doc)
> Biomolecular NMR, Bijvoet Center
> Utrecht University
> Padualaan 8
> 3584 CH Utrecht
> The Netherlands
> P: +31-30-2539931
> F: +31-30-2537623<rect.py>

-- 
------------------------------------------------------------------------
Dean Waldow, Professor               (253) 535-7533
Department of Chemistry              (253) 536-5055 (FAX)
Pacific Lutheran University          wa...@ch...
Tacoma, WA  98447   USA              http://www.chem.plu.edu/waldow/
------------------------------------------------------------------------
---> CIRRUS and the Chemistry homepage: <" rel="nofollow">http://www.chem.plu.edu/> <----
------------------------------------------------------------------------

Hi Dean,

Funny, really. Last week I was just playing around a bit with creating
boxes in pymol, e.g. to create a bounding box, and I wanted to have it
transparent. So here's a script, giving you a function 'rect', which
takes two tuples, specifying the far edges of the box:

rect( [x0,y0,z0], [x1,y1,z1],name="box",rgbt=[1,1,0,0.5])

The rgbt argument specifies the color and transparency. Feel free to
go through the code to see how things are done (although you won't
hear me say it's perfect). In case you have any suggestions, also feel
free to contact me, either on or off list.

I hope it helps. Cheers,

Tsjerk

On Wed, Apr 23, 2008 at 5:22 PM, Dean Waldow <wa...@ch...> wrote:
>  Hi Folks,
>
> I am very new to pymol and have been learning a lot about using (mac)pymol.
> However, I seem to be unable to make a box which is transparent and has
> color. I have been able to make a box with the *.py script below but when I
> do the ray tracing to get a nice image the box turns to grey / black. I have
> also been able to to make prolate and oblate spheriods using ideas from the
> pymol wiki.
>
> My eventual goal is to have about three slabs or boxes with spheroids at the
> interface of these slabs and my pdb results from a monte carlo simulation
> where the spheriods highlight the changes in shape of my copolymers at the
> interface.
>
> Has anyone succeeded in making colored transparent boxes? Or might there be
> another strategy?
>
> Thanks,
>
> Dean Waldow
>
> Here is the script (modified from one that makes a bounding box I believe)
> that makes my current solid box which turns grey with I issue the ray
> command:
>
>
> from pymol.cgo import *
> from pymol import cmd
> #
> # SEGMENT     1
> box = [
>    LINEWIDTH, 1.0,
>    BEGIN, VERTEX,
>    COLOR, 0.0, 0.0, 0.0,
>
> # Face 1
>    VERTEX,   55.000,   55.000,   55.000,
>    VERTEX,   55.000,    5.000,   55.000,
>    VERTEX,   55.000,    5.000,    5.000,
>
>    VERTEX,   55.000,    5.000,    5.000,
>    VERTEX,   55.000,   55.000,    5.000,
>    VERTEX,   55.000,   55.000,   55.000,
>
> # Face 2
>    VERTEX,    5.000,   55.000,   55.000,
>    VERTEX,    5.000,    5.000,   55.000,
>    VERTEX,    5.000,    5.000,    5.000,
>
>    VERTEX,    5.000,    5.000,    5.000,
>    VERTEX,    5.000,   55.000,    5.000,
>    VERTEX,    5.000,   55.000,   55.000,
>
> # Face 3
>    VERTEX,   55.000,   55.000,   55.000,
>    VERTEX,    5.000,   55.000,   55.000,
>    VERTEX,    5.000,   55.000,    5.000,
>
>    VERTEX,    5.000,   55.000,    5.000,
>    VERTEX,   55.000,   55.000,    5.000,
>    VERTEX,   55.000,   55.000,   55.000,
>
> # Face 4
>    VERTEX,   55.000,    5.000,   55.000,
>    VERTEX,    5.000,    5.000,   55.000,
>    VERTEX,    5.000,    5.000,    5.000,
>
>    VERTEX,    5.000,    5.000,    5.000,
>    VERTEX,   55.000,    5.000,    5.000,
>    VERTEX,   55.000,    5.000,   55.000,
>
> # Face 5
>    VERTEX,   55.000,   55.000,   55.000,
>    VERTEX,    5.000,   55.000,   55.000,
>    VERTEX,    5.000,    5.000,   55.000,
>
>    VERTEX,    5.000,    5.000,   55.000,
>    VERTEX,   55.000,    5.000,   55.000,
>    VERTEX,   55.000,   55.000,   55.000,
>
> # Face 6
>    VERTEX,   55.000,   55.000,    5.000,
>    VERTEX,    5.000,   55.000,    5.000,
>    VERTEX,    5.000,    5.000,    5.000,
>
>    VERTEX,    5.000,    5.000,    5.000,
>    VERTEX,   55.000,    5.000,    5.000,
>    VERTEX,   55.000,   55.000,    5.000,
>
>    END
>    ]
>
> obj = box
>
> cmd.load_cgo(obj,'segment',   1)
>
>
>
> --
>
> ------------------------------------------------------------------------
>
> Dean Waldow, Professor               (253) 535-7533
>
> Department of Chemistry              (253) 536-5055 (FAX)
>
> Pacific Lutheran University          wa...@ch...
>
> Tacoma, WA  98447   USA              http://www.chem.plu.edu/waldow/
>
> ------------------------------------------------------------------------
>
> ---> CIRRUS and the Chemistry homepage: <" rel="nofollow">http://www.chem.plu.edu/> <----
>
> ------------------------------------------------------------------------
>
>
>
>
> -------------------------------------------------------------------------
>  This SF.net email is sponsored by the 2008 JavaOne(SM) Conference
>  Don't miss this year's exciting event. There's still time to save $100.
>  Use priority code J8TL2D2.
>
> http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone
> _______________________________________________
>  PyMOL-users mailing list
>  PyM...@li...
>  https://lists.sourceforge.net/lists/listinfo/pymol-users
>
>



-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

Hi Folks,

I am very new to pymol and have been learning a lot about using (mac) 
pymol. However, I seem to be unable to make a box which is  
transparent and has color. I have been able to make a box with the  
*.py script below but when I do the ray tracing to get a nice image  
the box turns to grey / black. I have also been able to to make  
prolate and oblate spheriods using ideas from the pymol wiki.

My eventual goal is to have about three slabs or boxes with spheroids  
at the interface of these slabs and my pdb results from a monte carlo  
simulation where the spheriods highlight the changes in shape of my  
copolymers at the interface.

Has anyone succeeded in making colored transparent boxes? Or might  
there be another strategy?

Thanks,

Dean Waldow

Here is the script (modified from one that makes a bounding box I  
believe) that makes my current solid box which turns grey with I  
issue the ray command:

from pymol.cgo import *
from pymol import cmd
#
# SEGMENT     1
box = [
    LINEWIDTH, 1.0,
    BEGIN, VERTEX,
    COLOR, 0.0, 0.0, 0.0,

# Face 1
    VERTEX,   55.000,   55.000,   55.000,
    VERTEX,   55.000,    5.000,   55.000,
    VERTEX,   55.000,    5.000,    5.000,

    VERTEX,   55.000,    5.000,    5.000,
    VERTEX,   55.000,   55.000,    5.000,
    VERTEX,   55.000,   55.000,   55.000,

# Face 2
    VERTEX,    5.000,   55.000,   55.000,
    VERTEX,    5.000,    5.000,   55.000,
    VERTEX,    5.000,    5.000,    5.000,

    VERTEX,    5.000,    5.000,    5.000,
    VERTEX,    5.000,   55.000,    5.000,
    VERTEX,    5.000,   55.000,   55.000,

# Face 3
    VERTEX,   55.000,   55.000,   55.000,
    VERTEX,    5.000,   55.000,   55.000,
    VERTEX,    5.000,   55.000,    5.000,

    VERTEX,    5.000,   55.000,    5.000,
    VERTEX,   55.000,   55.000,    5.000,
    VERTEX,   55.000,   55.000,   55.000,

# Face 4
    VERTEX,   55.000,    5.000,   55.000,
    VERTEX,    5.000,    5.000,   55.000,
    VERTEX,    5.000,    5.000,    5.000,

    VERTEX,    5.000,    5.000,    5.000,
    VERTEX,   55.000,    5.000,    5.000,
    VERTEX,   55.000,    5.000,   55.000,

# Face 5
    VERTEX,   55.000,   55.000,   55.000,
    VERTEX,    5.000,   55.000,   55.000,
    VERTEX,    5.000,    5.000,   55.000,

    VERTEX,    5.000,    5.000,   55.000,
    VERTEX,   55.000,    5.000,   55.000,
    VERTEX,   55.000,   55.000,   55.000,

# Face 6
    VERTEX,   55.000,   55.000,    5.000,
    VERTEX,    5.000,   55.000,    5.000,
    VERTEX,    5.000,    5.000,    5.000,

    VERTEX,    5.000,    5.000,    5.000,
    VERTEX,   55.000,    5.000,    5.000,
    VERTEX,   55.000,   55.000,    5.000,

    END
    ]

obj = box

cmd.load_cgo(obj,'segment',   1)


-- 
------------------------------------------------------------------------
Dean Waldow, Professor               (253) 535-7533
Department of Chemistry              (253) 536-5055 (FAX)
Pacific Lutheran University          wa...@ch...
Tacoma, WA  98447   USA              http://www.chem.plu.edu/waldow/
------------------------------------------------------------------------
---> CIRRUS and the Chemistry homepage: <" rel="nofollow">http://www.chem.plu.edu/> <----
------------------------------------------------------------------------