pymol-users — Collaborative support and tips for PyMOL users

Re: [PyMOL] Re: PyMOL-users digest, Vol 1 #210 - 2 msgs

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

On Wed, 13 Nov 2002, Michael Ford wrote:

> This list really needs a reflector (ala AMBER mail reflector) so that we
> can benefit from each others pains.  It would really be in everyone's
> best interest. (less repetition of answers, less asking of questions
> already answered!)
>
> Just my humble opinion,
>
> (yes I realize there are other things to work on!)

Michael,

I am not sure what you mean exactly by a "reflector", but there is
an archive of the mailing list located at:

http://sourceforge.net/mailarchive/forum.php?forum_id=60

You can browse the archive (currently 640 messages) cronologically or
search using keywords.

Cheers,
Warren

[PyMOL] Re: PyMOL-users digest, Vol 1 #211 - 1 msg

[<kk...@ga...>]

> Date: Wed, 13 Nov 2002 15:26:22 -0500
> From: Michael Ford <mf...@cc...>
> To: pym...@li...
> Subject: [PyMOL] Re: PyMOL-users digest, Vol 1 #210 - 2 msgs
> 
> This list really needs a reflector (ala AMBER mail reflector) so that we
> can benefit from each others pains.  It would really be in everyone's
> best interest. (less repetition of answers, less asking of questions
> already answered!)
> 
> Just my humble opinion,
> 
> (yes I realize there are other things to work on!)
> 
> Mike Ford
> 

Well that's of course correct if this can be achieved.
I have a different suggestion, though.
I guess it is time for a book totally devoted in the
graphical presentation of (biological) molecules.
Of course there will be considerable contents about
computer graphics in such a book, but it is still possible
to compile such a book so that the topics most important for
people who wish to use some packages to prepare molecular graphics
are appropriately emphasized and clearly explained.

The problem of an FAQ is always that new comers often do not even
know how to describe their problems adequately.
Just like hunting for integral formular in a math table,
we rookies just do not know what our problems are like in those
very valuable references.
An introductory book will be very very good for us.

Since Warren has started his work in an environment which I think
is the best (Python I mean, due to the flexibility of it.),
I think it a great idea if someone can write such a book with
PyMol as the example package.
That will be an ideal book for me if there is one.

Regards,
K.K.Liang
IAMS, Academia Sinica

[PyMOL] Re: PyMOL-users digest, Vol 1 #210 - 2 msgs

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

This list really needs a reflector (ala AMBER mail reflector) so that we
can benefit from each others pains.  It would really be in everyone's
best interest. (less repetition of answers, less asking of questions
already answered!)

Just my humble opinion,

(yes I realize there are other things to work on!)




Mike Ford

pym...@li... wrote:
> 
> Send PyMOL-users mailing list submissions to
>         pym...@li...
> 
> To subscribe or unsubscribe via the World Wide Web, visit
>         https://lists.sourceforge.net/lists/listinfo/pymol-users
> or, via email, send a message with subject or body 'help' to
>         pym...@li...
> 
> You can reach the person managing the list at
>         pym...@li...
> 
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of PyMOL-users digest..."
> 
> Today's Topics:
> 
>    1. Color plotting of electron density contours? (wg...@ch...)
>    2. RE: Color plotting of electron density contours? (DeLano, Warren)
> 
> --__--__--
> 
> Message: 1
> Date: Tue, 12 Nov 2002 13:27:17 -0800
> From: wg...@ch...
> To: pym...@li...
> Subject: [PyMOL] Color plotting of electron density contours?
> 
> Hi Folks:
> 
> Is there a way to display a cross-section of electron density
> (false)-color-coded for electron density?  In other words, I would like
> to produce a 2-D plot that looks like a contour map (eg: output of CCP4
> npo) but color-coded with respect to electron density.  A continuum, if
> possible, would actually be better than a series of contour lines.
> 
> Has this by any chance been implemented in pymol or anywhere?
> 
> Many thanks,
> 
> Bill Scott
> 
> William G. Scott
> 
> Associate Professor
> Department of Chemistry and Biochemistry
> and The Center for the Molecular Biology of RNA
> Sinsheimer Laboratories
> University of California at Santa Cruz
> Santa Cruz, California 95064
> USA
> 
> phone:  +1-831-459-5367 (office)
>                 +1-831-459-5292 (lab)
> fax:         +1-831-4593139  (fax)
> 
> --__--__--
> 
> Message: 2
> Subject: RE: [PyMOL] Color plotting of electron density contours?
> Date: Tue, 12 Nov 2002 13:54:14 -0800
> From: "DeLano, Warren" <wa...@su...>
> To: <wg...@ch...>,
>         <pym...@li...>
> 
> Bill,
> 
> There has been some discussion of this desirable feature, but it doesn't =
> currently exist.
> 
> Cheers,
> Warren
> 
> > -----Original Message-----
> > From: wg...@ch... [mailto:wg...@ch...]
> > Sent: Tuesday, November 12, 2002 1:27 PM
> > To: pym...@li...
> > Subject: [PyMOL] Color plotting of electron density contours?
> >=20
> >=20
> > Hi Folks:
> >=20
> > Is there a way to display a cross-section of electron density =20
> > (false)-color-coded for electron density?  In other words, I=20
> > would like=20
> > to produce a 2-D plot that looks like a contour map (eg:=20
> > output of CCP4=20
> > npo) but color-coded with respect to electron density.  A=20
> > continuum, if=20
> > possible, would actually be better than a series of contour lines.
> >=20
> > Has this by any chance been implemented in pymol or anywhere?
> >=20
> > Many thanks,
> >=20
> > Bill Scott
> >=20
> >=20
> >=20
> > William G. Scott
> >=20
> > 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
> >=20
> > phone:  +1-831-459-5367 (office)
> >                 +1-831-459-5292 (lab)
> > fax:         +1-831-4593139  (fax)
> >=20
> >=20
> >=20
> >=20
> > -------------------------------------------------------
> > This sf.net email is sponsored by:=20
> > To learn the basics of securing your web site with SSL,=20
> > click here to get a FREE TRIAL of a Thawte Server Certificate:=20
> > http://www.gothawte.com/rd522.html
> > _______________________________________________
> > PyMOL-users mailing list
> > PyM...@li...
> > https://lists.sourceforge.net/lists/listinfo/pymol-users
> >=20
> 
> --__--__--
> 
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
> 
> End of PyMOL-users Digest

RE: [PyMOL] Color plotting of electron density contours?

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

Bill,

There has been some discussion of this desirable feature, but it doesn't =
currently exist.

Cheers,
Warren


> -----Original Message-----
> From: wg...@ch... [mailto:wg...@ch...]
> Sent: Tuesday, November 12, 2002 1:27 PM
> To: pym...@li...
> Subject: [PyMOL] Color plotting of electron density contours?
>=20
>=20
> Hi Folks:
>=20
> Is there a way to display a cross-section of electron density =20
> (false)-color-coded for electron density?  In other words, I=20
> would like=20
> to produce a 2-D plot that looks like a contour map (eg:=20
> output of CCP4=20
> npo) but color-coded with respect to electron density.  A=20
> continuum, if=20
> possible, would actually be better than a series of contour lines.
>=20
> Has this by any chance been implemented in pymol or anywhere?
>=20
> Many thanks,
>=20
> Bill Scott
>=20
>=20
>=20
> William G. Scott
>=20
> 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
>=20
> phone:  +1-831-459-5367 (office)
>                 +1-831-459-5292 (lab)
> fax:         +1-831-4593139  (fax)
>=20
>=20
>=20
>=20
> -------------------------------------------------------
> This sf.net email is sponsored by:=20
> To learn the basics of securing your web site with SSL,=20
> click here to get a FREE TRIAL of a Thawte Server Certificate:=20
> http://www.gothawte.com/rd522.html
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20

[PyMOL] Color plotting of electron density contours?

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

Hi Folks:

Is there a way to display a cross-section of electron density  
(false)-color-coded for electron density?  In other words, I would like 
to produce a 2-D plot that looks like a contour map (eg: output of CCP4 
npo) but color-coded with respect to electron density.  A continuum, if 
possible, would actually be better than a series of contour lines.

Has this by any chance been implemented in pymol or anywhere?

Many thanks,

Bill Scott



William G. Scott

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

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

[PyMOL] PyObjC for OS X

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

Howdie Citizens:

There is a new PyObjC web page at 
http://pyobjc.sourceforge.net/index.php complete with a truly tasteful 
icon.

[PyMOL] mixing pymol and powerpoint (or equivalent) in a presentation

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

Hi Folks:

Awhile ago I suggested using "hyperlinks" in powerpoint to call pymol 
in order to embed this in a presentation.  The disadvantages of this 
are that it requires a lag for pymol startup time, powerpoint warns you 
about the possibility that you are opening a macrovirus with a warning 
that you can't turn off in preferences even though it claims you can 
(as if pymol, rather than a microsoft product, was the software that 
could be mistaken for a virus), etc.

I think someone already suggested running powerpoint from within pymol.

This in fact works FAR better.  Here's how to do it in OS X, although I 
imagine it would be similar in other operating systems but with 
slightly different syntax.

First, define an alias, for example,

alias pymol  /Applications/PyMOL/Darwin/pymol.com -q -e 
/Users/homedirectory/pymol/alias.pml

The -q and -e options give you a full screen that is blank.  Here I 
tell it to read a file that contains further aliases in  
/Users/homedirectory/pymol/alias.pml


Second, divide your powerpoint presentations up into subsets that flank 
the positions in which you would want to insert a pymol-based 
demonstration.  Save each of these as a powerpoint "show" or "package" 
with a .pps suffix.  Check the option to show at full screen when 
opening.  (Keep a normal ppt version for future edits, as saving in 
this format isn't readily reversible.)

Third, use the python os.system()  command to open the powerpoint show 
file.

[The os.system() command lets you run any operating system command, 
program, shell script, etc,  eg:  os.system("date") runs the unix date 
command, which can be very handy if you are like me and don't know what 
day and time it is.]

On OS X you can use the      open filename   command as the equivalent 
of double-clicking a file to open it.  I imagine there is something 
similar for windows but I don't know what it is.

Here is part of my /Users/homedirectory/pymol/alias.pml  file to give 
an idea for how this is implemented:

alias 1, os.system("open /Users/wgscott/pymol/part_1/part_1.pps");
alias 2, @/Users/wgscott/pymol/low.pml;
alias 3, mstop; mclear; hide all; os.system("open 
/Users/wgscott/pymol/part_2/part_2.pps");
alias 4, @/Users/wgscott/pymol/high.pml


So when I invoke pymol at the command line using the above alias for 
pymol, I will get a black screen, blank, with the PyMOL>  prompt at the 
bottom left.

If I issue 1 at the prompt, i.e.,

PyMOL>  1

Then the file /Users/wgscott/pymol/part_1/part_1.pps opens.  This will 
go faster if powerpoint has already been started.  Then powerpoint 
takes over the screen and I go through the powerpoint presentation to 
the end.  At the end, the file spontaneously shuts and I am back to the 
pymol screen.  I have to click on it (although would prefer a better 
way) and then I type in the screen 2, i.e.,

PyMOL>  2

and this runs another pymol script that plays a movie for me, 
/Users/wgscott/pymol/low.pml

When I am done, I type 3,

PyMOL>  3

and we are back to the second part of my powerpoint presentation.  
mstop; mclear; hide all; clears the screen and movie memory and then 
the next presentation is opened again and I can go through it.  Upon 
termination, I get a blank pymol screen back, click on it, enter 4, and 
I am into my next pymol movie, scripted in high.pml

Both powerpoint and pymol remain open but in the background, so 
transition times are kept to a minimum.

  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)

RE: [PyMOL] help with surface parameters

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

Scott,

> From: Scott Classen [mailto:cl...@uc...]
>=20
> Hello fellow PyMOLers,
> 	Is the surface in PyMOL a solvent accessible surface or=20
> a molecular=20
> surface? It looks like a solvent accessible surface to me. Is=20
> there any=20
> way to change the radius of the water probe that is used to=20
> create the=20
> surface?

PyMOL's default surface is a water contact surface (approximates a =
Connolly surface).

>I noticed that there are a few surface settings, but I can't=20
> figure out what effects they are having on the displayed surface. Can=20
> anybody shed light on these commands? What are their default=20
> settings?=20

You can use the settings editor to get the default (except if you're =
using the native OSX version on a mac).

> What are the high and low values they can take?
>=20
> surface_best
> surface_normal
> surface_proximity
> surface_quality

These settings haven't yet been documented, but they will be in an =
upcoming version of the manual. =20

>   I would like to create a fairly tight molecular surface and I just=20
> can't figure it out. ANy help would be appreciated.

show surface
set surface_quality=3D1
set solvent_radius=3D0.8
rebuild

WARNING: PyMOL may crash if solvent_radius is too low.  If it does, try =
incrementing it by 0.1 until it stabilizes.

Cheers,
Warren

[PyMOL] help with surface parameters

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

Hello fellow PyMOLers,
	Is the surface in PyMOL a solvent accessible surface or a molecular 
surface? It looks like a solvent accessible surface to me. Is there any 
way to change the radius of the water probe that is used to create the 
surface? I noticed that there are a few surface settings, but I can't 
figure out what effects they are having on the displayed surface. Can 
anybody shed light on these commands? What are their default settings? 
What are the high and low values they can take?

surface_best
surface_ normal
surface_ proximity
surface_ quality

  I would like to create a fairly tight molecular surface and I just 
can't figure it out. ANy help would be appreciated.

Thanks in advance,
Scott



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

[PyMOL] PyMOL movie example (SRP S-domain assembly)

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

Hello,

We have just finished making an animation of SRP S-domain assembly (based 
on stuctures we recently determined) with the Yale Morph Server and PyMOL.
  Since other users who are new to making movies with PyMOL (just like I 
was up to month ago) might be interested in looking at the script we used 
to combine the various assembly steps as yet another example, I attach the 
URL:

http://www.mssm.edu/students/jovinl02/research/srp_assembly_movie.html

Ciao, Luca

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

[PyMOL] practical PyMOL FAQ

[Kristian R. <kri...@be...>]

Hello all,

In case somebody is new to the mailing list and wonders what problems 
have already been solved, it might be a good idea to take a look at:

http://www.rubor.de/bioinf/pymol_tips.html

which is basically a collection of examples for doing things with molecules.
I have compiled a lot of recent postings there. However, the topics 
around Stereo 3D and MacOSX were not included (i know nothing about both 
of them).


Kristian

RE: [PyMOL] heavy atom selection

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

Tara:

One easy way is simply

(not hydro)

Wildcards in atom names are currently disabled because nucleic acid =
chemists use asterices in atom names.  However it is better to use the =
element symbol, since there is no guarantee that an atom name will start =
with the element:

(elem c,n,o,s)

Cheers,
Warren



> -----Original Message-----
> From: Tara Sprules [mailto:tsp...@ua...]
> Sent: Thursday, November 07, 2002 1:38 PM
> To: pym...@so...
> Subject: [PyMOL] heavy atom selection
>=20
>=20
> Hi,
>=20
> I am using PyMOL for OSX, and would like to select heavy=20
> atoms for a fit.
> Looking at the manual pages it seems as though the term=20
> hetatm exists, but
> it is not recognized when I try to use it. How can I select=20
> heavy atoms? I
> tried making a selection ie select heavy=3D (name c*,n*,o*,s*)- but
> obviously have the wrong wildcard.
>=20
> Thanks,
>=20
> Tara
>=20
> Tara Sprules
> Post-Doctoral Fellow
> Department of Chemistry
> University of Alberta
>=20
>=20
>=20
> -------------------------------------------------------
> This sf.net email is sponsored by: See the NEW Palm=20
> Tungsten T handheld. Power & Color in a compact size!
> http://ads.sourceforge.net/cgi-bin/redirect.pl?palm0001en
> _______________________________________________
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> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20

[PyMOL] heavy atom selection

[Tara S. <tsp...@ua...>]

Hi,

I am using PyMOL for OSX, and would like to select heavy atoms for a fit.
Looking at the manual pages it seems as though the term hetatm exists, but
it is not recognized when I try to use it. How can I select heavy atoms? I
tried making a selection ie select heavy= (name c*,n*,o*,s*)- but
obviously have the wrong wildcard.

Thanks,

Tara

Tara Sprules
Post-Doctoral Fellow
Department of Chemistry
University of Alberta

RE: [PyMOL] .py scripts on OS 10.1

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

The native OSX version doesn't support the Tkinter-based user interface, =
but you can use the unaccelerated versions of PyMOL available in Fink or =
GNU/Darwin.

Warren


> -----Original Message-----
> From: robert del vecchio [mailto:del...@cs...]
> Sent: Tuesday, November 05, 2002 9:00 AM
> To: pym...@li...
> Subject: [PyMOL] .py scripts on OS 10.1
>=20
>=20
> 	I am using PyMol 0.84 for Mac OS 10.1(10.1.5) and was=20
> wondering if=20
> it is possible to run .py scripts such as ScriptBox.py.
> When I start PyMol by clicking on the 10.1 icon and then try=20
> to run .py=20
> scripts (run scriptx.py) I get some error messages including the=20
> following:
> 	"import _tkinter # If this fails your Python may not be=20
> configured=20
> for Tk
> 	ImportError: No module named _tkinter"
> Is there a way to configure Python properly or is this not=20
> possible on=20
> the Mac?  Thanks for your help.
> Bob Del Vecchio
>=20
> Robert Del Vecchio
> Cold Spring Harbor Laboratory
> Demerec Building
> 1 Bungtown Road
> Cold Spring Harbor, NY  11724
> email: del...@cs...
> tel: (516)367-8314
>=20
>=20
>=20
> -------------------------------------------------------
> This sf.net email is sponsored by: See the NEW Palm=20
> Tungsten T handheld. Power & Color in a compact size!
> http://ads.sourceforge.net/cgi-bin/redirect.pl?palm0001en
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20

[PyMOL] .py scripts on OS 10.1

[robert d. v. <del...@cs...>]

	I am using PyMol 0.84 for Mac OS 10.1(10.1.5) and was wondering if 
it is possible to run .py scripts such as ScriptBox.py.
When I start PyMol by clicking on the 10.1 icon and then try to run .py 
scripts (run scriptx.py) I get some error messages including the 
following:
	"import _tkinter # If this fails your Python may not be configured 
for Tk
	ImportError: No module named _tkinter"
Is there a way to configure Python properly or is this not possible on 
the Mac?  Thanks for your help.
Bob Del Vecchio

Robert Del Vecchio
Cold Spring Harbor Laboratory
Demerec Building
1 Bungtown Road
Cold Spring Harbor, NY  11724
email: del...@cs...
tel: (516)367-8314

Re: [PyMOL] Getting started with movies for moving through a presentation

[Lieven B. <li...@ul...>]

Kersey Black wrote:
> 3)  Where can I find the source to the "scripted animation" Demo
> (arginine conformations)?

The source for all the demos is in the the file
".../modules/pmg_tk/Demo.py" 
starting from the PyMol base directory. The arginine demo is in the
method 
"anime":

   def anime(self,cleanup=0):
      if not cleanup:
         cmd.disable()
         cmd.delete("arg")
         cmd.fragment("arg")
         cmd.zoom("arg",2)
         cmd.show("sticks","arg")
         cmd.feedback('dis','sel','res')
         for a in xrange(1,181):
            cmd.set("suspend_updates",1,quiet=1)
            cmd.edit("(arg and n;cd)","(arg and n;cg)")
            cmd.torsion("6")
            cmd.unpick()
            cmd.edit("(arg and n;cb)","(arg and n;ca)")
            cmd.torsion("2")
            cmd.unpick()
            cmd.set("suspend_updates",0,quiet=1)
            cmd.refresh()
         cmd.feedback('ena','sel','res')
      else:
         cmd.delete("arg")

-- 
Lieven Buts
Department of Ultrastructure
Brussels Free University

[PyMOL] Density & Isosurface

[Yves B. <yve...@wa...>]

Dear Pymolers,

Is there a way to display isosurface built from an electron density map a=
round a 
ligand=3F It works well with the isomesh command but so far I'm only able=
 to display 
the whole electron density map using isosurface.

Thanks - Yves

RE: [PyMOL] colors

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

> I just discovered that I can't set colors with more than one=20
> decimal point
> of precision.  Is there any way around this?  I'm trying to get a
> background that blends in with part of a web page.
>=20

Not true... just the output is rounded.  The exact color is whatever you =
set it to.

PyMOL>set_color test,[0.555,0.666,0.777]
 Color: "test" defined as [ 0.6, 0.7, 0.8 ].

print cmd.get_color_tuple("test")
PyMOL>print cmd.get_color_tuple("test")
(0.55500000715255737, 0.66600000858306885, 0.77700001001358032)

--
mailto:wa...@su...
Warren L. DeLano, Ph.D.=20
Informatics Manager=20
Sunesis Pharmaceuticals, Inc.=20
341 Oyster Point Blvd.=20
S. San Francisco, CA 94080=20
(650)-266-3606 FAX:(650)-266-3501

[PyMOL] colors

[Nat E. <na...@bi...>]

I just discovered that I can't set colors with more than one decimal point
of precision.  Is there any way around this?  I'm trying to get a
background that blends in with part of a web page.

----------------------------------------------------------------------------
Nathaniel Echols                                                  Programmer
na...@bi...                                        Gerstein Lab
203-589-6765                                                 Yale University
----------------------------------------------------------------------------

[PyMOL] Getting started with movies for moving through a presentation

[Kersey B. <kb...@js...>]

Hi Pymolers,

Sorry for a newbie question, but here goes.

I am trying to get started with movies and am having problems with the 
understanding the paradigm (states vs frames and how actions are 
associated with frames, etc).  So, a couple of questions arise.

1)  Perhaps I misunderstanding the utility of movies.  I am thinking of 
using a sequence of frames that I could move through 1 by 1 as a way of 
moving through a presentation.  [I would be doing this in PyMOL so I 
have slways have complete interactivity, and not as a quicktime movie.] 
  Each frame would differ enough that I do not want to try to type in 
all the required pymol commands individually, nor try to do it all with 
the GUI on the fly.   (e.g. I am thinking of something like starting by 
showing a protein, then show a cartoon, then go back to sticks, then 
zoom into the active site, etc.)
Is this reasonable, or is there a better way to effectively apply 
"functions" containing a sequence of PyMOL commands to move through a 
presentation.  Would it be better to do this as a bunch of individual 
scripts which I call from the command line?  (perhaps with scirptBox, 
though I have not yet got it up and running on my mac -- has anyone 
done this?)?  Any thoughts would be great.

2)  I have been using the manual, the list archives, and a couple of 
small tutorials on the web, but remain a bit lost on movie creation.  
Are there examples which use movies towards the purpose  I describe 
above which might give more hints on how to define 
states/frames/associated actions, etc.  Most of the examples I have 
found go a different direction (thus, point 1)).

I am using 0.84beta on OSX 10.2.1 -- it great -- thanks for all the 
effort in the creation of PyMOL and the port to OS X.
I also have it on my SGI, if the full GUI would make any of this more 
obvious.

3)  Where can I find the source to the "scripted animation" Demo 
(arginine conformations)?

4)  Can transparency be applied to sticks?
[saw the previous post, but could not find an answer]

Thanks for any help.

Kersey

[PyMOL] (no subject)

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

Hi Lieven:

I don't have windows pymol or access currently to a windows machine, so 
I will have to tell you how I did it on the Mac version and then hope 
it is essentially identical with windows.

I did this about 6 months ago in order to hyperlink quicktime to 
Powerpoint in XP.  I am assuming hyperlinking to Pymol would work the 
same way, since it works the same way on a Mac.  But you never know 
with Windows since 90% of the operating system seems to be dedicated to 
preventing you from using your computer.

Open up powerpoint and create a new slide.

In it put a word or picture or something.

Then select that word or picture or whatever it is.

Go to insert > hyperlink

and then put in the full file hierarchy path to your pymol application


Then when you are in presentation mode, you click on this and it starts 
pymol.  On XP it seemed to embed it in situ (at least when I was using 
quicktime).  In OS X it changes over to the pymol display.  That's the 
basis for my claim that it works better in XP.  I apologize if this 
doesn't.

HTH,

Bill Scott




William G. Scott

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

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

RE: [PyMOL] manual docking of multiple molecules and DNA fragments

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

Jules,

	Unfortunately, PyMOL molecular editing features are not really =
documented yet. =20

	You can move entire object independently using the "MovF" and "RotF" =
mouse actions.  With the normal three-button mouse configuration in =
Editing Mode, that would be shift-middle-click and shift-left-click, =
respectively.  You can change the origin of rotation with the "Orig" =
action, control-shift-middle click.

	By the way, Be sure that no atoms are "picked" before attempting this.  =
If the pick selections (pk1, pkfrag1, ...) are present, then you will =
end up only moving pieces of the picked molecule.  You can can first =
ctrl-middle click away from any atom to unpick.


Warren



> -----Original Message-----
> From: Jules Jacobsen [mailto:jo...@he...]
> Sent: Thursday, October 31, 2002 6:39 AM
> To: pym...@li...
> Subject: [PyMOL] manual docking of multiple molecules and DNA=20
> fragments
>=20
>=20
>=20
> Does anyone know of a way to dock (read move independantly)=20
> two or more
> molecules in one window? I am aware of the rotate and=20
> translate commands
> but these are really not quick or easy to use. If there isn't=20
> any way of
> doing this can i then add this to a wish list of functions for future
> releases. This would be especially good if it could work in=20
> conjunction
> with the sculpting wizard. Also is there any way of adding=20
> DNA/RNA bases
> to the fragment library?
>=20
> thanks in advance
>=20
> Jules
>=20
>=20
>=20
> -------------------------------------------------------
> This sf.net email is sponsored by: Influence the future=20
> of Java(TM) technology. Join the Java Community=20
> Process(SM) (JCP(SM)) program now.=20
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> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20

[PyMOL] manual docking of multiple molecules and DNA fragments

[Jules J. <jo...@he...>]

Does anyone know of a way to dock (read move independantly) two or more
molecules in one window? I am aware of the rotate and translate commands
but these are really not quick or easy to use. If there isn't any way of
doing this can i then add this to a wish list of functions for future
releases. This would be especially good if it could work in conjunction
with the sculpting wizard. Also is there any way of adding DNA/RNA bases
to the fragment library?

thanks in advance

Jules

[PyMOL] Re: using PyMol in PowerPoint

[Lieven B. <li...@ul...>]

wg...@ch... wrote:
> Also, don't overlook the fact that pymol itself is a movie player.  In
> powerpoint you can create what is called a hyperlink to pymol, and then
> you can just load in your macro (pml script) and your movie starts
> playing embedded in powerpoint.  

Could you provide some more details on this procedure. So far I have
only managed to include an icon/object in PowerPoint that starts PyMol 
in an extra window (with a specified script).

-- 
Lieven Buts
Vrije Universiteit Brussel

RE: [PyMOL] How to get a suurface on small molecule in active site?

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

By default, PyMOL doesn't surface PDB HETATMs.

To surface all atoms,

set surface_mode=3D1

To surface all atoms except hydrogens,

set surface_mode=3D2

Cheers,
Warren



> -----Original Message-----
> From: Kersey Black [mailto:kb...@js...]
> Sent: Wednesday, October 30, 2002 3:09 PM
> To: pym...@li...
> Cc: Kersey Black
> Subject: [PyMOL] How to get a suurface on small molecule in=20
> active site?
>=20
>=20
> Hi Pymolers,
>=20
> I am trying to show a surface on a small molecule in the=20
> active site. =20
> I can create surfaces on protein residues  without any problem, but I=20
> can not get a surface around the small organic structure.  I=20
> have tried=20
> this on an SGI and using the 0.84beta on OS X.
> I am obviously missing something.  Any help out there would be great.
>=20
> After loading the hapten, I try things like ...
>    show surface, hap
>    set transparency=3D0.5, hap
> But I do not get a surface, with or without the transparency
>=20
> Cheers,
>=20
> Kersey
>=20
>=20
>=20
> -------------------------------------------------------
> This sf.net email is sponsored by: Influence the future=20
> of Java(TM) technology. Join the Java Community=20
> Process(SM) (JCP(SM)) program now.=20
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> _______________________________________________
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> PyM...@li...
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>=20