pymol-users — Collaborative support and tips for PyMOL users

[PyMOL] pymol and povray

[Craig S. <boi...@ma...>]

I have a apple G4 powerbook using OS10.2.  Is it possible to write out 
a pov-ray type script file that could be directly input into pov-ray?


Craig L. Smith, Ph. D.
Molecular Microbiology
Washington University School of Medicine
660 South Euclid Box 8230
Voice: (314) 362-9054
Fax: (314) 362-1232
e-mail: sm...@bo...

RE: [PyMOL] Calpha-Calpha distance

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

PyMOL is currently just a little too smart in this area -- it checks to =
see whether the CA atoms are connected through C and N atoms.  The next =
version will support CA traces with just CA positions.=20

In the meantime, you might want to look into the CGO capability, which =
lets you draw arbitrary kinds of graphics without this kind of trickery.

- Warren

PS. Here is one of the examples "cgo01.py" included with PyMOL: "run =
cgo01.py"

# this is a trivial example of creating a cgo object consisting of a
# a single state=20

from pymol.cgo import *
from pymol import cmd

# first we create a list of floats containing a GL rendering stream

obj =3D [
   BEGIN, LINES,
   COLOR, 1.0, 1.0, 1.0,
  =20
   VERTEX, 0.0, 0.0, 0.0,
   VERTEX, 1.0, 0.0, 0.0,
  =20
   VERTEX, 0.0, 0.0, 0.0,
   VERTEX, 0.0, 2.0, 0.0,
  =20
   VERTEX, 0.0, 0.0, 0.0,
   VERTEX, 00, 0.0, 3.0,

   END
   ]

# then we load it into PyMOL

cmd.load_cgo(obj,'cgo01')

# move the read clipping plane back a bit=20

cmd.clip('far',-5)

> -----Original Message-----
> From: Daniel John Rigden [mailto:da...@ce...]
> Sent: Wednesday, October 23, 2002 10:54 AM
> To: pym...@li...
> Subject: [PyMOL] Calpha-Calpha distance
>=20
>=20
> Hi all
>=20
> I have a PDB file which uses a series of pseudo-Calpha=20
> positions to draw
> an arrow.  The positions are 3.0A apart.  This is OK for them=20
> to be joined
> in a Calpha trace made in, for example, O and RASMOL, but=20
> PYMOL must have
> a more stringent cutoff.  I've had a look but I can't see how=20
> to change
> this, or even if that's possible.
>=20
> Thanks for your help.
>=20
> Daniel
>=20
>=20
> +-------------------------------------------------------------
> ------------+
> |                       Dr Daniel John Rigden                =20
>             |
> | CENARGEN/EMBRAPA                 | e-mail:=20
> da...@ce...   |
> | Parque Estacao Biologica         |=20
> http://www.cenargen.embrapa.br       |
> | PqEB - Final - Av. W3 Norte      |  Phone:  +55=20
> (61)448-4741            |
> | 70770-900, Brasilia-D.F.-BRAZIL  |  Fax:    +55=20
> (61)340-3658            |
> +-------------------------------------------------------------
> ------------+
>=20
>=20
>=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
> http://ads.sourceforge.net/cgi-bin/redirect.pl?sunm0002en
>=20
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20

[PyMOL] Calpha-Calpha distance

[Daniel J. R. <da...@ce...>]

Hi all

I have a PDB file which uses a series of pseudo-Calpha positions to draw
an arrow.  The positions are 3.0A apart.  This is OK for them to be joined
in a Calpha trace made in, for example, O and RASMOL, but PYMOL must have
a more stringent cutoff.  I've had a look but I can't see how to change
this, or even if that's possible.

Thanks for your help.

Daniel


+-------------------------------------------------------------------------+
|                       Dr Daniel John Rigden                             |
| CENARGEN/EMBRAPA                 | e-mail: da...@ce...   |
| Parque Estacao Biologica         | http://www.cenargen.embrapa.br       |
| PqEB - Final - Av. W3 Norte      |  Phone:  +55 (61)448-4741            |
| 70770-900, Brasilia-D.F.-BRAZIL  |  Fax:    +55 (61)340-3658            |
+-------------------------------------------------------------------------+

Re: [PyMOL] Need help with selections

[Daniel K. <dan...@ma...>]

Hi Aaron, 

> I am somewhat new to PYMOL and was trying to create a selection of atoms.
> What I need to do is select all atoms of a protein that are within 5
> angstroms of an inhibitor (the protein and inhibitor are separate
> molecules).  I cannot figure out how to do this from the examples in the
> manual. I will want to use this selection to make a surface of the
> selection afterward.
> 

You might try this. Select a central atom of your ligand (ALT + left mouse button). Pymol will name this selection (lb).

select bindingsite = (lb around 5) and not HETATM)   # PDB-style, this will select all not HETATM atoms around your selected atom
			or 
select bindingsite = (lb around 5) and not ligand)   # if your small molecule is named ligand

show surface, bindingsite

Cheers
Daniel
 
-- 
  Daniel Kuhn
  Department of Pharmaceutical Chemistry
  Philipps-University of Marburg
  Marbacher Weg 6                           Phone: (+49)6421 28-25071
  35037 Marburg                             Fax:   (+49)6421 28-28994
  Germany

RE: [PyMOL] distance parameters

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

> From: Jules Jacobsen [mailto:jo...@he...]
>=20
>=20
> you can change most of the parameters using set dash_n where=20
> n=3D length,
> width, gap, radius. Unfortunately dash_color doesn't exist.
>=20
=20
...but you can change the color of a distance object

color red,dist01

Warren

Re: [PyMOL] distance parameters

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

you can change most of the parameters using set dash_n where n= length,
width, gap, radius. Unfortunately dash_color doesn't exist.

hope this helps

Jules

On Tue, 22 Oct 2002, franck coste wrote:

> Hi,
> I'd like to know if it's possible to change the parameters of the
> DISTANCE command (color, radius, ...)
> Thanks,
> Franck Coste.

RE: [PyMOL] CMYK colors

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

Thanks for the suggestion?

For now, why not just redefine the existing colors?=20

No need for a leading underscore...

set_color green=3D [0.00 , 0.53 , 0.22]

etc.

Note that there are default atom colors such as "carbon", "nitrogen", =
"oxygen", "hydrogen", "sulfur", etc. which should also be redefined.

set_color carbon=3D [0.00 , 0.53 , 0.22]

etc,=20

Warren


> -----Original Message-----
> From: Gil Prive [mailto:pr...@uh...]
> Sent: Friday, October 18, 2002 1:38 PM
> To: pym...@li...
> Subject: [PyMOL] CMYK colors
>=20
>=20
>=20
> This is not directly PyMOL specific, but it addresses a=20
> problem I think=20
> a lot of us have encountered in preparing hardcopy outputs.
>=20
> Some RGB triplets do have equivalents in CMYK space, and as a=20
> result, a=20
> figure that looks great on a screen can come out with unpredictable=20
> colors when printed.
>=20
> Most applications do a good job with RGB-to-CMYK conversions=20
> for photos,=20
> but do not do such a good job with graphics that use pure primary=20
> colors.  For example, reds are generally OK, but pure blues=20
> and greens=20
> do not translate very well.
>=20
> Here are some RGB values that are within the CMYK gamut  (i.e. are=20
> "CMYK-safe"):
>=20
>=20
> ##
> #optimized rgb values for cmyk output:
> set_color _dblue=3D [0.05 , 0.19 , 0.57]
> set_color _blue=3D  [0.02 , 0.50 , 0.72]
> set_color _mblue=3D [0.5  , 0.7  , 0.9 ]
> set_color _lblue=3D [0.86 , 1.00 , 1.00]
>=20
> set_color _green=3D [0.00 , 0.53 , 0.22]
> set_color _lgreen=3D[0.50 , 0.78 , 0.50]
>=20
> set_color _yellow=3D[0.95 , 0.78 , 0.00]
>=20
> set_color _orange=3D[1.00 , 0.40 , 0.0 ]
>=20
> # these are trivial
> set_color _red=3D   [1.00 , 0.00 , 0.00]
> set_color _mred=3D  [1.00 , 0.40 , 0.40]
> set_color _lred=3D  [1.00 , 0.80 , 0.80]
> set_color _vlred=3D [1.00 , 0.90 , 0.90]
> set_color _white=3D [1.00 , 1.00 , 1.00]
> set_color _vlgray=3D[0.95 , 0.95 , 0.95]
> set_color _lgray=3D [0.90 , 0.90 , 0.90]
> set_color _gray=3D  [0.70 , 0.70 , 0.70]
> set_color _dgray=3D [0.50 , 0.50 , 0.50]
> set_color _vdgray=3D[0.30 , 0.30 , 0.30]
> set_color _black=3D [0.00 , 0.00 , 0.00]
> ##
>=20
>=20
> There may be a more elegant way to do this (specific to the OS and=20
> post-PyMOL application), but this is a simple solution.
>=20
>=20
> Wishlist:
> It would be useful to specify a "CMYK mode" in PyMOL, so that=20
> the color=20
> palate uses RGB colors that have good CMYK equivalents.  This would=20
> simplify color selection when preparing hardcopy figures.
>=20
>=20
> With apologies to color-matching gurus,
> Gil
>=20
>=20
> =
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D
> Gil Priv=E9
> Ontario Cancer Institute
> University of Toronto
>=20
> pr...@uh...
> http://xtal.uhnres.utoronto.ca/prive
> =
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D
>=20
>=20
>=20
> -------------------------------------------------------
> This sf.net email is sponsored by:
> Access Your PC Securely with GoToMyPC. Try Free Now
> https://www.gotomypc.com/s/OSND/DD
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20

[PyMOL] Pymol 0.82-Error

[Marc S. <mar...@mp...>]

Hi there,

Today I stumbled over a bug in Pymol:

If I load a certain molecule (can be provided if needed) into Pymol 0.82 
together with rubor.py from Christian Rothers rTools, and do some 
operations on it (detailed log can also be provided) after setting the 
display-quality to "Maximum Performance" and back to "Maximum Quality, 
Pymol crashes with the following error-message:

"""
PyMOL>rebuild
NULL-POINTER-ERROR: in RepSphere.c line 379
  PyMOL: abrupt program termination.
"""

This could be reproduced, so it might be worth looking at it.

-- 
Bye,  Marc Saric

Max-Planck-Institut fuer molekulare Physiologie
Otto-Hahn-Str.11  44227 Dortmund  phone:0231/133-2168

[PyMOL] distance parameters

[franck c. <fc...@cn...>]

Hi,
I'd like to know if it's possible to change the parameters of the
DISTANCE command (color, radius, ...)
Thanks,
Franck Coste.

[PyMOL] CMYK colors

[Gil P. <pr...@uh...>]

This is not directly PyMOL specific, but it addresses a problem I think=20
a lot of us have encountered in preparing hardcopy outputs.

Some RGB triplets do have equivalents in CMYK space, and as a result, a=20
figure that looks great on a screen can come out with unpredictable=20
colors when printed.

Most applications do a good job with RGB-to-CMYK conversions for photos,=20
but do not do such a good job with graphics that use pure primary=20
colors.  For example, reds are generally OK, but pure blues and greens=20
do not translate very well.

Here are some RGB values that are within the CMYK gamut  (i.e. are=20
"CMYK-safe"):


##
#optimized rgb values for cmyk output:
set_color _dblue=3D [0.05 , 0.19 , 0.57]
set_color _blue=3D  [0.02 , 0.50 , 0.72]
set_color _mblue=3D [0.5  , 0.7  , 0.9 ]
set_color _lblue=3D [0.86 , 1.00 , 1.00]

set_color _green=3D [0.00 , 0.53 , 0.22]
set_color _lgreen=3D[0.50 , 0.78 , 0.50]

set_color _yellow=3D[0.95 , 0.78 , 0.00]

set_color _orange=3D[1.00 , 0.40 , 0.0 ]

# these are trivial
set_color _red=3D   [1.00 , 0.00 , 0.00]
set_color _mred=3D  [1.00 , 0.40 , 0.40]
set_color _lred=3D  [1.00 , 0.80 , 0.80]
set_color _vlred=3D [1.00 , 0.90 , 0.90]
set_color _white=3D [1.00 , 1.00 , 1.00]
set_color _vlgray=3D[0.95 , 0.95 , 0.95]
set_color _lgray=3D [0.90 , 0.90 , 0.90]
set_color _gray=3D  [0.70 , 0.70 , 0.70]
set_color _dgray=3D [0.50 , 0.50 , 0.50]
set_color _vdgray=3D[0.30 , 0.30 , 0.30]
set_color _black=3D [0.00 , 0.00 , 0.00]
##


There may be a more elegant way to do this (specific to the OS and=20
post-PyMOL application), but this is a simple solution.


Wishlist:
It would be useful to specify a "CMYK mode" in PyMOL, so that the color=20
palate uses RGB colors that have good CMYK equivalents.  This would=20
simplify color selection when preparing hardcopy figures.


With apologies to color-matching gurus,
Gil


=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D
Gil Priv=E9
Ontario Cancer Institute
University of Toronto

pr...@uh...
http://xtal.uhnres.utoronto.ca/prive
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D

Re: [PyMOL] multi-step movie

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

Hello Gabriel,

Your Questions:

> 1. How can you make a molecule rotate 10 times only,

go to http://www.rubor.de/bioinf and download the movieScript module
and issue the following commands:

mvClear
mvRot 1-500,x,3600
mvCmd 501,mstop
movie

Explanation:
This tells movieScript to rotate the molecule in frames 1 to 500 around 
3600 degrees, then calls the mstop command in frame 501.


> 2. Is there any script command, that put the script on
> "hold" until you press the mouse or the keyboard
> button ? This is useful for multi-step movie.

I think this should be done using the raw_input("press any key")
function from a python script.


> 3. Is there any possibility to do zoom-in , for
> example, into the active site.

of course, there is (e.G. 'actsite' is your active site subselection):

hide all         # molecule gets invisible
orient actsite   # now the active site fills out all the screen
move z,-200      # zoom out
move x,50        # move a little to the side

# Now your molecule is ready to come to the scene:
show cartoon    # make the molecule visible
mvClear
mvSinmove 1-100,x,-50
mvSinmove 1-100,z,200
mvCmd 101,mstop
movie

best wishes,

   Kristian Rother

[PyMOL] Measuring an angle between two planes

[Julien C. <juj...@fr...>]

Hi there,

I made two selections of atoms of one single molecule and I  would like=20=

to get the angle between the average planes of each selection.
How can I do that ?

Thanks for the help

Julien Chiron
Laboratoire de Valorisation de la Chimie Fine
Service 552
Facult=E9 des Sciences de Saint J=E9r=F4me
13397 Marseille CEDEX 20
FRANCE
Tel:   33 (0)4 91 28 81 92
Fax : 33 (0)4 91 28 83 23=

RE: [PyMOL] What's in a selection

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

Atom selections aren't directly exposed to Python, but you can have =
PyMOL build a Python list containing whatever information you need:

Using PyMOL commands:

list=3D[]
iterate (name ca),list.append((resi,resn))
print list

[('ASP', '1'), ('CYS', '2'), ('ALA', '3'), ('TRP', '4'), ('HIS', '5'), =
('LEU',
 '6'), ('GLY', '7'), ('GLU', '8'), ('LEU', '9'), ('VAL', '10'), ('TRP', =
'11'),=20
('CYS', '12'), ('THR', '13')]

or using a Python script (in PyMOL):

from pymol import cmd,stored
stored.list=3D[]
cmd.iterate("(name ca)","stored.list.append((resi,resn))")
print stored.list

[('1', 'ASP'), ('2', 'CYS'), ('3', 'ALA'), ('4', 'TRP'), ('5', 'HIS'), =
('6', '
LEU'), ('7', 'GLY'), ('8', 'GLU'), ('9', 'LEU'), ('10', 'VAL'), ('11', =
'TRP'),=20
('12', 'CYS'), ('13', 'THR')]

Cheers,
Warren

> -----Original Message-----
> From: ml...@um... [mailto:ml...@um...]
> Sent: Thursday, October 17, 2002 12:03 PM
> To: pym...@li...
> Subject: [PyMOL] What's in a selection
>=20
>=20
>=20
>=20
> Hi,
>=20
> How can I tell which atoms are in a selection?  For example,=20
> I've opened up a
> pdb file and selected all non-backbone atoms within five=20
> angstroms of the active
> site.  Now I want to get a list of the atoms in that=20
> selection.  My selection
> was called "nearby" and I tried "print nearby" but got a NameError.
>=20
> Sorry if the answer's obvious and I've just missed it.
>=20
> thanks,
>=20
> -michael
>=20
>=20
> -------------------------------------------------------
> This sf.net email is sponsored by: viaVerio will pay you up to
> $1,000 for every account that you consolidate with us.
> http://ad.doubleclick.net/clk;4749864;7604308;v?
> http://www.viaverio.com/consolidator/osdn.cfm
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20

[PyMOL] What's in a selection

[<ml...@um...>]

Hi,

How can I tell which atoms are in a selection?  For example, I've opened up a
pdb file and selected all non-backbone atoms within five angstroms of the active
site.  Now I want to get a list of the atoms in that selection.  My selection
was called "nearby" and I tried "print nearby" but got a NameError.

Sorry if the answer's obvious and I've just missed it.

thanks,

-michael

[PyMOL] multi-step movie

[gabriel r. <gab...@ya...>]

Hi.
Few questions about movies :
1. How can you make a molecule rotate 10 times only,
using script commands ? right now the only way is to
press the stop-butoon at the lower-left pannel, but i
want the script to stop it after 10 rounds.
2. Is there any script command, that put the script on
"hold" until you press the mouse or the keyboard
button ? This is useful for multi-step movie.
3. Is there any possibility to do zoom-in , for
example, into the active site.
Thanks
Gabi. 

__________________________________________________
Do you Yahoo!?
Faith Hill - Exclusive Performances, Videos & More
http://faith.yahoo.com

[PyMOL] RE: MacOSX and Three button mice.

[Andy C. <afc...@li...>]

Ok. Thanks all. Cracked it.

The Macally driver was indeed the culprit. I had installed it way back in
OSX 10.1 or maybe before that even when the standard Apple driver did
nothing for my scroll wheel etc. I had just kept updating it thinking it was
needed. Just run the uninstaller (which you can get by downloading from
http://www.macally.com/techsupport/drivers.html ) in case, like me, you had
ditched it. A system reboot is needed.

In 10.2.1 at least all Macally mouse functions are supported by the Apple
driver and proper 3 button control is present in PyMOL. :-)

Uninstall seems to be the only option as the Macally utility for customising
what the buttons do on an application by application basis does not include
an option of excluding an application such as PyMOL. Correct me if I missed
something though. :-(

-- 
.-Dr-Andy-Calder----------.
| Materials Modelling Group\
| Materials Science & Eng.  \
| University of Liverpool   /
| UK .---------------------'

Re: [PyMOL] MacOSX and Three button mice.

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

Yes, my Kensington Optical Elite mouse (which actually has five buttons)=20=

works fine.  The middle button is a scroll wheel which is also=20
clickable.  Clicking it does exactly as you expect it should.  I'm using=20=

OS X 10.1.5 though, not 10.2.  My office mate has just got 10.2 however,=20=

and she seems to have no problems with the same type of mouse.

The only problem I have is that I haven't figured out the command to get=20=

back from the secondary set of mouse commands to the main one.  If you=20=

know what it is you could let me know!

Bronwyn

On Wednesday, October 16, 2002, at 10:00  PM, Andy Calder wrote:

>> I have a microsoft intellimouse explorer, OS 10.2.1, and can't seem =
to=20
>> get
>> the mouse to function as a three button mouse. I have apparently=20
>> normal left
>> and right button function (+/- control, shift, both) but no middle=20
>> button. I
>> could use the wheel button if I could define it, but I haven't=20
>> succeeded. I
>> would appreciate advice on how to fix this mouse, or what else to do.
>
> I have MacOS X 10.2.1 but I use a Macally iOptinet mouse which is a=20
> similar
> type of wheel mouse function to yours.
>
> I too cannot get my middle button to function. Eg Move.
>
> What I have done in the past is to define in the Macally mouse =
software=20
> that
> middle button is something like ctrl R-button and then in PyMol use
> cmd.button to change Move to be ctrl-R button. Its OK if you don=92t =
want=20
> all
> the mouse functions but a pain nonetheless.
>
> Has anyone got real 3 button functioning in PyMOL (OSX)?
>
> --
> .-Dr-Andy-Calder----------.
> | Materials Modelling Group\
> | Materials Science & Eng.  \
> | University of Liverpool   /
> | UK .---------------------'
>
> -------------------------------------------------------
> This sf.net email is sponsored by: viaVerio will pay you up to
> $1,000 for every account that you consolidate with us.
> http://ad.doubleclick.net/clk;4749864;7604308;v?
> http://www.viaverio.com/consolidator/osdn.cfm
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>
>
Bronwyn Carlisle
Biochemistry Department
University of Otago
Dunedin
New Zealand

Tel 64 3 479 7704

RE: [PyMOL] MacOSX and Three button mice.

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

Great -- another high traffic day on the PyMOL list!   I do hope =
everyone is aware that you can get the PyMOL list batched into a =
*single* daily message.  That way you can still keep up with PyMOL =
informati without being flooded.  Here's how

Surf to http://lists.sourceforge.net/lists/listinfo/pymol-users , enter =
your email address, and click select "Edit Options", then set digest =
mode to "on", enter password and submit.

Onto the topic at hand:  MacOSX 3 button mice.

Based on Evan's success (below), it sounds to me like the problem has to =
do with third-party mouse driver software suppressing the normal =
middle-button mouse event.  OSX barely supports the middle button, so it =
isn't surprising that third parties don't even bother.

Deactivation of mouse software is complicated by the fact that with =
PyMOL, the Mac OSX icon you launch is not the one which ends up being =
active (the reasons for this are important but technical...). =20

Thus, my advice would be (1) avoid programmable mouse driver software =
althougher (just don't install it), or failing that (2) try deactivating =
the software for all of the PyMOL application icons in the PyMOL folder =
(as well as in the "Darwin" sub-folder).

Cheers,
Warren

-----Original Message-----
From: J. Evan Sadler [mailto:es...@im...]
Sent: Wednesday, October 16, 2002 8:27 AM
To: DeLano, Warren
Subject: Re: [PyMOL] MacOSX and Three button mice.


Warren,

Great suggestion to try vanilla. I was programming the mouse from within =
System Preferences, choosing the Microsoft IntelliPoint application =
under "Other". Doing the same, but checking "Disable IntelliPoint =
features..." specifically for application "PyMOL", enabled all L,M,R =
mouse functions as expected under PyMOL. This setting allows the mouse =
to use the OS10 mouse software instead of IntelliPoint.=20

The key points seem to be:

1. Choose the correct PyMOL application icon to define the application =
within the IntelliPoint application.

2. Disable Intellipoint features for PyMOL.=20

Alternatively, I suppose one could simply not install the extra mouse =
software.

Evan



From: "DeLano, Warren" <wa...@su...>
Date: Wed, 16 Oct 2002 08:07:29 -0700
To: "J. Evan Sadler" <es...@im...>
Subject: RE: [PyMOL] MacOSX and Three button mice.




Evan,
=20
Thanks for your detailed response!
=20
Two more questions for you specifically: =20
=20
1. Are there any other programs you have which do regonize the middle =
button as such?
=20
2. Have you tried a plain-old-vanilla intellimouse without any =
programmability?  I haven't installed additional software to get my =
mouse to work, and I'm wondering if somehow the extra software is =
getting the way.  By the way, how are you programming the mouse?
=20
Cheers,
Warren
=20

-----Original Message-----=20
From: J. Evan Sadler [mailto:es...@im...]=20
Sent: Wed 10/16/2002 7:56 AM=20
To: DeLano, Warren; Andy Calder=20
Cc: pym...@li...=20
Subject: Re: [PyMOL] MacOSX and Three button mice.


I am using the 0.84 version, launching by clicking an alias of the 10.2
application icon in the dock. Pymol does appear in the menu bar, and I =
have
both GUI (PyMOL) and viewer (PyMOL Viewer) windows.

The mouse is a 5 button (counting the wheel button) Intellimouse =
Explorer
3.0 USB mouse, with current intellipoint software for OS10. I have
discovered the following:

1. Program specific settings chosen for PyMol 10.2 are ignored - Global
settings trump.

2. Program specific settings chosen instead for PyMOL (NOT the =
application
icons designated by 10.1 or 10.2) are recognized.

3. Programming the wheel button as "click" or "secondary click" =
correctly
reproduces the behavior of the left or right buttons, respectively.

4. Programming the wheel button as "control+click" or "control+secondary
click" etc works as expected for all combinations in the viewer window =
that
apply to L or R buttons.

5. Nothing I have tried will convince the wheel button to behave as a =
middle
button. For example, command+/-option+click or secondary click are =
ignored;
behavior is same as click or secondary click.

Evan Sadler

> From: "Warren L. DeLano" <wa...@su...>
> Date: Wed, 16 Oct 2002 07:16:37 -0700 (PDT)
> To: Andy Calder <afc...@li...>
> Cc: <pym...@li...>

> Hmm... I've been using a 3-button Microsoft USB Intellimouse with =
PyMOL
> just fine, and the middle mouse button is fully functional under =
10.2.1.
> I didn't need to do any kind of configuration, it just worked.  Thus, =
I
> am flummoxed as to why it doesn't work for you as well!
>
> 1. Are you using the latest beta version (0.84)?
> 2. How are you launching PyMOL?
> 3. Does 'PyMOL' appear in the menu bar?
> 4. Does an external GUI appear?
>
> (The last 2 questions are to insure that PyMOL is getting properly
> initialized).
>
> Since I can't reproduce the problem, it's going to be tough for me to
> solve it.
>
> Does anyone else have an idea what might be causing this problem?
>
> How widespread is the lack of middle-button function on a Mac?
>
> Cheers,
> Warren
>

Re: [PyMOL] MacOSX and Three button mice.

[J. E. S. <es...@im...>]

I am using the 0.84 version, launching by clicking an alias of the 10.2
application icon in the dock. Pymol does appear in the menu bar, and I have
both GUI (PyMOL) and viewer (PyMOL Viewer) windows.

The mouse is a 5 button (counting the wheel button) Intellimouse Explorer
3.0 USB mouse, with current intellipoint software for OS10. I have
discovered the following:

1. Program specific settings chosen for PyMol 10.2 are ignored - Global
settings trump.

2. Program specific settings chosen instead for PyMOL (NOT the application
icons designated by 10.1 or 10.2) are recognized.

3. Programming the wheel button as "click" or "secondary click" correctly
reproduces the behavior of the left or right buttons, respectively.

4. Programming the wheel button as "control+click" or "control+secondary
click" etc works as expected for all combinations in the viewer window that
apply to L or R buttons.

5. Nothing I have tried will convince the wheel button to behave as a middle
button. For example, command+/-option+click or secondary click are ignored;
behavior is same as click or secondary click.

Evan Sadler

> From: "Warren L. DeLano" <wa...@su...>
> Date: Wed, 16 Oct 2002 07:16:37 -0700 (PDT)
> To: Andy Calder <afc...@li...>
> Cc: <pym...@li...>

> Hmm... I've been using a 3-button Microsoft USB Intellimouse with PyMOL
> just fine, and the middle mouse button is fully functional under 10.2.1.
> I didn't need to do any kind of configuration, it just worked.  Thus, I
> am flummoxed as to why it doesn't work for you as well!
> 
> 1. Are you using the latest beta version (0.84)?
> 2. How are you launching PyMOL?
> 3. Does 'PyMOL' appear in the menu bar?
> 4. Does an external GUI appear?
> 
> (The last 2 questions are to insure that PyMOL is getting properly
> initialized).
> 
> Since I can't reproduce the problem, it's going to be tough for me to
> solve it.
> 
> Does anyone else have an idea what might be causing this problem?
> 
> How widespread is the lack of middle-button function on a Mac?
> 
> Cheers,
> Warren
> 

Re: [PyMOL] MacOSX and Three button mice.

[Chris R. <chr...@va...>]

> Has anyone got real 3 button functioning in PyMOL (OSX)?
>
>
I have real 3 button functioning when I use the "native" version of 
PyMOL for OSX. Additionally, when I use the X-window version of PyMOL I 
have the "middle" button set as cmd-click, which is the equivalent of a 
middle-click. I am using a Kensington 5-button optical mouse. You can 
program this mouse so that the buttons mean different things for 
different programs, which is quite useful.

Chris


Department of Biochemistry
606 Light Hall
Vanderbilt University
Nashville, TN
Phone: (615) 343-5682

Re: [PyMOL] MacOSX and Three button mice.

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

On Wed, 16 Oct 2002, Andy Calder wrote:

> > I have a microsoft intellimouse explorer, OS 10.2.1, and can't seem to get
> > the mouse to function as a three button mouse. I have apparently normal left
> > and right button function (+/- control, shift, both) but no middle button. I
> > could use the wheel button if I could define it, but I haven't succeeded. I
> > would appreciate advice on how to fix this mouse, or what else to do.
>
> I have MacOS X 10.2.1 but I use a Macally iOptinet mouse which is a similar
> type of wheel mouse function to yours.
>
> I too cannot get my middle button to function. Eg Move.
(snip)
> Has anyone got real 3 button functioning in PyMOL (OSX)?

Hmm... I've been using a 3-button Microsoft USB Intellimouse with PyMOL
just fine, and the middle mouse button is fully functional under 10.2.1.
I didn't need to do any kind of configuration, it just worked.  Thus, I
am flummoxed as to why it doesn't work for you as well!

1. Are you using the latest beta version (0.84)?
2. How are you launching PyMOL?
3. Does 'PyMOL' appear in the menu bar?
4. Does an external GUI appear?

(The last 2 questions are to insure that PyMOL is getting properly
initialized).

Since I can't reproduce the problem, it's going to be tough for me to
solve it.

Does anyone else have an idea what might be causing this problem?

How widespread is the lack of middle-button function on a Mac?

Cheers,
Warren

[PyMOL] MacOSX and Three button mice.

[Andy C. <afc...@li...>]

> I have a microsoft intellimouse explorer, OS 10.2.1, and can't seem to ge=
t
> the mouse to function as a three button mouse. I have apparently normal l=
eft
> and right button function (+/- control, shift, both) but no middle button=
. I
> could use the wheel button if I could define it, but I haven't succeeded.=
 I
> would appreciate advice on how to fix this mouse, or what else to do.

I have MacOS X 10.2.1 but I use a Macally iOptinet mouse which is a similar
type of wheel mouse function to yours.

I too cannot get my middle button to function. Eg Move.

What I have done in the past is to define in the Macally mouse software tha=
t
middle button is something like ctrl R-button and then in PyMol use
cmd.button to change Move to be ctrl-R button. Its OK if you don=B9t want all
the mouse functions but a pain nonetheless.

Has anyone got real 3 button functioning in PyMOL (OSX)?

--=20
.-Dr-Andy-Calder----------.
| Materials Modelling Group\
| Materials Science & Eng.  \
| University of Liverpool   /
| UK .---------------------' =20

RE: [PyMOL] distance sequence output

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

> From: Kristian Rother=20

> In this and other recent questions inside and outside this=20
> forum i have=20
> discovered that many of them could be solved quite easy if=20
> there was an=20
> easy way to access the atomic coordinates directly from the PyMOL API.
>=20
> Is this achievable somehow?

The actual C-langauge arrays aren't exposed, but there are at least =
three different ways you can modify coordinates from within Python:

#####=20
(1) You can get a python object which contains the molecular =
information, modify the coordinates in that object, load the modified =
molecule into PyMOL, update the modified coordinates to the original =
model, and then delete the modified object.

(in a python script)

from pymol import cmd

model =3D cmd.get_model("pept")
for a in model.atom:
   a.coord=3D[ -a.coord[1], a.coord[0], a.coord[2]]

cmd.load_model(model,"tmp")
cmd.update("pept","tmp")
cmd.delete("tmp")

######
(2) Another approach is the "alter_state" function, which can perform =
the same transformation in a single PyMOL command statement:

alter_state 1,pept,(x,y)=3D(-y,x)

Likewise sub-selections can be transformed as well:

alter_state 1,(pept and name ca),(x,y,z)=3D(x+5,y,z)

#######
(3) A third approach is to use alter_state with the global "stored" =
object:

(in Python script)

from pymol import cmd
from pymol import stored

stored.xyz =3D []
cmd.iterate_state(1,"pept","stored.xyz.append([x,y,z])")

# at this point, stored.xyz is a native Python array holding
# the coordinates, which you can modify as required

stored.xyz =3D map(lambda v:[-v[1],v[0],v[2]],stored.xyz)

# and now you can update the internal coordinate sets

cmd.alter_state(1,"pept","(x,y,z)=3Dstored.xyz.pop(0)")

#####

Approaches 2 gives the best performance, approach 3 gives more =
flexibility, and approach 1 gives you a reusable and fully modifiable =
Python object.

Cheers,
Warren

Re: [PyMOL] Mouse problems

[J. E. S. <es...@im...>]

Yes, in that case the behavior is the same as just using the left button.

Evan

> From: Jules Jacobsen <jo...@he...>
> Date: Mon, 14 Oct 2002 22:58:05 +0100 (BST)
> To: "J. Evan Sadler" <es...@im...>
> Cc: pym...@li...
> Subject: Re: [PyMOL] Mouse problems
> 
> Have you tried using both left and right mouse buttons at the same time
> instead of the middle button?
> 
> Jules
> 
> On Mon, 14 Oct 2002, J. Evan Sadler wrote:
> 
>> I have a microsoft intellimouse explorer, OS 10.2.1, and can't seem to get
>> the mouse to function as a three button mouse. I have apparently normal left
>> and right button function (+/- control, shift, both) but no middle button. I
>> could use the wheel button if I could define it, but I haven't succeeded. I
>> would appreciate advice on how to fix this mouse, or what else to do.
>> 
>> Evan Sadler
>> 
>> 
>> 
>> -------------------------------------------------------
>> This sf.net email is sponsored by:ThinkGeek
>> Welcome to geek heaven.
>> http://thinkgeek.com/sf
>> _______________________________________________
>> PyMOL-users mailing list
>> PyM...@li...
>> https://lists.sourceforge.net/lists/listinfo/pymol-users
>> 
> 

Re: [PyMOL] Mouse problems

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

Have you tried using both left and right mouse buttons at the same time
instead of the middle button?

Jules

On Mon, 14 Oct 2002, J. Evan Sadler wrote:

> I have a microsoft intellimouse explorer, OS 10.2.1, and can't seem to get
> the mouse to function as a three button mouse. I have apparently normal left
> and right button function (+/- control, shift, both) but no middle button. I
> could use the wheel button if I could define it, but I haven't succeeded. I
> would appreciate advice on how to fix this mouse, or what else to do.
>
> Evan Sadler
>
>
>
> -------------------------------------------------------
> This sf.net email is sponsored by:ThinkGeek
> Welcome to geek heaven.
> http://thinkgeek.com/sf
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>