pymol-users — Collaborative support and tips for PyMOL users

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
>

[PyMOL] Mouse problems

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

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 

RE: [PyMOL] Pymol and povray 3.5

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

> From: J. Evan Sadler [mailto:es...@im...]

> I have povray3.5 working from within pymol, but adjacent=20
> colors on surfaces
> show jagged lines instead of smooth. I gather that patching=20
> povray3.1 fixed
> this. Is there a way to do the same for povray3.5?

I've heard that PovRay3.5 supports color-interpolated triangles by =
default (no patching required).  If this is in fact the case, then all =
we would need to do is make a few minor changes to PyMOL's source code =
so that it spits out the new PovRay primitives. =20

Can someone track down the details and summarize what needs to be done?=20

Right now I am quite busy adding session saves-and-restores to PyMOL, a =
much sought-after feature that will greatly increase (re)usability.  The =
next version will have this, but it will take at least a few more weeks =
to tie up all of the loose ends...

Cheers,
Warren

[PyMOL] Pymol and povray 3.5

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

I have povray3.5 working from within pymol, but adjacent colors on surfaces
show jagged lines instead of smooth. I gather that patching povray3.1 fixed
this. Is there a way to do the same for povray3.5?

Evan Sadler

Re: [PyMOL] distance sequence output

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

Yuuki,

   I've glanced at the code and found that there's no way to get that
information out directly right now.  The dist command only returns the
average distance drawn -- this is because a single distance command can be
used to draw distances to many atoms.  To accomplish your goal, you would
need to temporarily copy each state into a separate object, issue a
distance command to measure it, and then delete the temporary object.

   We need to add more "measuring" tools to PyMOL:  Is the following
proposed list complete?

get_distance
get_angle
get_dihedral

In each case, you would only be measuring one set of atoms and you would
get a number if measuring a single state (default), or you would get a
list if measuring the value for all states (of those atoms).

Sound reasonable?

Cheers,
Warren


On Sat, 12 Oct 2002, Yuuki Komata wrote:

> Hi all,
>
>   I'm making sequenced pictures to be a movie. Each picture
> contains distance between atoms, and I can SEE them changing in
> the movie. Does someone know whether PyMol can output this sequenced
> atom distance to a file, and how? Normal text format will be O.K.
>
>   Thanks a lot.
>
>   Yuuki
>
> ----
> Yuuki Komata  ko...@co...
>
>
> -------------------------------------------------------
> 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
>

[PyMOL] Phosphate trace for nucleic acids

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

 >Question 1, CA-trace:
 >
 >show ribbon
 >set ribbon_sampling=1
 >
 >(NOTE: requires all main chain atoms to be present, but not necessarily 
visible
 > -- CA-only models will be supported later on).

(thanks Warren!!)

...and similarly, should you ever want to show the phosphate trace of a 
nucleic acid molecule:

def p_trace(selection="(all)"):
	s = str(selection)
	cmd.hide('lines',"("+s+")")
	cmd.hide('spheres',"("+s+")")
	cmd.hide('sticks',"("+s+")")
	cmd.hide('ribbon',"("+s+")")
	cmd.show('cartoon',"("+s+")")
	cmd.set('cartoon_sampling',1,"("+s+")")
	cmd.set('cartoon_tube_radius',0.5,"("+s+")")
cmd.extend('p_trace',p_trace)

and then:

p_trace (selection)

...

-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] distance sequence output

[Yuuki K. <ko...@co...>]

Hi all,

  I'm making sequenced pictures to be a movie. Each picture
contains distance between atoms, and I can SEE them changing in
the movie. Does someone know whether PyMol can output this sequenced
atom distance to a file, and how? Normal text format will be O.K.

  Thanks a lot.

  Yuuki

----
Yuuki Komata  ko...@co...

[PyMOL] util.py

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

> From: Xavier I. Ambroggio=20
>=20
> Dr. Delano,
>=20
> First of all, thank you for developing PyMOL. I want to=20
> modify the util.py
> to create another color scheme, similar to the util.cba* schemes. How
> would I do this and what would I need to do with the modified util.py
> script to get the PyMOL program to accept the new util.cba*=20
> command? As

1. Put the code below into a Python file (".py" file).
2. Run the file from within PyMOL ("run filename.py").
3. You can now use your new command as=20

mycba=20

or

mycba (atom selection)

You may want to put the code into $HOME/.pymolrc.py (unix) or =
$PYMOLPATH/pymolrc.py (windows) so that the new  command will always be =
available.

--

from pymol import cmd

def mycba(selection=3D"(all)"):
   s =3D str(selection)  =20
   cmd.color("magenta","("+s+")")
   cmd.color("oxygen","(elem O and "+s+")")
   cmd.color("nitrogen","(elem N and "+s+")")
   cmd.color("sulfur","(elem S and "+s+")")
   cmd.color("hydrogen","(elem H and "+s+")")
   cmd.color("pink","(elem C and "+s+")")

cmd.extend("mycba",mycba)

RE: [PyMOL] (no subject)

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

Question 1, CA-trace: =20

show ribbon
set ribbon_sampling=3D1

(NOTE: requires all main chain atoms to be present, but not necessarily =
visible -- CA-only models will be supported later on).

Question 2, Alignment of structural homologs (requires version 0.82).

load prot1.pdb
load prot2.pdb
align prot1,prot2////ca

This will perform a sequence alignment and then an iterative =
alpha-carbon superposition of matched residues.

Cheers,
Warren


-----Original Message-----
From: Craig Smith [mailto:boi...@ma...]
Sent: Wednesday, October 09, 2002 3:19 PM
To: pym...@li...
Subject: [PyMOL] (no subject)


Hello,=20


On the advice of a friend, I recently downloaded the OSX beta version of =
PyMOL. So far I'm very,very impressed. I have two questions: 1. How do =
you display a simple CA trace. I saw the selection for a backbone trace. =
2. I want to rms-fit two structural homologs. How is this done in PyMOL? =
I tried using the fit command and kept getting errors.=20


Thanks for you help=20



Craig L. Smith, Ph. D.=20
Molecular Microbiology=20
Washington University School of Medicine=20
660 South Euclid Box 8230=20
Voice: (314) 362-9054=20
Fax: (314) 362-1232=20
e-mail: sm...@bo...=20

RE: [PyMOL] Need help with selections

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

Thanks to the previous responders!  In addition, versions 0.82 and =
beyond support a more intuitive distance selection phrase:

"... within ... of ..."

For example:

load lig.pdb
load prot.pdb
select site,prot within 6 of lig
show surface, site

Note that if the ligand and protein are in the same object and the =
ligand isn't composed of PDB HETATM's, then you may need to specifically =
exclude their presence from the surface calculation:

flag ignore,lig
rebuild

Cheers,
Warren

> -----Original Message-----
> From: aar...@gs... [mailto:aar...@gs...]
> Sent: Friday, October 11, 2002 12:36 PM
> To: pym...@li...
> Subject: [PyMOL] Need help with selections
>=20
>=20
> Hello,
>=20
> I am somewhat new to PYMOL and was trying to create a=20
> 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=20
> examples in the
> manual. I will want to use this selection to make a surface of the
> selection afterward.
>=20
> Thanks,
>=20
> Aaron
>=20
>=20
> Aaron B. Miller
> Computational Chemist
> GlaxoSmithKline R & D
> Five Moore Drive, North M1407
> RTP, NC 27709-3398
> (919) 483-6069  Fax (919) 315-0430
> Aar...@gs...
>=20
>=20
>=20
>=20
> -------------------------------------------------------
> 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
>=20

Re: [PyMOL] Need help with selections

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

Hello Aaron,

* aar...@gs... <aar...@gs...> [2002-10-11 15:36] wrote:
> Hello,
> 
> 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.

If your molecule objects are called, for example, prot and inhib, you
could use something like:

  select interface, (prot and (inhib around 5.))
  show surface, interface

by creating a named selection, it can be easier to do subsequent
manipulations of your representation.

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

Re: [PyMOL] Need help with selections

[Ezequiel H P. <za...@SL...>]

select ligands, (byres gmp expand 5 and psd)

selects whole residues from molecule psd within 5 A from gmp


aar...@gs... wrote:
> Hello,
> 
> 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.
> 
> Thanks,
> 
> Aaron
> 
> 
> Aaron B. Miller
> Computational Chemist
> GlaxoSmithKline R & D
> Five Moore Drive, North M1407
> RTP, NC 27709-3398
> (919) 483-6069  Fax (919) 315-0430
> Aar...@gs...
> 
> 
> 
> 
> -------------------------------------------------------
> 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

-- 
--
  Ezequiel Panepucci, Ph.D. - Laboratory of Prof. Axel Brunger
  HHMI - Stanford University
  Phone: 650-736-1714
  Cell:  650-714-9414

[PyMOL] Need help with selections

[<aar...@gs...>]

Hello,

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.

Thanks,

Aaron


Aaron B. Miller
Computational Chemist
GlaxoSmithKline R & D
Five Moore Drive, North M1407
RTP, NC 27709-3398
(919) 483-6069  Fax (919) 315-0430
Aar...@gs...

Re: [PyMOL] Again: How does the density wizard works?

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

On Fri, 11 Oct 2002, Marc Saric wrote:

> Hi all,
>
> Some time ago I asked if someone knows how the density-wizard in Pymol
> works, but did not get an answer, so I ask again! :-)

Persistence is sometimes necessary....

> I searched the archives for this, but found nothing (at least not under
> "wizard" and "density wizard"), therefore my question:

The answer:

1. Load a map
2. Load a model structure
3. Activate the Density Wizard
4. Control-middle click to pick any atom in the model to get
   the map drawn about it.

Each of the blue rows in the Wizard is a pop-up menu.

You can select multiple or different maps to be displayed at different
levels as you traverse the model.

Cheers,
Warren

[PyMOL] Again: How does the density wizard works?

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

Hi all,

Some time ago I asked if someone knows how the density-wizard in Pymol 
works, but did not get an answer, so I ask again! :-)

I searched the archives for this, but found nothing (at least not under
"wizard" and "density wizard"), therefore my question:

I know how to load and display CCP4 and XPLOR/CNS-maps in Pymol and how
to make them visible from the commandline (isomesh bla, bla, ...), but I
don't understand the density wizard:

If I've loaded a map, I'm not able to make some parts of it visible with
the wizard, and also not if I'm trying to update an existing isomesh
created at the commandline.

So maybe I'm overlooking something really simple, but it did not work at
all so far.

If someone could point out how this thing is supposed to work???

Thanks in advance!


-- 
Bye,  Marc Saric

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

[PyMOL] (no subject)

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

Hello,

On the advice of a friend, I recently downloaded the OSX beta version 
of PyMOL.  So far I'm very,very impressed.  I have two questions:  1.  
How do you display a simple CA trace. I saw the selection for a 
backbone trace.  2.  I want to rms-fit two structural homologs.  How is 
this done in PyMOL?  I tried using the fit command and kept getting 
errors.

Thanks for you help


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] Stereographics CrystalEyes problem

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

Yep, we ran into the same problem with our ESGI emitters and FireGL2 =
cards -- we ended up having to buy new StereoGraphics (E-2) emitters for =
the Linux machines  (~$200).

http://www.qualixdirect.com/
part # SV-008-A-PC-E2=20

Cheers,
Warren


> -----Original Message-----
> From: Viktor Hornak [mailto:ho...@cs...]
> Sent: Tuesday, October 08, 2002 2:19 PM
> To: Schubert, Carsten
> Cc: pymol-users
> Subject: Re: [PyMOL] Stereographics CrystalEyes problem
>=20
>=20
> Carsten,
>=20
> your guess sounds very likely to me. Unfortunately, we only=20
> have "ESGI"=20
> emitters so I cannot confirm it for sure (but I bet you're right).
> Thanks a lot for the tip.
>=20
> Cheers,
> -Viktor
>=20
>=20
> Schubert, Carsten wrote:
> > just a wild guess, but in order to get stereo to work on my=20
> PC (under=20
> > W2K) with a Oxygen GVX card I had to use a "ENT" emitter from=20
> > Stereographics. As far as I recall the regular emitters used on the=20
> > SGI's, type "ESGI", did not work.
> >=20
> > Hope it helps.
> >=20
> > Cheers
> >         Carsten
> >=20
> > -----Original Message-----
> > From: Viktor Hornak [mailto:ho...@cs...]
> > Sent: Tuesday, October 08, 2002 15:45
> > To: pymol-users
> > Subject: [PyMOL] Stereographics CrystalEyes problem
> >=20
> >=20
> > Hello,
> >=20
> > I followed the discussion on 3D stereo support in PyMOL and saw that
> > many people were able to get PyMOL in stereo with FireGL or Nvidia
> > cards. Finally I got the chance to try it out myself with a=20
> new NVIDIA
> > Quadro4 XGL 900. I am running PyMOL on RedHat 7.3 wiht the=20
> latest nvidia
> > drivers (1.0-3123). There were no problems to get=20
> accelerated X up with
> > blazingly fast PyMOL rendering. So next, I tried to get=20
> stereo working.
> > I am using Stereographics emitter and CrystalEyes which=20
> I've been using
> > with our SGIs (so that I know they are functional; in fact=20
> PyMOL works
> > in stereo on our SGIs without a problem). I plugged the=20
> emmiter into the
> > DIN on my Quadro4 card, put   Option "Stereo" "3"   into my
> > XF86Config-4, restarted X and hoped that things will just work.
> > According to XFree log file, X was really initiated in=20
> stereo mode. The
> > emmiter light turned on when I started PyMOL. I switched to 'quad
> > buffered stereo' and the molecule getss rendered in stereo=20
> but when I
> > look at it with CrystalEyes glasses nothing changes. I=20
> still see double
> > rendered image on the screen, which means that the emmiter does not
> > synchronize glasses correctly (or at all).
> > I tried to change some options in XF86Config-4 but nothing=20
> helped, so I
> > was wondering if someone experienced the same problem. Do=20
> Stereographics
> > emmiter and CrystalEyes glasses work with Quadro4 at all?=20
> Do I need to
> > get a different emmiter or glasses? Any help appreciated...
>=20
>=20
>=20
>=20
> -------------------------------------------------------
> 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
>=20

Re: [PyMOL] Stereographics CrystalEyes problem

[Viktor H. <ho...@cs...>]

Carsten,

your guess sounds very likely to me. Unfortunately, we only have "ESGI" 
emitters so I cannot confirm it for sure (but I bet you're right).
Thanks a lot for the tip.

Cheers,
-Viktor


Schubert, Carsten wrote:
> just a wild guess, but in order to get stereo to work on my PC (under 
> W2K) with a Oxygen GVX card I had to use a "ENT" emitter from 
> Stereographics. As far as I recall the regular emitters used on the 
> SGI's, type "ESGI", did not work.
> 
> Hope it helps.
> 
> Cheers
>         Carsten
> 
> -----Original Message-----
> From: Viktor Hornak [mailto:ho...@cs...]
> Sent: Tuesday, October 08, 2002 15:45
> To: pymol-users
> Subject: [PyMOL] Stereographics CrystalEyes problem
> 
> 
> Hello,
> 
> I followed the discussion on 3D stereo support in PyMOL and saw that
> many people were able to get PyMOL in stereo with FireGL or Nvidia
> cards. Finally I got the chance to try it out myself with a new NVIDIA
> Quadro4 XGL 900. I am running PyMOL on RedHat 7.3 wiht the latest nvidia
> drivers (1.0-3123). There were no problems to get accelerated X up with
> blazingly fast PyMOL rendering. So next, I tried to get stereo working.
> I am using Stereographics emitter and CrystalEyes which I've been using
> with our SGIs (so that I know they are functional; in fact PyMOL works
> in stereo on our SGIs without a problem). I plugged the emmiter into the
> DIN on my Quadro4 card, put   Option "Stereo" "3"   into my
> XF86Config-4, restarted X and hoped that things will just work.
> According to XFree log file, X was really initiated in stereo mode. The
> emmiter light turned on when I started PyMOL. I switched to 'quad
> buffered stereo' and the molecule getss rendered in stereo but when I
> look at it with CrystalEyes glasses nothing changes. I still see double
> rendered image on the screen, which means that the emmiter does not
> synchronize glasses correctly (or at all).
> I tried to change some options in XF86Config-4 but nothing helped, so I
> was wondering if someone experienced the same problem. Do Stereographics
> emmiter and CrystalEyes glasses work with Quadro4 at all? Do I need to
> get a different emmiter or glasses? Any help appreciated...

RE: [PyMOL] Stereographics CrystalEyes problem

[Schubert, C. <Car...@3d...>]

Hi Viktor,

just a wild guess, but in order to get stereo to work on my PC (under W2K)
with a Oxygen GVX card I had to use a "ENT" emitter from Stereographics. As
far as I recall the regular emitters used on the SGI's, type "ESGI", did not
work.

Hope it helps.

Cheers

	Carsten



-----Original Message-----
From: Viktor Hornak [mailto:ho...@cs...]
Sent: Tuesday, October 08, 2002 15:45
To: pymol-users
Subject: [PyMOL] Stereographics CrystalEyes problem


Hello,

I followed the discussion on 3D stereo support in PyMOL and saw that 
many people were able to get PyMOL in stereo with FireGL or Nvidia 
cards. Finally I got the chance to try it out myself with a new NVIDIA 
Quadro4 XGL 900. I am running PyMOL on RedHat 7.3 wiht the latest nvidia 
drivers (1.0-3123). There were no problems to get accelerated X up with 
blazingly fast PyMOL rendering. So next, I tried to get stereo working. 
I am using Stereographics emitter and CrystalEyes which I've been using 
with our SGIs (so that I know they are functional; in fact PyMOL works 
in stereo on our SGIs without a problem). I plugged the emmiter into the 
DIN on my Quadro4 card, put   Option "Stereo" "3"   into my 
XF86Config-4, restarted X and hoped that things will just work. 
According to XFree log file, X was really initiated in stereo mode. The 
emmiter light turned on when I started PyMOL. I switched to 'quad 
buffered stereo' and the molecule getss rendered in stereo but when I 
look at it with CrystalEyes glasses nothing changes. I still see double 
rendered image on the screen, which means that the emmiter does not 
synchronize glasses correctly (or at all).
I tried to change some options in XF86Config-4 but nothing helped, so I 
was wondering if someone experienced the same problem. Do Stereographics 
emmiter and CrystalEyes glasses work with Quadro4 at all? Do I need to 
get a different emmiter or glasses? Any help appreciated...

Thanks,
-Viktor
-- 
=================================================================== 
Viktor Hornak
CSB computational facility
SUNY at Stony Brook               E-mail: vik...@su... 
===================================================================



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[PyMOL] Stereographics CrystalEyes problem

[Viktor H. <ho...@cs...>]

Hello,

I followed the discussion on 3D stereo support in PyMOL and saw that 
many people were able to get PyMOL in stereo with FireGL or Nvidia 
cards. Finally I got the chance to try it out myself with a new NVIDIA 
Quadro4 XGL 900. I am running PyMOL on RedHat 7.3 wiht the latest nvidia 
drivers (1.0-3123). There were no problems to get accelerated X up with 
blazingly fast PyMOL rendering. So next, I tried to get stereo working. 
I am using Stereographics emitter and CrystalEyes which I've been using 
with our SGIs (so that I know they are functional; in fact PyMOL works 
in stereo on our SGIs without a problem). I plugged the emmiter into the 
DIN on my Quadro4 card, put   Option "Stereo" "3"   into my 
XF86Config-4, restarted X and hoped that things will just work. 
According to XFree log file, X was really initiated in stereo mode. The 
emmiter light turned on when I started PyMOL. I switched to 'quad 
buffered stereo' and the molecule getss rendered in stereo but when I 
look at it with CrystalEyes glasses nothing changes. I still see double 
rendered image on the screen, which means that the emmiter does not 
synchronize glasses correctly (or at all).
I tried to change some options in XF86Config-4 but nothing helped, so I 
was wondering if someone experienced the same problem. Do Stereographics 
emmiter and CrystalEyes glasses work with Quadro4 at all? Do I need to 
get a different emmiter or glasses? Any help appreciated...

Thanks,
-Viktor
-- 
=================================================================== 
Viktor Hornak
CSB computational facility
SUNY at Stony Brook               E-mail: vik...@su... 
===================================================================

RE: [PyMOL] PyMol fruit-menu incompatability on OS X

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

William,

	You might want to try using the "top" utility to determine whether or =
not some other process is soaking up CPU while PyMOL is=20


-----Original Message-----
From: William Scott [mailto:wg...@hy...]
Sent: Saturday, October 05, 2002 7:13 PM
To: pym...@li...
Subject: [PyMOL] PyMol fruit-menu incompatability on OS X


Hi:

I've noticed that the performance of pymol on my laptop after an OS X=20
upgrade to 10.2 (and corresponding pymol 0.84 upgrade) was much worse. =20
Although I think 10.2.1 is definitely slower and more buggy than=20
10.1.5, I tracked down the main culprit:  A $7 piece of shareware=20
called Fruit Menu.  (It lets you put whatever you want in the=20
upper-left corner blue apple pulldown, much like OS 9 favorites).  I=20
disabled something called an Application Enhancer that gets installed=20
with Fruit Menu by moving it from its original Library folder location=20
to a new one, logged out and back in again.  (This temporarily disables=20
fruit menu, but it is a small price to pay).  When I then log back in=20
again, pymol is significantly speedier (although I still think it=20
worked better under 10.1.5.)

This is much more of a problem on my 500MHz iBook, which is what I use=20
with pymol for oral presentations, than it is with faster machines.  I=20
am suspicious that this problem actually doesn't arise on dual=20
processor machines.

I've also noticed that this same Application Enhancer thing screws up=20
OroborOSX, my X-windows manager.  A similar cure works.

Anyway I thought I would pass this along in case anyone is having=20
problems like this on 10.2.x with pymol.  If anyone has a better=20
workaround, I'd like to know ...


All the best,

Bill Scott




 =20



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Welcome to geek heaven.
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