pymol-users — Collaborative support and tips for 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... 
===================================================================



-------------------------------------------------------
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] 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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RE: [PyMOL] hardware stereo

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

Samy,

   Try increasing your refresh rate.  You need a vertical refresh in the =
100+ Hz range to avoid flicker.  If that doesn't do the trick, then =
perhaps there is something wrong with the emitter?

Warren

-----Original Message-----
From: Samy Meroueh [mailto:me...@go...]
Sent: Sunday, October 06, 2002 11:07 AM
To: pym...@li...
Subject: [PyMOL] hardware stereo


Hello,=20
  I recently purchased an ATI FIRE gl2 graphics card,=20
a nuvision emitter and glasses for 3D stereo viewing
with pymol.  I am currently running windows xp.  When
switch to hardware stereo and I put the glasses on I
notice heavy flickering  though I am able to see the=20
molecule in 3D.  THe flickering is extermely uncomfortable
and I am wondering if there is a way to get rid of
it.=20

-best regards, Samy.





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Welcome to geek heaven.
http://thinkgeek.com/sf
_______________________________________________
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[PyMOL] hardware stereo

[Samy M. <me...@go...>]

Hello, 
  I recently purchased an ATI FIRE gl2 graphics card, 
a nuvision emitter and glasses for 3D stereo viewing
with pymol.  I am currently running windows xp.  When
switch to hardware stereo and I put the glasses on I
notice heavy flickering  though I am able to see the 
molecule in 3D.  THe flickering is extermely uncomfortable
and I am wondering if there is a way to get rid of
it. 

-best regards, Samy.

[PyMOL] PyMol fruit-menu incompatability on OS X

[William S. <wg...@hy...>]

Hi:

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

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

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

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


All the best,

Bill Scott




  

[PyMOL] Re: [o-info] Q&A Quadro4 900 XGL under Linux

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

On Thu, 3 Oct 2002, Alwyn Jones wrote:

> >Quadro4 900 XGL under Linux
>
> we now have this card running on a linux system (AMD XP1700).
>
> the stereo performance is stellar with a suitable high refresh
> monitor, NuVision glasses and emitter.
>
> the only problem comes when you switch back to mono with F1. the
> performance (as judged by spin, for example) then drops by ~10.

There has been some discussion of this on the PyMOL list as well.  All
nVidia stereo-capable cards experience this problem with O and PyMOL when
stereo is enabled (but not activated).  I think the GLUT library is
partly to blame, but the problem is specific to nVidia hardware.

Presumably this is because both programs are opening a GLUT stereo window
under mono mode -- nVidia's hardware or drivers have a unique problem with
this configuration, which competiting options (ATI, SGI, 3DLabs) do
not share.  Note that this problem is not OS-dependent -- it also occurs
under Windows -- and it doesn't matter which OEM manufacturer built the
card -- the problem lies with nVidia chips or low-level drivers.

> if you start with a mono visual (i.e. setenv STEREO OFF), performance
> is again excellent.

> this is the first linux stereo card that i have seen that i can recommend.

I think this "bug" is a major drawback with nVidia cards.  My experience
has been that the FireGL2's are a better choice for stereo under Linux,
with the caveat that you have to be very careful about running a version
of Linux compatible with their fickle drivers.  The new ATI FireGL X1 may
offer the best stereo performance of any card available right now, but I
haven't yet had the privilege of being able to try one.

Considering the importance of stereographics to structural biology,
computational chemistry, and bioinformatics, I really hope one or both
manufacturers will start taking stereo support under Linux (as well
as Windows) more seriously.

The pharmaceutical industry as well as thousands of academic researchers
have a significant amount of money to waiting to be spent on solid PC
stereo-graphics solutions, if and when such solutions become available.

Cheers,
Warren

[PyMOL] numbering problem

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

   I am trying to make png sequence, but it doesn't work like I wish.
There're 800 pdb files in sequence, and 400-499 numbered files are made 
after the 800 file was made. When run script to make movie, PyMol reads 
1-399, 500-800, and then 400-499. I don't know why it happens. Some module 
of PyMol reads the date of files to make sequence? ...I don't know. 

   I don't like making 500-800 files to make date sequence, because it's 
rather big calculation. Can I make right-sequenced movie, and how?

   many thanks,
   Yuuki

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