pymol-users — Collaborative support and tips for PyMOL users

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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[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...

[PyMOL] Density wizard

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

Hi Pymolers,

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.

Thanks in advance!

I'm using Pymol 0.82 on SuSE Linux 8.0 with Python 2.2, which gives me 
the following (obviously not lethal) error-message on startup:

[...]
/usr/lib/python2.1/site-packages/pymol/modules/pymol/__init__.py:69: 
RuntimeWarning: Python C API version mismatch for module pcatch: This 
Python has API version 1011, module pcatch has version 1010.
   _cmd.runpymol() # only returns if we are running pretend GLUT
/usr/lib/python2.1/site-packages/pymol/modules/pymol/xray.py:15: 
RuntimeWarnin
g: Python C API version mismatch for module sglite: This Python has API 
version
  1011, module sglite has version 1010.
   import sglite
/usr/lib/python2.1/site-packages/pymol/modules/pymol/xray.py:15: 
RuntimeWarnin
g: Python C API version mismatch for module ExtensionClass: This Python 
has API
  version 1011, module ExtensionClass has version 1010.
   import sglite
  OpenGL based graphics front end:
   GL_VENDOR: VA Linux Systems Inc.
   GL_RENDERER: Mesa DRI G400 20010622 AGP 1x x86
   GL_VERSION: 1.2 Mesa 3.4.2



-- 
Bye,  Marc Saric

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

[PyMOL] FYI: nvidia stereo + twinview does not work

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

Hi People,
For your information, the latest Nvidia driver does not support stereo
with a dual monitor (aka TwinView) configuration.

It might work if you have 2 graphics cards though I haven't tried that.

Does any one know if this is possible with any of the ati firegl cards?

Thanks,

Zac

Re: [PyMOL] spheres in very large ppdb files

[<pm...@ua...>]

Quoting Ronald L Koder <ko...@ma...>:

> I'm relatively new to PyMOL, and I've been repeatedly running into
> a problem with the pdb files I use, namely that whenever I try to use the
> show spheres command the program crashes.  The same scripts work for
> smaller proteins, so I'm guessing I need to find some way to increase the
> memory allocation for the image, or something of the sort.
> 
> Anyone have any ideas?

Ronald,

how much RAM do you have in your machine ?... To render 1bgy (31486 atoms) with
spheres, my linux box uses more than 256 Mb of physical RAM, maybe that´s the
problem (I have 512 Mb).

Paulo
 
> BTW, I'm using the win32 build and one of the files I'm having problems
> with is 1BGY, (the cytochrome BC1 complex)
> 
> Thanks,
> 
> _____________________________________________
> Ronald L. Koder, Ph.D.
> Postdoctoral Fellow
> The Johnson Foundation
> Dept. of Biochemistry and Biophysics
> University of Pennsylvania School of Medicine
> Room 1004 Stellar-Chance Bldg.
> Philadelphia, PA 19104-6059
> ko...@ma...
> _____________________________________________
> 
> 
> 
> 
> -------------------------------------------------------
> 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] spheres in very large ppdb files

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

Ron,

	This appears to be a Windows specific problem.  I can view spheres with =
1bgy.pdb just fine under Linux (albeit 168 MB of RAM...), but it blows =
out on Windows.

However, if you lower the sphere_quality (which only affects OpenGL =
quality), it holds together:

load 1bgy.pdb
set sphere_quality=3D0
show sph
ray

My suspicion is that PyMOL is trying to allocate a larger block of RAM =
than Windows can give it in order to hold the sphere graphics =
primitives.

Cheers,
Warren


-----Original Message-----
From: Ronald L Koder [mailto:ko...@ma...]
Sent: Wednesday, October 02, 2002 12:23 PM
To: pym...@li...
Subject: [PyMOL] spheres in very large ppdb files


I'm relatively new to PyMOL, and I've been repeatedly running into
a problem with the pdb files I use, namely that whenever I try to use =
the
show spheres command the program crashes.  The same scripts work for=20
smaller proteins, so I'm guessing I need to find some way to increase =
the=20
memory allocation for the image, or something of the sort.

Anyone have any ideas?

BTW, I'm using the win32 build and one of the files I'm having problems=20
with is 1BGY, (the cytochrome BC1 complex)

Thanks,

_____________________________________________
Ronald L. Koder, Ph.D.
Postdoctoral Fellow
The Johnson Foundation
Dept. of Biochemistry and Biophysics
University of Pennsylvania School of Medicine
Room 1004 Stellar-Chance Bldg.
Philadelphia, PA 19104-6059
ko...@ma...
_____________________________________________




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[PyMOL] spheres in very large ppdb files

[<ko...@ma...>]

I'm relatively new to PyMOL, and I've been repeatedly running into
a problem with the pdb files I use, namely that whenever I try to use the
show spheres command the program crashes.  The same scripts work for 
smaller proteins, so I'm guessing I need to find some way to increase the 
memory allocation for the image, or something of the sort.

Anyone have any ideas?

BTW, I'm using the win32 build and one of the files I'm having problems 
with is 1BGY, (the cytochrome BC1 complex)

Thanks,

_____________________________________________
Ronald L. Koder, Ph.D.
Postdoctoral Fellow
The Johnson Foundation
Dept. of Biochemistry and Biophysics
University of Pennsylvania School of Medicine
Room 1004 Stellar-Chance Bldg.
Philadelphia, PA 19104-6059
ko...@ma...
_____________________________________________

Re: [PyMOL] Meaning of the get_view block

[<pm...@ua...>]

Quoting Serge Cohen <co...@em...>:

> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA1
> 
> Hi again,
> 
> I posted a question few days ago about the way to center on a particular
> zone of a structure without using the zoom command (which would touch a
> lot of view parameters at once).
Dear Serge,

I think that the following code works in the way you want - it brings the
selection to center of the screen, at the same setting it as the center of
rotation:

    cmd.origin(selection)
    m = cmd.get_view(0)
    n = m[0:9]+(0.0,0.0)+m[11:]
    cmd.set_view(n)


Regards,
Paulo

Re: [PyMOL] get_view

[<pm...@ua...>]

Dear Luca and Serge,


> > PS: If any one as some info on the previous questions I asked (get_view
> > blocks...), really don't fill shy about it. I did not have any answer
> > (even off list)
> 

here is the meaning of the rotation matrix:

set_view (\

#rotation matrix, describes the orientation of
#the object relative to coordinate system:
    -0.423272938,    0.519671082,   -0.742144108,\
     0.565680504,   -0.488278866,   -0.664524078,\
    -0.707710445,   -0.701090038,   -0.087292627,\
#Position of the object relative to world coordinates:
     0.000000000,    0.000000000, -108.510879517,\
#Coordinates of the object rotation center:
    21.806344986,   33.097042084,   26.156803131,\
#Near and far clipping planes, and the orthoscopic flag:
    81.724128723,  141.037658691,    0.000000000 )


Quoting Luca Jovine <luc...@ma...>:

> On Wednesday, October 2, 2002, at 10:10 AM, Serge Cohen wrote:
> 
> Actually, I would also be very interested in knowing what the matrix
> output by get_view exactly means...  also because it would be really nice
> if one could save the *transformed* coordinates of a molecule, so it could
> be imported into other programs in exactly the same orientation as in
> PyMOL (even though I find myself using other programs less and less,
> sometimes one still needs them...)

Here is a simple script that saves the molecule
with coordinates from the current orientation.

# Adds the command save_transformed
# Usage: save_transformed object, file
def save_transformed(object,file):
    m = cmd.get_view(0)
    ttt = [m[0], m[1], m[2], 0.0,
           m[3], m[4], m[5], 0.0,
           m[6], m[7], m[8], 0.0,
           0.0,   0.0,  0.0, 1.0]
    cmd.transform_object(object,ttt)
    cmd.save(file,object)

cmd.extend('save_transformed',save_transformed)


Cheers,
Paulo

Re: [PyMOL] get_view

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

* Luca Jovine <luc...@ma...> [2002-10-02 10:53] wrote:

> On Wednesday, October 2, 2002, at 10:10 AM, Serge Cohen wrote:
>=20
> > PS: If any one as some info on the previous questions I asked (get_view=
=20
> > blocks...), really don't fill shy about it. I did not have any answer=
=20
> > (even off list)
>=20
> Actually, I would also be very interested in knowing what the matrix=20
> output by get_view exactly means...  also because it would be really nice=
=20
> if one could save the *transformed* coordinates of a molecule, so it coul=
d=20
> be imported into other programs in exactly the same orientation as in=20
> PyMOL (even though I find myself using other programs less and less,=20
> sometimes one still needs them...)

Actually maybe the answer you are looking for was given back in July
when Warren answered someone else's question with:

* Warren L. DeLano <wa...@su...> [2002-07-07 11:13] wrote:

> cmd.get_view() returns a tuple which can be passed to cmd.set_view(...)
>=20
> ie.=20
>=20
> set_view (\
>     -0.745493710,   -0.657504320,   -0.109211229,\
>      0.235591769,   -0.413225234,    0.879625380,\
>     -0.623487175,    0.630026162,    0.462960035,\
>      2.252975464,    1.815253615,  -55.481048584,\
>     -3.770999908,   -6.882999897,   18.787000656,\
>     43.924808502,   75.804443359,    0.000000000 )
>=20
> or
>=20
> cmd.set_view((\
>     -0.745493710,   -0.657504320,   -0.109211229,\
>      0.235591769,   -0.413225234,    0.879625380,\
>     -0.623487175,    0.630026162,    0.462960035,\
>      2.252975464,    1.815253615,  -55.481048584,\
>     -3.770999908,   -6.882999897,   18.787000656,\
>     43.924808502,   75.804443359,    0.000000000 ))
>=20
> or
>=20
> vu=3Dcmd.get_view()
>=20
> ...
>=20
> cmd.set_view(vu)
>=20
> in vu[...]:
>=20
> 0-8 is the 3x3 rotation matrix
> 9-11 is the camera location (I think -- been a while...)
> 12-14 is the origin of rotation
> 15-16 are the clipping distances
> and 17 is the orthoscopic flag.

Hope that helps,
Robert
--=20
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] get_view

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

On Wednesday, October 2, 2002, at 10:10 AM, Serge Cohen wrote:

> PS: If any one as some info on the previous questions I asked (get_view 
> blocks...), really don't fill shy about it. I did not have any answer 
> (even off list)

Actually, I would also be very interested in knowing what the matrix 
output by get_view exactly means...  also because it would be really nice 
if one could save the *transformed* coordinates of a molecule, so it could 
be imported into other programs in exactly the same orientation as in 
PyMOL (even though I find myself using other programs less and less, 
sometimes one still needs them...)

-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
--------------------------------------------------------

Re: [PyMOL] Colouring according to B-factor

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

Serge,

* Serge Cohen <co...@em...> [2002-10-02 16:10] wrote:
> Title says it all...
>=20
> Is it possible to draw a protein (back-bone, cartoon, sticks...) with a=
=20
> colouring scheme according to the crystallographic B-factor of each=20
> atoms?

I have a color_b.py python script on my PyMOL web page that you can use.
it has a number of options including the selection and two types of
colouring schemes (rainbow versus a blue-magenta-red gradient) and
two types of binning of the colours (equal number of atoms in each
colour or equal spacing of colours along the B-factor range).

See http://biophysics.med.jhmi.edu/rlc/work/pymol to download.
There are other scripts there as well.

Cheers,
Robert
--=20
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

[PyMOL] Colouring according to B-factor

[Serge C. <co...@em...>]

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

Title says it all...

Is it possible to draw a protein (back-bone, cartoon, sticks...) with a 
colouring scheme according to the crystallographic B-factor of each 
atoms?

Thanks for the help

Serge.

PS: If any one as some info on the previous questions I asked (get_view 
blocks...), really don't fill shy about it. I did not have any answer 
(even off list)


- ----------------------------------------------------
Serge Cohen

GPG Key ID: 1024D/69B1D346
- ----------------------------------------------------
-----BEGIN PGP SIGNATURE-----
Version: GnuPG v1.0.7 (Darwin)

iD8DBQE9mv5FMygj1Wmx00YRAv+CAJ4zTpe8DPLwhXF8b5IDpCsSAQwZpgCggsfd
69I1HGciE849hCzxpv69aGo=
=vdj3
-----END PGP SIGNATURE-----

Re: [PyMOL] rpm installation problems

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

Hi Dirk

Perfect, thanks.  Guess it's not just my pymol understanding that's
incomplete...

Now.. why is the text in the top, grey window suddenly enormous in the new
version? - this is a little inconvenient for get_view, for example.

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            |
+-------------------------------------------------------------------------+



On Wed, 2 Oct 2002, Dirk Kostrewa wrote:

> Hi Daniel,
>
> AFAIK, rpm complains if you want to install a newer package version over an
> older one. In the case of an update, just issue the command "rpm -Uhv
> pymol-0.82-1.rh70.py152.i386.rpm".
>
> Best regards,
>
> Dirk.
>
> --
>
> ***************************************************************
> Dirk Kostrewa
> Paul Scherrer Institut             E-mail: dir...@ps...
> Life Sciences, OSRA/007             Phone: +41-56-310-4722
> CH-5232 Villigen PSI                  Fax: +41-56-310-4556
> Switzerland                      Internet: http://www.sb.psi.ch
> ***************************************************************
>
> On Wednesday 02 October 2002 14:31, Daniel John Rigden wrote:
> > Hi everyone
> >
> > I'm trying to install version 0.82 to replace 0.78.  The relevant rpms are
> > pymol-0.82-1.rh70.py152.i386.rpm and pymol-0.78-3.rh70.py152.i386.rpm.
> >
> > However, I get a load of messages of the following type
> >
> > [root@dodo progs]# rpm -ivh pymol-0.82-1.rh70.py152.i386.rpm
> > Preparing...                ###########################################
> > [100%]
> > file
> > /usr/lib/python1.5/site-packages/pymol/examples/package/redhat/pymol-0.78-2
> >.rh72.py21n.spec from install of pymol-0.82-1.rh70.py152 conflicts with file
> > from package pymol-0.78-3.rh70.py152 file
> > /usr/lib/python1.5/site-packages/pymol/modules/ExtensionClass.so from
> > install of pymol-0.82-1.rh70.py152 conflicts with file from package
> > pymol-0.78-3.rh70.py152
> > file /usr/lib/python1.5/site-packages/pymol/modules/_cmd.so from install
> > of pymol-0.82-1.rh70.py152 conflicts with file from package
> > pymol-0.78-3.rh70.py152
> > file /usr/lib/python1.5/site-packages/pymol/modules/_glu_nummodule.so from
> > install of pymol-0.82-1.rh70.py152 conflicts with file from package
> > pymol-0.78-3.rh70.py152
> > file /usr/lib/python1.5/site-packages/pymol/modules/_glumodule.so from
> > install of pymol-0.82-1.rh70.py152 conflicts with file from package
> > pymol-0.78-3.rh70.py152
> > etc etc
> >
> > I tried renaming the /usr/lib/python1.5/site-packages/pymol/ directory,
> > but that didn't help.
> >
> > I believe I can force rpm to install the new stuff anyway, but is it safe
> > to do so in this case?
> >
> > 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            |
> >
> > +-------------------------------------------------------------------------+
> >
> >
> >
> >
> >
> > -------------------------------------------------------
> > 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] rpm installation problems

[Dirk K. <dir...@ps...>]

Hi Daniel,

AFAIK, rpm complains if you want to install a newer package version over =
an=20
older one. In the case of an update, just issue the command "rpm -Uhv=20
pymol-0.82-1.rh70.py152.i386.rpm".

Best regards,

Dirk.

--=20

***************************************************************
Dirk Kostrewa
Paul Scherrer Institut             E-mail: dir...@ps...
Life Sciences, OSRA/007             Phone: +41-56-310-4722
CH-5232 Villigen PSI                  Fax: +41-56-310-4556
Switzerland                      Internet: http://www.sb.psi.ch
***************************************************************

On Wednesday 02 October 2002 14:31, Daniel John Rigden wrote:
> Hi everyone
>
> I'm trying to install version 0.82 to replace 0.78.  The relevant rpms =
are
> pymol-0.82-1.rh70.py152.i386.rpm and pymol-0.78-3.rh70.py152.i386.rpm.
>
> However, I get a load of messages of the following type
>
> [root@dodo progs]# rpm -ivh pymol-0.82-1.rh70.py152.i386.rpm
> Preparing...                ###########################################
> [100%]
> file
> /usr/lib/python1.5/site-packages/pymol/examples/package/redhat/pymol-0.=
78-2
>.rh72.py21n.spec from install of pymol-0.82-1.rh70.py152 conflicts with =
file
> from package pymol-0.78-3.rh70.py152 file
> /usr/lib/python1.5/site-packages/pymol/modules/ExtensionClass.so from
> install of pymol-0.82-1.rh70.py152 conflicts with file from package
> pymol-0.78-3.rh70.py152
> file /usr/lib/python1.5/site-packages/pymol/modules/_cmd.so from instal=
l
> of pymol-0.82-1.rh70.py152 conflicts with file from package
> pymol-0.78-3.rh70.py152
> file /usr/lib/python1.5/site-packages/pymol/modules/_glu_nummodule.so f=
rom
> install of pymol-0.82-1.rh70.py152 conflicts with file from package
> pymol-0.78-3.rh70.py152
> file /usr/lib/python1.5/site-packages/pymol/modules/_glumodule.so from
> install of pymol-0.82-1.rh70.py152 conflicts with file from package
> pymol-0.78-3.rh70.py152
> etc etc
>
> I tried renaming the /usr/lib/python1.5/site-packages/pymol/ directory,
> but that didn't help.
>
> I believe I can force rpm to install the new stuff anyway, but is it sa=
fe
> to do so in this case?
>
> 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         =
   |
>
> +----------------------------------------------------------------------=
---+
>
>
>
>
>
> -------------------------------------------------------
> 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] rpm installation problems

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

Hi everyone

I'm trying to install version 0.82 to replace 0.78.  The relevant rpms are
pymol-0.82-1.rh70.py152.i386.rpm and pymol-0.78-3.rh70.py152.i386.rpm.

However, I get a load of messages of the following type

[root@dodo progs]# rpm -ivh pymol-0.82-1.rh70.py152.i386.rpm
Preparing...                ###########################################
[100%]
file
/usr/lib/python1.5/site-packages/pymol/examples/package/redhat/pymol-0.78-2.rh72.py21n.spec
from install of pymol-0.82-1.rh70.py152 conflicts with file from package
pymol-0.78-3.rh70.py152 file
/usr/lib/python1.5/site-packages/pymol/modules/ExtensionClass.so from
install of pymol-0.82-1.rh70.py152 conflicts with file from package
pymol-0.78-3.rh70.py152
file /usr/lib/python1.5/site-packages/pymol/modules/_cmd.so from install
of pymol-0.82-1.rh70.py152 conflicts with file from package
pymol-0.78-3.rh70.py152
file /usr/lib/python1.5/site-packages/pymol/modules/_glu_nummodule.so from
install of pymol-0.82-1.rh70.py152 conflicts with file from package
pymol-0.78-3.rh70.py152
file /usr/lib/python1.5/site-packages/pymol/modules/_glumodule.so from
install of pymol-0.82-1.rh70.py152 conflicts with file from package
pymol-0.78-3.rh70.py152
etc etc

I tried renaming the /usr/lib/python1.5/site-packages/pymol/ directory,
but that didn't help.

I believe I can force rpm to install the new stuff anyway, but is it safe
to do so in this case?

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] translation vs rotation

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

There is also a translate function similar to "rotate", the docs for =
these don't exist yet, because the implementation isn't finished.  =
However, feel free to used them in the following forms:

translate vector,object-name,state

   vector needs to be something like [x,y,z]

   translate [1,0,0],pept

rotate axis,angle,object-name,state

   axis can be either the letter x,y,z or a 3D vector [x,y,z]

   rotate x,90,pept
   rotate [1,1,1],10,pept

Cheers,
Warren

-----Original Message-----
From: Byron Delabarre [mailto:by...@SL...]
Sent: Tuesday, October 01, 2002 12:32 PM
To: PyM...@li...
Subject: Re: [PyMOL] translation vs rotation


Mark -

For the label colours, I don't think you can colour independantly. You
can work around this by creating duplicate atoms, colouring them the
colour you want for the labels, and then labelling the duplicate atoms.

Can't help with the move objects - maybe try redefining your screen
centre? I'm sure there is a better way than that however...

Byron DeLaBarre
Stanford

PS - apologies if this showed up 3x on the list - the Mozilla mailer has =

been getting fussy.

Mark Pfuhl wrote:

 > Hello!
 > This is a follow up to a recent question on 'moving' several objects
 > independently. In the answer there is only reference to the rotate
 > command. But is there also a way to translate the objects
 > independently? I tried the move command but that does not take an
 > object name as an argument. I know objects can be translated
 > interactively by using the mouse editing mode but is there a way to =
do
 > so in a script?
 > Another question: Is there a way to set the colour for labels
 > explicitely and independently from the object that they belong to?
 > thanks,
 > mark





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Re: [PyMOL] translation vs rotation

[Byron D. <by...@SL...>]

Mark -

For the label colours, I don't think you can colour independantly. You
can work around this by creating duplicate atoms, colouring them the
colour you want for the labels, and then labelling the duplicate atoms.

Can't help with the move objects - maybe try redefining your screen
centre? I'm sure there is a better way than that however...

Byron DeLaBarre
Stanford

PS - apologies if this showed up 3x on the list - the Mozilla mailer has 
been getting fussy.

Mark Pfuhl wrote:

 > Hello!
 > This is a follow up to a recent question on 'moving' several objects
 > independently. In the answer there is only reference to the rotate
 > command. But is there also a way to translate the objects
 > independently? I tried the move command but that does not take an
 > object name as an argument. I know objects can be translated
 > interactively by using the mouse editing mode but is there a way to do
 > so in a script?
 > Another question: Is there a way to set the colour for labels
 > explicitely and independently from the object that they belong to?
 > thanks,
 > mark

Re: [PyMOL] translation vs rotation

[Byron D. <by...@SL...>]

Mark -

For the label colours, I don't think you can colour independantly. You 
can work around this by creating duplicate atoms, colouring them the 
colour you want for the labels, and then labelling the duplicate atoms.

Can't help with the move objects - maybe try redefining your screen 
centre? I'm sure there is a better way than that however...

Byron DeLaBarre
Stanford

Mark Pfuhl wrote:

> Hello!
> This is a follow up to a recent question on 'moving' several objects 
> independently. In the answer there is only reference to the rotate 
> command. But is there also a way to translate the objects 
> independently? I tried the move command but that does not take an 
> object name as an argument. I know objects can be translated 
> interactively by using the mouse editing mode but is there a way to do 
> so in a script?
> Another question: Is there a way to set the colour for labels 
> explicitely and independently from the object that they belong to?
> thanks,
> mark

Re: [PyMOL] translation vs rotation

[Byron D. <by...@SL...>]

Mark -

For the label colours, I don't think you can colour independantly. You 
can work around this by creating duplicate atoms, colouring them the 
colour you want for the labels, and then labelling the duplicate atoms.

Can't help with the move objects - maybe try redefining your screen 
centre? I'm sure there is a better way than that however...

Byron DeLaBarre
Stanford

Mark Pfuhl wrote:

> Hello!
> This is a follow up to a recent question on 'moving' several objects 
> independently. In the answer there is only reference to the rotate 
> command. But is there also a way to translate the objects 
> independently? I tried the move command but that does not take an 
> object name as an argument. I know objects can be translated 
> interactively by using the mouse editing mode but is there a way to do 
> so in a script?
> Another question: Is there a way to set the colour for labels 
> explicitely and independently from the object that they belong to?
> thanks,
> mark

[PyMOL] Smooth Surfaces

[Evan S. <st...@sa...>]

I'm trying to generate the smoothest possible surface while using PyMol
0.82 under XP.

I've tried increasing surface_quality but there appears to be a value
above which no more polygons are generated. I've also tried playing with
surface_best, surface_poor, and surface_moderate with unpredictable
results.

Is there an inherent limit to the smoothness of a surface in PyMol? Or, is
it possible for me to get more polygons?

--
Evan Stein
Structural Biology Program
Skirball Institute / NYU School of Medicine
540 First Avenue Lab 3-4
New York, NY 10016

phone: (212) 263-8968
fax: (212) 263-8951
email: st...@sa...
URL: http://saturn.med.nyu.edu/~stein