pymol-users — Collaborative support and tips for PyMOL users

[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...
_____________________________________________




-------------------------------------------------------
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] 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...   |
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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

[PyMOL] translation vs rotation

[Mark P. <mp...@le...>]

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
-- 
Mark Pfuhl                  phone : 44 (0) 116 223 1544
Department of Biochemistry                     252 3054
Leicester University        fax   :            223 1503
University Road             home  :            255 3262
Leicester LE1 7RH           email : mp...@le...
UK                    http://www.le.ac.uk/biochem/mp84/

RE: [PyMOL] moving one segment relative to the rest

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

Shohei,

The easiest way to do this is to split the objects and then use the =
rotate command.

# save as a ".pml" file...

load 1FJ1.pdb

# split PDB file

create anti=3D(chain F)=20
create fab=3D(chain A,B)

# delete original object

delete 1FJ1

# color objects

color green,fab
color pink,anti

# color interface

select inter =3D (byres ((fab within 5 of anti)\
   or (anti within 5 of fab)))

color yellow,inter

# splay apart

orient
origin fab
rotate y,60,fab
origin anti
rotate y,-60, anti

# zoom interface region

zoom inter
show sph,inter
disable inter

-----Original Message-----
From: Shohei Koide [mailto:sk...@uc...]
Sent: Monday, September 30, 2002 12:14 PM
To: pym...@li...
Subject: [PyMOL] moving one segment relative to the rest


Hello,

I am wondering if one can move one segment (in my case, an antigen=20
protein) relative to the rest of the complex (antibody) using PyMOL.=20
So far I have only been able to translate/rotate the entire complex.=20
I would like to manually "undock" the complex for an illustration=20
purpose.

Thanks.

Shohei Koide


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[PyMOL] moving one segment relative to the rest

[Shohei K. <sk...@uc...>]

Hello,

I am wondering if one can move one segment (in my case, an antigen 
protein) relative to the rest of the complex (antibody) using PyMOL. 
So far I have only been able to translate/rotate the entire complex. 
I would like to manually "undock" the complex for an illustration 
purpose.

Thanks.

Shohei Koide

[PyMOL] RE: pyMol help (Ball & Sticks)

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

From: George Nicola

>I've tried several settings and commands but cannot figure out how to =
make=20
>a simple ball-and-stick representation of a molecule.  Can it be done =
in=20
>Pymol?

George,

Yes, but it is non-obvious:

hide lines
show sticks
show spheres
set stick_radius=3D0.1
set sphere_scale=3D0.25

You can change the two numbers above to fit preferences.

Cheers,
Warren

Antw: [PyMOL] Re: Stereo3D hardware recommendation

[Manfred B. <Man...@ms...>]

>>> Marc Saric <mar...@mp...> 29.09.2002 18:28 >>>

....
> Nuvision and Crystaleyes wireless glasses and emitters are 
> interchangeable. 

Be carefull! Unfortunately I had to find out that this only works  in
one way:  Nuvission glasses do work with Nuvission and Stereographics 
emitters. But a Nuvission emitter CANNOT drive stereographics
(Crystaleyes) glasses. Therefore I still would buy Nuvission glasses,
but never again a Nuvission emitter.


Manfred

[PyMOL] Re: Stereo3D hardware recommendation

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

> Because of the mono-performance issue, I decide to
> change my graphics card to ATI Fire GL2 (or 3 / 4).

That might be a good idea if you wan't to use stereo heavily, if you use 
it only rarely, a nVidia-based board might also be ok (although the 
Quadro-cards are also quite expensive, and there's no hacked driver for 
Linux, you need to modify the graphics-hardware to fool the driver).
Otoh there is also a new Radeon 9x00-based "professional" chip called 
Fire GL X1

http://mirror.ati.com/products/workstation/fireglx1/index.html

which apparently comes with stereo-enabled Linux-drivers (don't know 
exactly, wether the Linux-drivers really have stereo, but it is 
mentioned that the card as such such is stereo-capable). Don't know 
about any issues regarding stereo-performance for this board.

You might take this on your list of alternatives (but I don't know the 
price).


> My first question is: how will the different cards
> affect the stereo-viewing performance (at 1280x1024)?
> Is it necessary to go for a high-end card (and pay
> extra cash)?

In general: From the specs and the benchmarks/reviews I've read, all 
cards should be able to do what you want (display macromolecules in 
Pymol in stereo). More expensive cards might be better at handling 
larger models/more textures etc. but I would think that even the cheapes 
of them should be able to run sufficiently fast on the mentioned 
PC-hardware. Have a look at ViewPerf-numbers, if they seem to be 
reasonable (> 5-10 fps for most of the tests) the card should be ok for you.


> For the stereo glasses, I called Stereo Graphics and
> their CrystalEyes3 + Emitter boundle costs about $900.
> I also called NuVision and their 60GX + Emitter cost
> about $300. My second question is: what's the
> difference between these two? Can the difference
> justify the extra $600?

I've had a look at both Nuvision and Stereographics-glasses, and both 
are professional-grade (vs. the ELSA Revelator or other semi-pro or 
hobby sollutions, which are even cheaper, but are also very small).

Nuvision and Crystaleyes wireless glasses and emitters are 
interchangeable. Crystaleyes are normaly a bit larger, but the Nuvision 
shutters are big enough that you don't have a restricted field of view 
(which you have with the Revelator etc.).

Due to the smaller size they might also be a bit less heavy.

If you want the cheapest "pro"-sollution, I would go for the Nuvision, 
they are good enough. If -for some reason- you really want maximum-sized 
shutters, you need Crystaleyes.

Maybe you can test at least one of the two at your next crystallography 
department or CAD-office?

-- 
Bye,  Marc Saric

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