pymol-users — Collaborative support and tips for PyMOL users

[PyMOL] Version 0.78 Release w/ RPMs

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

PyMOL Version 0.78 is now available for download from
http://pymol.sf.net

I'm pleased to announce my first release of PyMOL Linux RPMs, which were
made possible with assistance from Stephen Adler (Brookhaven NL).  These
should greatly simplify the installation process for RedHat 7.x users.
Thanks a bunch Stephen!!!

Along with bufixes, version 0.78 contains a prelimarily release of
PyMOL's new "Sculpting" capability.  With "Auto-Sculpting" on in Editing
Mode, you can simply CTRL-click-and-drag atoms to where you want them to
go, and then PyMOL will do its best to make sure that bonds, angles,
planarity, chirality, and van der Waals radii are maintained.  It's not
particularly realistic, but it sure looks cool -- as if your molecules
were made of "gummy" worms candy... =20

- Warren

Re: [PyMOL] Another stupid user question...

[Stephen A. <ad...@bn...>]

Warren,

in launch_pymol.py there is the following code


   sys.path.append(os.environ['PYMOL_PATH']+'/modules')

It looks to me like your adding $PYMOL_PATH/modules to
the path of modules searched by python. Right now,
there is no modules directory in the final installation.
Should I create one and put all the .so files in there?

Right now I define

    $PYMOL_PATH=/usr/lib/python2.1/site-packages/pymol

Where pymol has a bunch of .so files and some directories
(no modules directory) with various __init__.py files.
But it still starts up fine. Its like the sys.path.append
does not seem to do much.

What do you suggest?

Steve.

Re: [PyMOL] Another stupid user question...

[Stephen A. <ad...@bn...>]

Warren,

This is what I'm going to do. I've kludge up the installation
on my PC to run pymol. I've been able to download a .pdb file
from the PDB and actually display a protien structure. (Really
cool!) I'm going to try and rationalize my kludges so that anyone
who installs the rpm's just has to type 'pymol' under linux and
bingo, their off and running. There are a couple of tricks I
can apply to the installation to make it integrate better with
redhat linux.

Also, I'm going to shy away from pulling the code out of CVS.
Since I'm building RPM's, this does suggest some kind of stable
release, even tho it's a moving target. So that fact that you
went through the trouble of putting a .tar.gz file for .73 must
mean that .73 has some significance of some sort. Maybe in the
near future I can work on some kind of nightly build option or
something which does pull the code right out of CVS.

Cheers Steve.

DeLano, Warren wrote:

> Stephen,
> 
> Glad to see you're interested!  O'Reilly was a blast...
> 
> Right now PyMOL is more of a continuous process rather than a discrete
> set of release stages.  Try building off of the CVS source.
> 
> In theory, the 'ext' distribution contains all the dependencies you need
> (including Pmw and Numeric), but most of those are now getting to be
> quite out of date.  Yu're best off assembling all of the necessary
> dependencies from their respective web sites.  Please use Python 2.1 or
> greater.
> 
> PyMOL isn't really a well behaved Python module, right now.  That will
> change soon.  The problem is that PyMOL needs a bit more coddling than a
> normal Python module in order to run.  You can stick all of PyMOL under
> /usr/lib/python2.1/site-packages/pymol, but you'll need to adjust
> PYMOLPATH accordingly in the "pymol.com" script, and you'll want to copy
> or link that script to someplace useful (such as /usr/local/bin).
> 
> 
>>Ok, after googling the term Numeric I've come across
>>Numpy which looks to be Numeric. From what I can tell, it
>>looks like Numeric (or Numpy) is not distributed with redhat
>>and thus a seperate installation is necessary. Thus the
>>numeric rpms on the pymol site. If this were to be done
>>right, the numeric rpms should be located in the numpy
>>site, rather than the pymol site. I'm wondering if this
>>goes for Pwm as well....
>>
> 
> - Warren
> 

RE: [PyMOL] Another stupid user question...

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

Stephen,

Glad to see you're interested!  O'Reilly was a blast...

Right now PyMOL is more of a continuous process rather than a discrete
set of release stages.  Try building off of the CVS source.

In theory, the 'ext' distribution contains all the dependencies you need
(including Pmw and Numeric), but most of those are now getting to be
quite out of date.  Yu're best off assembling all of the necessary
dependencies from their respective web sites.  Please use Python 2.1 or
greater.

PyMOL isn't really a well behaved Python module, right now.  That will
change soon.  The problem is that PyMOL needs a bit more coddling than a
normal Python module in order to run.  You can stick all of PyMOL under
/usr/lib/python2.1/site-packages/pymol, but you'll need to adjust
PYMOLPATH accordingly in the "pymol.com" script, and you'll want to copy
or link that script to someplace useful (such as /usr/local/bin).

> Ok, after googling the term Numeric I've come across
> Numpy which looks to be Numeric. From what I can tell, it
> looks like Numeric (or Numpy) is not distributed with redhat
> and thus a seperate installation is necessary. Thus the
> numeric rpms on the pymol site. If this were to be done
> right, the numeric rpms should be located in the numpy
> site, rather than the pymol site. I'm wondering if this
> goes for Pwm as well....

- Warren

[PyMOL] YASUQ

[Stephen A. <ad...@bn...>]

Sorry about flooding the e-mail list with the following questions
comments....

My attempt at rebuilding a version 0.73 of pymol failed. It did
so becuase of the following detail. In the build area, there is
a module directory which contains the following....

[root@newadler modules]# pwd
/usr/src/redhat/BUILD/pymol/modules
[root@newadler modules]# ls -Fa
./        ExtensionClass.so*  _openglmodule.so*      pmg_wx/
../       _glumodule.so*      _opengl_nummodule.so*  pymol/
chempy/   _glu_nummodule.so*  openglutil_num.so*     sglite.so*
_cmd.so*  _glutmodule.so*     openglutil.so*
CVS/      launch_pymol.py     pmg_tk/


When doing the rpm build, the rpm package manager takes care of
moving all the directories into /usr/lib/python2.1/site-packages/
But the files in the 'modules' directory, are left orphand.
The question is where to put them, since putting them in the
directory /usr/lib/python2.1/site-packages/ seems a bit wonko.
For now, I'm going to put them in /usr/lib/python2.1/site-packages/pymol
for a lack of a better place to put them. Maybe it will become
clear where they should go after screwing around a bit with
this rpm build.

Cheers. Steve.

[PyMOL] Another stupid user question...

[Stephen A. <ad...@bn...>]

Ok, after googling the term Numeric I've come across
Numpy which looks to be Numeric. From what I can tell, it
looks like Numeric (or Numpy) is not distributed with redhat
and thus a seperate installation is necessary. Thus the
numeric rpms on the pymol site. If this were to be done
right, the numeric rpms should be located in the numpy
site, rather than the pymol site. I'm wondering if this
goes for Pwm as well....

comments?

Steve.

[PyMOL] New to pymol

[Stephen A. <ad...@bn...>]

Hi,

I want to build updated RPM's for pymol. I see that version 0.73
is on sourceforge. I also see that there are version 0.68 rpm
packages for redhat. I also see that there is a version 0.77
of pymol binaries for windows.

so, in order to get the most out of this rpm hack, what should
I do? Should I try and do a CVS checkout of .77 and build that?
Or should I just stick with .73? also, what about Pwm and Numeric.
Are the versions in the current RPM's sufficient?

Thanks.

Steve.

RE: [PyMOL] Installing from source on a linux box

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

Michael,

   Try checking out a new copy of the source code from the current CVS
repository -- the Makefiles have been simplified somewhat, so
compilation under Linux may go easier.  You should only need to change
the Python version in one place : )

Read "INSTALL.linux-rh7x"

Cheers,
Warren


--
mailto:wa...@su...
Warren L. DeLano, Ph.D.
Informatics Manager
Sunesis Pharmaceuticals, Inc.
341 Oyster Point Blvd.
S. San Francisco, CA 94080
(650)-266-3606  FAX:(650)-266-3501



> -----Original Message-----
> From: Michael George Lerner [mailto:ml...@um...]
> Sent: Monday, January 28, 2002 1:44 PM
> To: pym...@so...
> Subject: [PyMOL] Installing from source on a linux box
>=20
>=20
>=20
> Hi,
>=20
> I have PyMol up and running on my windows partition .. the=20
> installation
> was super easy.  Now, I want to set it up on my Linux=20
> partition.  I have
> Mandrake 8.1 installed, which means that my default python=20
> version is 2.1.
> It also means that many things (Numeric, zlib, etc..) are=20
> pre-installed
> for me.
>=20
> So, I downloaded the PyMol sources and tried to install it.  In the
> external packages bit, it looked like the only thing I need=20
> is glut.  So,
> I changed the setenv BASE line in build.com to point to the=20
> right place
> (/home/mglerner/src/pymol/ext in my case) and changed the setenv
> PYMOL_TARGETS line to say "glut-linux" and did "./build.com".  I also
> tried "./build.com glut-linux" for variety .. both seemed to work.
>=20
> Then I went up a directory into the main pymol directory.  I=20
> then moved
> Rules.linux to Rules.make and edited it.  There were many instances of
> -lpython1.5 .. I changed all of them to -lpython2.1.  It was=20
> still having
> some trouble finding libpython2.1, so I added=20
> -L/usr/lib/python2.1/config
> to the LIB_DIRS line.  After typing make, things get pretty=20
> far, but it
> doesn't get far enough.  I wasn't sure how many of the error=20
> messages to
> include, but I've tacked on the last screen or so of output=20
> at the end of
> this message.
>=20
> There were some things that made me think that various parts=20
> of this build
> process were really looking for python sources in the ext=20
> directory, so I
> placed a copy of the python 2.1 sources there just in case.  It didn't
> seem to help.
>=20
> Sorry if this is a dumb question,
>=20
> -michael
>=20
> ------ begin output from make ------
>=20
> make[2]: Entering directory `/home/mglerner/src/pymol/contrib/modules'
> rm -f *.o *~
> rm -f *.a tags TAGS config.c Makefile.pre python sedscript
> rm -f *.so *.sl so_locations
> VERSION=3D`../../ext/bin/python -c "import sys; print=20
> sys.version[:3]"`; \
> installdir=3D`../../ext/bin/python -c "import sys; print sys.prefix"`; =
\
> exec_installdir=3D`../../ext/bin/python -c "import sys; print
> sys.exec_prefix"`; \make -f ./Makefile.pre.in VPATH=3D. srcdir=3D. \
>         VERSION=3D$VERSION \
>         installdir=3D$installdir \
>         exec_installdir=3D$exec_installdir \
>         Makefile
> /bin/sh: ../../ext/bin/python: No such file or directory
> /bin/sh: ../../ext/bin/python: No such file or directory
> /bin/sh: ../../ext/bin/python: No such file or directory
> make[3]: Entering directory `/home/mglerner/src/pymol/contrib/modules'
> make[3]: *** No rule to make target=20
> `/lib/python/config/Makefile', needed
> by `sedscript'.  Stop.
> make[3]: Leaving directory `/home/mglerner/src/pymol/contrib/modules'
> make[2]: *** [boot] Error 2
> make[2]: Leaving directory `/home/mglerner/src/pymol/contrib/modules'
> make[1]: *** [make-modules] Error 2
> make[1]: Leaving directory `/home/mglerner/src/pymol/contrib'
> make: *** [.contrib] Error 2
>=20
> ------ end output from make ------
>=20
> --
> This isn't a democracy;|                        _  |Michael Lerner
>  it's a cheer-ocracy.  | ASCII ribbon campaign ( ) |   Michigan
> -Torrence,  Bring It On|  - against HTML email  X  |  Biophysics
>                        |                       / \ | mlerner@umich
>=20
>=20
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20

Re: [PyMOL] RE: Resolution increase

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

A good tip when rendering unusual aspect ratio images
is to set the viewport with the same aspect ratio as
the final rendered image to better use the image area. 

It also helps to avoid unexpected crops due to the change in the
aspect ratio.

Cheers,
	Zac

On Mon, 4 Feb 2002, DeLano, Warren wrote:

> Jason,
> 
>    The resolution field in images is not uniformly supported or
> understood, so the safest policy is to ignore it and stick with 72 dpi
> for your images. As far as I can tell from the man page, PNG format
> doesn't even support a DPI field.  Just make sure that your image
> contain enough pixels to look good when reduced.  The page layout staff
> at the journal are usually professionals and will take care of adjusting
> the final image size and resolution provided that you give them enough
> pixels to start with.
> 
>    For example, if you are submitting something which will end up being
> 4x3 inches when published, then you want to give them a 4x300=1200 by
> 3x300=900 pixel image.  Thus, use the command "ray 1200,900" and then
> save the file.  For submission, you'll probably need to use Photoshop or
> the ImageMagick "convert" command to convert this file into something
> they can handle.
> 
> To cite PyMOL, either use the URL:
>    
>        Warren L. DeLano "The PyMOL Molecular Graphics System."
>        DeLano Scientific, San Carlos, CA, USA. http://www.pymol.org
> 
> or cite the manual as a book
> 
>        Warren L. DeLano (2002) "The PyMOL User's Manual" 
>        DeLano Scientific, San Carlos, CA, USA.
> 
> Cheers,
> Warren
> 
> --
> mailto:wa...@su...
> Warren L. DeLano, Ph.D.
> Informatics Manager
> Sunesis Pharmaceuticals, Inc.
> 341 Oyster Point Blvd.
> S. San Francisco, CA 94080
> (650)-266-3606  FAX:(650)-266-3501
> 
> 
> 
> > -----Original Message-----
> > From: Jason Yano [mailto:jk...@br...]
> > Sent: Monday, February 04, 2002 10:33 AM
> > To: DeLano, Warren
> > Subject: Resolution increase
> > 
> > 
> > Hey Warren,
> > 	I want use one of the images that I made in PyMOL for 
> > publication,
> > but I would like to increase the output resolution to 300 
> > dpi, right now
> > the program spits out images at 72 dpi. I have tried to do this
> > artificially in photoshop, but the image doesn't look any 
> > better. Whats
> > the easest way to increase the resolution?
> > 
> > By the way how would you like me to reference the program in the
> > publication?
> > 
> > 
> > Thanks,
> > 
> > 
> > Jason
> > 
> > 
> > 
> 
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
> 

--
 Ezequiel Panepucci - Laboratory of Prof. Axel Brunger
 HHMI - Stanford University
 Phone: 650-926-5127
 Cell:  650-714-9414

[PyMOL] RE: Resolution increase

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

Jason,

   The resolution field in images is not uniformly supported or
understood, so the safest policy is to ignore it and stick with 72 dpi
for your images. As far as I can tell from the man page, PNG format
doesn't even support a DPI field.  Just make sure that your image
contain enough pixels to look good when reduced.  The page layout staff
at the journal are usually professionals and will take care of adjusting
the final image size and resolution provided that you give them enough
pixels to start with.

   For example, if you are submitting something which will end up being
4x3 inches when published, then you want to give them a 4x300=3D1200 by
3x300=3D900 pixel image.  Thus, use the command "ray 1200,900" and then
save the file.  For submission, you'll probably need to use Photoshop or
the ImageMagick "convert" command to convert this file into something
they can handle.

To cite PyMOL, either use the URL:
  =20
       Warren L. DeLano "The PyMOL Molecular Graphics System."
       DeLano Scientific, San Carlos, CA, USA. http://www.pymol.org

or cite the manual as a book

       Warren L. DeLano (2002) "The PyMOL User's Manual"=20
       DeLano Scientific, San Carlos, CA, USA.

Cheers,
Warren

--
mailto:wa...@su...
Warren L. DeLano, Ph.D.
Informatics Manager
Sunesis Pharmaceuticals, Inc.
341 Oyster Point Blvd.
S. San Francisco, CA 94080
(650)-266-3606  FAX:(650)-266-3501



> -----Original Message-----
> From: Jason Yano [mailto:jk...@br...]
> Sent: Monday, February 04, 2002 10:33 AM
> To: DeLano, Warren
> Subject: Resolution increase
>=20
>=20
> Hey Warren,
> 	I want use one of the images that I made in PyMOL for=20
> publication,
> but I would like to increase the output resolution to 300=20
> dpi, right now
> the program spits out images at 72 dpi. I have tried to do this
> artificially in photoshop, but the image doesn't look any=20
> better. Whats
> the easest way to increase the resolution?
>=20
> By the way how would you like me to reference the program in the
> publication?
>=20
>=20
> Thanks,
>=20
>=20
> Jason
>=20
>=20
>=20

RE: [PyMOL] map rendering

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

Jose,=20

   I'm not sure what you mean by weak (invisible, ??), but try adjusting
the setting "mesh_radius"

set mesh_radius=3D0.025
ray

set mesh_radius=3D0.05
ray

set mesh_raidus=3D0.1
ray

etc.

also, try enabling antialiasing

set antialias=3D1

Cheers,
Warren



--
mailto:wa...@su...
Warren L. DeLano, Ph.D.
Informatics Manager
Sunesis Pharmaceuticals, Inc.
341 Oyster Point Blvd.
S. San Francisco, CA 94080
(650)-266-3606  FAX:(650)-266-3501



> -----Original Message-----
> From: Jose Casasnovas [mailto:jos...@cb...]
> Sent: Monday, January 28, 2002 7:18 AM
> To: pym...@li...
> Subject: [PyMOL] map rendering
>=20
>=20
> I am trying to render a figure with several ribbons and a map.  After=20
> rendering either in Pymol or Povray ribbons came fine, but=20
> map is very=20
> weak.  Any help on settings to get a map render properly.
>=20
> Thanks,
>=20
> Jose
> ________________________________________
> Jose M Casasnovas Ph.D.
> Karolinska Institutet
> Department of Biosciences
> NOVUM, Center for Biotechnology
> Halsov=E4gen 7
> S-141 57 HUDDINGE
> Sweden
> Ph.  46 8 6089133
> Fax. 46 8 7745538
> email: jos...@cb...
>=20
>=20
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20

[PyMOL] Installing Glut and Pymol on Tru64 Unix

[Culhane, A. <a.c...@uc...>]

Dear Pymol
I am having lots of difficulty installing Pymol (and its dependencies) on
Tru64 5.1.  I already had python2.1, Numpy, Tcl, Tk etc installed. Hence I
choose not to re-install using the extensions.  I downloaded libpng, so all
I had to do was sort Glut. I have tried downloading this again from the
OpenGL web site, but it will fall over each time.  Hence Pymol falls over. I
would be very grateful if anyone can help or has experience of installing
these on Tru64 v5.1 (OSF1/DEC).
Thanks a million

Aedin Culhane
-------------------------------
Bioinformatics Group
Biochemistry Department
Lee Maltings,
University College Cork
Cork, Ireland

Re: [PyMOL] Installing from source on a linux box

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

Michael,

   Python dependencies are better handled in the current source archive
(available from the CVS repository).  See the "CVS Installation" section
of the web page.  You should be able to quickly adapt Rules.linux-rh7x
file to create a "Rules.make" for Mandrake.  

Cheers,
Warren

On Mon, 28 Jan 2002, Michael George Lerner wrote:

> I have PyMol up and running on my windows partition .. the
> installation was super easy.  Now, I want to set it up on my Linux
> partition.  I have Mandrake 8.1 installed, which means that my default
> python version is 2.1. It also means that many things (Numeric, zlib,
> etc..) are pre-installed for me.
> 
> So, I downloaded the PyMol sources and tried to install it.  In the
> external packages bit, it looked like the only thing I need is glut.  So,
> I changed the setenv BASE line in build.com to point to the right place
> (/home/mglerner/src/pymol/ext in my case) and changed the setenv
> PYMOL_TARGETS line to say "glut-linux" and did "./build.com".  I also
> tried "./build.com glut-linux" for variety .. both seemed to work.
> 
> Then I went up a directory into the main pymol directory.  I then moved
> Rules.linux to Rules.make and edited it.  There were many instances of
> -lpython1.5 .. I changed all of them to -lpython2.1.  It was still having
> some trouble finding libpython2.1, so I added -L/usr/lib/python2.1/config
> to the LIB_DIRS line.  After typing make, things get pretty far, but it
> doesn't get far enough.  I wasn't sure how many of the error messages to
> include, but I've tacked on the last screen or so of output at the end of
> this message.
> 
> There were some things that made me think that various parts of this build
> process were really looking for python sources in the ext directory, so I
> placed a copy of the python 2.1 sources there just in case.  It didn't
> seem to help.
> 
> Sorry if this is a dumb question,
> 
> -michael
> 
> ------ begin output from make ------
> 
> make[2]: Entering directory `/home/mglerner/src/pymol/contrib/modules'
> rm -f *.o *~
> rm -f *.a tags TAGS config.c Makefile.pre python sedscript
> rm -f *.so *.sl so_locations
> VERSION=`../../ext/bin/python -c "import sys; print sys.version[:3]"`; \
> installdir=`../../ext/bin/python -c "import sys; print sys.prefix"`; \
> exec_installdir=`../../ext/bin/python -c "import sys; print
> sys.exec_prefix"`; \make -f ./Makefile.pre.in VPATH=. srcdir=. \
>         VERSION=$VERSION \
>         installdir=$installdir \
>         exec_installdir=$exec_installdir \
>         Makefile
> /bin/sh: ../../ext/bin/python: No such file or directory
> /bin/sh: ../../ext/bin/python: No such file or directory
> /bin/sh: ../../ext/bin/python: No such file or directory
> make[3]: Entering directory `/home/mglerner/src/pymol/contrib/modules'
> make[3]: *** No rule to make target `/lib/python/config/Makefile', needed
> by `sedscript'.  Stop.
> make[3]: Leaving directory `/home/mglerner/src/pymol/contrib/modules'
> make[2]: *** [boot] Error 2
> make[2]: Leaving directory `/home/mglerner/src/pymol/contrib/modules'
> make[1]: *** [make-modules] Error 2
> make[1]: Leaving directory `/home/mglerner/src/pymol/contrib'
> make: *** [.contrib] Error 2
> 
> ------ end output from make ------
> 
> --
> This isn't a democracy;|                        _  |Michael Lerner
>  it's a cheer-ocracy.  | ASCII ribbon campaign ( ) |   Michigan
> -Torrence,  Bring It On|  - against HTML email  X  |  Biophysics
>                        |                       / \ | mlerner@umich
> 
> 
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
> 

[PyMOL] Resolution

[Jason Y. <jk...@br...>]

Hi All,
	I just wanted to know if there is an easy way to change the
resolution of the images from 72 pixels/inch to something like 150
pixels/inch either by a pymol command or a python one.



Jason

[PyMOL] Installing from source on a linux box

[Michael G. L. <ml...@um...>]

Hi,

I have PyMol up and running on my windows partition .. the installation
was super easy.  Now, I want to set it up on my Linux partition.  I have
Mandrake 8.1 installed, which means that my default python version is 2.1.
It also means that many things (Numeric, zlib, etc..) are pre-installed
for me.

So, I downloaded the PyMol sources and tried to install it.  In the
external packages bit, it looked like the only thing I need is glut.  So,
I changed the setenv BASE line in build.com to point to the right place
(/home/mglerner/src/pymol/ext in my case) and changed the setenv
PYMOL_TARGETS line to say "glut-linux" and did "./build.com".  I also
tried "./build.com glut-linux" for variety .. both seemed to work.

Then I went up a directory into the main pymol directory.  I then moved
Rules.linux to Rules.make and edited it.  There were many instances of
-lpython1.5 .. I changed all of them to -lpython2.1.  It was still having
some trouble finding libpython2.1, so I added -L/usr/lib/python2.1/config
to the LIB_DIRS line.  After typing make, things get pretty far, but it
doesn't get far enough.  I wasn't sure how many of the error messages to
include, but I've tacked on the last screen or so of output at the end of
this message.

There were some things that made me think that various parts of this build
process were really looking for python sources in the ext directory, so I
placed a copy of the python 2.1 sources there just in case.  It didn't
seem to help.

Sorry if this is a dumb question,

-michael

------ begin output from make ------

make[2]: Entering directory `/home/mglerner/src/pymol/contrib/modules'
rm -f *.o *~
rm -f *.a tags TAGS config.c Makefile.pre python sedscript
rm -f *.so *.sl so_locations
VERSION=`../../ext/bin/python -c "import sys; print sys.version[:3]"`; \
installdir=`../../ext/bin/python -c "import sys; print sys.prefix"`; \
exec_installdir=`../../ext/bin/python -c "import sys; print
sys.exec_prefix"`; \make -f ./Makefile.pre.in VPATH=. srcdir=. \
        VERSION=$VERSION \
        installdir=$installdir \
        exec_installdir=$exec_installdir \
        Makefile
/bin/sh: ../../ext/bin/python: No such file or directory
/bin/sh: ../../ext/bin/python: No such file or directory
/bin/sh: ../../ext/bin/python: No such file or directory
make[3]: Entering directory `/home/mglerner/src/pymol/contrib/modules'
make[3]: *** No rule to make target `/lib/python/config/Makefile', needed
by `sedscript'.  Stop.
make[3]: Leaving directory `/home/mglerner/src/pymol/contrib/modules'
make[2]: *** [boot] Error 2
make[2]: Leaving directory `/home/mglerner/src/pymol/contrib/modules'
make[1]: *** [make-modules] Error 2
make[1]: Leaving directory `/home/mglerner/src/pymol/contrib'
make: *** [.contrib] Error 2

------ end output from make ------

--
This isn't a democracy;|                        _  |Michael Lerner
 it's a cheer-ocracy.  | ASCII ribbon campaign ( ) |   Michigan
-Torrence,  Bring It On|  - against HTML email  X  |  Biophysics
                       |                       / \ | mlerner@umich

[PyMOL] map rendering

[Jose C. <jos...@cb...>]

I am trying to render a figure with several ribbons and a map.  After=20
rendering either in Pymol or Povray ribbons came fine, but map is very=20
weak.  Any help on settings to get a map render properly.

Thanks,

Jose
________________________________________
Jose M Casasnovas Ph.D.
Karolinska Institutet
Department of Biosciences
NOVUM, Center for Biotechnology
Halsov=E4gen 7
S-141 57 HUDDINGE
Sweden
Ph.  46 8 6089133
Fax. 46 8 7745538
email: jos...@cb...

Re: [PyMOL] png output

[Ben C. <ac...@em...>]

Jason Yano <jk...@br...> writes:

> Hi All,
> 	I just wanted to know if there was a way to include resolution
> and pixels per inch ie 150 or 300 rather than the default of 72
> pixles/inch in the .pml scritp ie
> 

Just provide `ray' with an optional width and height.

Ben

[PyMOL] png output

[Jason Y. <jk...@br...>]

Hi All,
	I just wanted to know if there was a way to include resolution
and pixels per inch ie 150 or 300 rather than the default of 72
pixles/inch in the .pml scritp ie


[1280x1024, 150pixels/inch]
ray 

png image_name.png


Jason

RE: [PyMOL] Electrostatic potential surface?

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

> From: Eric C. Peterson [mailto:ec...@ua...]

> I am putting some figures together for an upcoming manuscript=20
> and am trying
> to figure out a few details.  Some of the things I want to do may be
> possible, some not.  Here are the questions I have:
>=20
> 1. How do you display electrostatic potential on surface displays?

Not yet directly possible, but that will change soon. The nearest thing
you can achieve is to color by charge. =20

> 2. Can the colors of individual side chains be changed=20
> without affecting the
> surface?

If you want a uniform surface color,

set surface_color, <color-name>, <object-name>

For anything complicated, just create a second copy of the object.  Show
the surface in one and sticks in the other.  Then color independently.
=20
> 3. I have tried to assign SS manually, but the cartoon skips=20
> at certain
> sections (ie alpha helices).  What can I do to fix this?

Hmm.  This should happen unless those atoms are HETATMS.  To be sure:

show cartoon
alter all,type=3D'ATOM'
rebuild

I'm a little suspicious that there might be some lingering bugs in the
ribbon code.  If you have an example PDB file and script which
reproduces the problem, please send them to me.

[PyMOL] Fe-S clusters

[Jason Y. <jk...@br...>]

Hi All,
	I'm looking for a way to display a "ball and Stick" representation
of an Fe-S cluser, with a cartoon for the protein back bone. I can get the
spheres for the Fe-S cluster, but can't connect them. Here's the script so
far.

#Pymol script for Adx 1AYF
load C:\Documents and Settings\jkyano\My Documents\P450 pdb\1AYF_A.pdb,
ADX
bg white
### cut below here and paste into script ###
set_view (\
    -0.057087217,    0.618627429,   -0.783607304,\
     0.026588190,    0.785550535,    0.618226647,\
     0.998013437,    0.014458310,   -0.061293427,\
    -1.276597023,    0.201005965, -106.195739746,\
   -12.916477203,  -11.231512070,   -8.815745354,\
    74.405113220,  137.986404419,    0.000000000 )
### cut above here and paste into script ###
util.ss
color slate, ADX
hide everything, ADX
show cartoon, ADX
select fes =(resid 109)
show sphere, fes
color yellow, fes
alter (name s1), vdw=.75
alter (name s2), vdw=.75
rebuild
sel elem fe
color marine, fe

Thanks for the help,



Jason

[PyMOL] PyMOL-x86

[proclus r. <pr...@in...>]

Announcing PyMOL for GNU-Darwin on Intel architecture (x86)!

terminal shot
http://gnu-darwin.sourceforge.net/gdc/pymol.x86.png
sample graphic
http://gnu-darwin.sourceforge.net/gdc/pymol2.x86.png
installation script (for Intel only!)
http://gnu-darwin.sourceforge.net/gdc/pymol-x86

The installation script provides ncurses-5.2.x86.tgz python-2.2_1.x86.tgz
tcl-8.3.4_3.x86.tgz
tk-8.3.4_1.x86.tgz py22-numeric-20.2.1.x86.tgz py22-tkinter-2.2.x86.tgz and
pymol-0_73_1.x86.tgz.  
For more information about the x86 platform, see the ports and
packages page for GNU-Darwin-x86.

http://gnu-darwin.sourceforge.net/x86/

PyMOL now builds automatically with the ports system, and required source code
is in CVS.

http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/gnu-darwin/4Darwin-x86/ports/science/pymol/

BTW. This japanese Balsa now appears to be working pretty well ;-}.  Heave Ho!

Regards,
Michael L. Love
MacCHESS
Cornell University
http://www.gnu-darwin.org/


-- 
Visit proclus realm! http://proclus.tripod.com/
-----BEGIN GEEK CODE BLOCK-----
Version: 3.1
GMU/S d+@ s: a+ C++++ UBOULI++++$ P+ L+++(++++) E--- W++ N- !o K- w--- !O
M++@ V-- PS+++ PE Y+ PGP-- t+++(+) 5+++ X+ R tv-(--)@ b !DI D- G e++++
h--- r+++ y++++
------END GEEK CODE BLOCK------

[PyMOL] Electrostatic potential surface?

[Eric C. P. <ec...@ua...>]

First of all, I am quite impressed with this program, free or not.  I also
saw Dr. Wells speak at the Keystone conference in Breckenridge in January
where he presented some graphics using Rigimol.  Very nice.

I am putting some figures together for an upcoming manuscript and am trying
to figure out a few details.  Some of the things I want to do may be
possible, some not.  Here are the questions I have:

1. How do you display electrostatic potential on surface displays?

2. Can the colors of individual side chains be changed without affecting the
surface?

3. I have tried to assign SS manually, but the cartoon skips at certain
sections (ie alpha helices).  What can I do to fix this?

Any help is appreciated.  Thanks.


Eric Peterson
Ph.D. Candidate
Cell and Molecular Biology
19 West Avenue Annex
University of Arkansas
Fayetteville, AR 72701
(501) 575-3021
Fax (501) 575-8434

RE: [PyMOL] movie frame alterations

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

Don't you hate it when users outsmart the programmer?

This is a tough one.  The only solution I can think of is not memory
efficient, but it should work:

Load each frame of the movie into a separate segment or chain.  This
should allow you to independently address each frame...

# assume that the segment is '' (empty) in the PDB files...

load frame1.pdb,mov
alter (segi ''),segi=3D'1'
load frame2.pdb,mov
alter (segi ''),segi=3D'2'

etc.=20

You can use Python to make a loop by switching to the Python API as
follows:

from pymol import cmd
for a in range(1,30):
   cmd.load("frame%d.pdb"%a,"mov")
   cmd.alter("(segi '')","segi=3D'%d'"%a)

Then you should be able to say:

color red,/mov/1//101/ca
color red,/mov/2//101/ca
color red,/mov/3//101/ca

Good luck,

Warren


--
mailto:wa...@su...
Warren L. DeLano, Ph.D.
Informatics Manager
Sunesis Pharmaceuticals, Inc.
341 Oyster Point Blvd.
S. San Francisco, CA 94080
(650)-266-3606  FAX:(650)-266-3501



> -----Original Message-----
> From: Nat [mailto:nat...@ya...]
> Sent: Wednesday, January 23, 2002 7:39 PM
> To: pym...@li...
> Subject: [PyMOL] movie frame alterations
>=20
>=20
>=20
> Is it possible to make changes to the way individual frames=20
> are rendered?
> Specifically, I'm writing a Python script (translated=20
> literally from C,
> but I'm too tired to learn the Python API right now) to evaluate bond
> "quality" and highlight the distorted regions in a frame of a protein
> morph.  However, since the distortions tend to come in the middle of a
> morph, I want to examine each frame alone and apply highlighting only
> where applicable.
>=20
> Right now, treating individual frames as part of an object (i.e. for a
> movie) means that calls like 'color red, 101/ca' are applied to every
> state.  Is there some way to only run that command on one state?  In
> simple terms, I'm trying for a movie that changes color=20
> during its course
> to indicate bond quality.  It's much easier to do this if I=20
> can use movie
> objects, especially since it would be nice to be able to run this
> interactively.  Otherwise, I'm going to just create a very=20
> long pml file
> with all the commands.
>=20
> thanks,
> Nat
>=20
>=20
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20

[PyMOL] movie frame alterations

[Nat <nat...@ya...>]

Is it possible to make changes to the way individual frames are rendered?
Specifically, I'm writing a Python script (translated literally from C,
but I'm too tired to learn the Python API right now) to evaluate bond
"quality" and highlight the distorted regions in a frame of a protein
morph.  However, since the distortions tend to come in the middle of a
morph, I want to examine each frame alone and apply highlighting only
where applicable.

Right now, treating individual frames as part of an object (i.e. for a
movie) means that calls like 'color red, 101/ca' are applied to every
state.  Is there some way to only run that command on one state?  In
simple terms, I'm trying for a movie that changes color during its course
to indicate bond quality.  It's much easier to do this if I can use movie
objects, especially since it would be nice to be able to run this
interactively.  Otherwise, I'm going to just create a very long pml file
with all the commands.

thanks,
Nat

RE: [PyMOL] stereo pictures

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

> From: Ricardo Aparicio [mailto:apa...@if...]

> 1) what is the effect of command "stereo" in PyMol? Does it makes a
> confuse screen (like in O when one is not using stereo
> glasses)? If so,
> there is no sense in capture the image from the screen with
> png command.

No, it just fails altogether.=20

> 2) how to make stereo figures using PyMol. If necessary we have SGIs
> with stereo here.

Easy -- you do it the old fashion way:

png left.png
turn y,5
png right.png

And then use something like Photoshop or PowerPoint to combine the two
images into a single stereo-pair. =20

The above recipe gives you cross-eye.  You'll want to play with the
angle a bit and or negate it in order to do wall-eye stereo.

- Warren