PyMOL Wiki - User contributions [en]

CCTBX

2006-10-27T23:36:48Z

Rogerdodd:

=Computational Crystallography Toolbox=
[http://cctbx.sourceforge.net cctbx]

==Using With PyMol==

===On a Mac===
There is a page on the cctbx with special instructions for using it on the Mac [http://cci.lbl.gov/cctbx_build/mac_os_x_notes.html cctbx On Mac]. Note that you need to use the "Framework" build of PyMOL [http://delsci.com/frameworkpymol/ FrameWorkPyMol].

===Windows XP (Roger Dodd)===
1. Download and install python (to the default location - C:\Python24)

[http://www.python.org/ftp/python/2.4.1/python-2.4.1.msi Python-2.4.1]

1a. If you want to use the draw_symops.py or draw_symops_cctbx.py
scripts you also need to install numarray after installing python

[http://prdownloads.sourceforge.net/numpy/numarray-1.3.3.win32-py2.4.exe?download Numarray-1.3.3]

2. Download cctbx *without* python included and unpack into
C:\cctbx_build and C:\cctbx_sources (i.e. execute the file in C:\)

[http://cci.lbl.gov/cctbx_build/ cctbx]

3. Download pymol built against python 2.4 (but not including its own
python) and install in the default location

[http://delsci.com/rel/098/pymol-0_98rc5-bin-win32-py24.zip pymol-0_98rc5]

(Newer versions of PyMOL linked against an external python are available from Delano Scientific on request for holders of a valid subscription.)

4. Create 2 files (use notepad or wordpad or any other text editor) and
save in the C:\Program Files\Delano Scientific\PyMOL directory:

a) pymol.cmd

@cctbx.python -x "%~f0" %* & exit /b
import cctbx
import pymol

b) run.cmd

CALL C:\cctbx_build\setpaths_all.bat
CALL "C:\Program Files\Delano Scientific\PyMOL\pymol.cmd"

5. It's important to have python in your path variable (which you can access by going to control panel|system|advanced|environment variables), just add C:\python24 to the end of the path variable, separated by a semi-colon.

===Linux (Robert Campbell)===
When you run the setpaths.sh script, it adds the cctbx_build/bin directory to the *front* of your $PATH. In that directory is a shell script called "python" that sets the environment necessary to import cctbx. So, to get cctbx to work, you have to call python without prefixing a directory path. If you were like me and had:
/usr/bin/python $PYMOL_PATH/modules/launch_pymol.py $*
in your pymol.com file, then it would not run that cctbx_build/bin/python script. So you need to either change the above line to:
python $PYMOL_PATH/modules/launch_pymol.py $*
(assuming you've already run the setpaths.sh script) or you need to copy the cctbx_build/bin/python contents (without the actual "python" command) into your pymol.com file or some other file that you source before pymol.com.

Within pymol, type the command:
print sys.path
and you should now see the cctbx directories show up.

[[Category:PyMol_Integration|cctbx]]

CCTBX

2006-10-27T23:35:37Z

Rogerdodd:

=Computational Crystallography Toolbox=
[http://cctbx.sourceforge.net cctbx]

==Using With PyMol==

===On a Mac===
There is a page on the cctbx with special instructions for using it on the Mac [http://cci.lbl.gov/cctbx_build/mac_os_x_notes.html cctbx On Mac]. Note that you need to use the "Framework" build of PyMOL [http://delsci.com/frameworkpymol/ FrameWorkPyMol].

===Windows XP (Roger Dodd)===
1. Download and install python (to the default location - C:\Python24)

[http://www.python.org/ftp/python/2.4.1/python-2.4.1.msi Python-2.4.1]

1a. If you want to use the draw_symops.py or draw_symops_cctbx.py
scripts you also need to install numarray after installing python

[http://prdownloads.sourceforge.net/numpy/numarray-1.3.3.win32-py2.4.exe?download Numarray-1.3.3]

2. Download cctbx *without* python included and unpack into
C:\cctbx_build and C:\cctbx_sources (i.e. execute the file in C:\)

[http://cci.lbl.gov/cctbx_build/ cctbx]

3. Download pymol built against python 2.4 (but not including its own
python) and install in the default location

[http://delsci.com/rel/098/pymol-0_98rc5-bin-win32-py24.zip pymol-0_98rc5]

(Newer versions of PyMOL linked against an external python are available from Delano Scientific on request for holders of a valid description.)

4. Create 2 files (use notepad or wordpad or any other text editor) and
save in the C:\Program Files\Delano Scientific\PyMOL directory:

a) pymol.cmd

@cctbx.python -x "%~f0" %* & exit /b
import cctbx
import pymol

b) run.cmd

CALL C:\cctbx_build\setpaths_all.bat
CALL "C:\Program Files\Delano Scientific\PyMOL\pymol.cmd"

5. It's important to have python in your path variable (which you can access by going to control panel|system|advanced|environment variables), just add C:\python24 to the end of the path variable, separated by a semi-colon.

===Linux (Robert Campbell)===
When you run the setpaths.sh script, it adds the cctbx_build/bin directory to the *front* of your $PATH. In that directory is a shell script called "python" that sets the environment necessary to import cctbx. So, to get cctbx to work, you have to call python without prefixing a directory path. If you were like me and had:
/usr/bin/python $PYMOL_PATH/modules/launch_pymol.py $*
in your pymol.com file, then it would not run that cctbx_build/bin/python script. So you need to either change the above line to:
python $PYMOL_PATH/modules/launch_pymol.py $*
(assuming you've already run the setpaths.sh script) or you need to copy the cctbx_build/bin/python contents (without the actual "python" command) into your pymol.com file or some other file that you source before pymol.com.

Within pymol, type the command:
print sys.path
and you should now see the cctbx directories show up.

[[Category:PyMol_Integration|cctbx]]

CCTBX

2006-10-27T23:32:44Z

Rogerdodd:

=Computational Crystallography Toolbox=
[http://cctbx.sourceforge.net cctbx]

==Using With PyMol==

===On a Mac===
There is a page on the cctbx with special instructions for using it on the Mac [http://cci.lbl.gov/cctbx_build/mac_os_x_notes.html cctbx On Mac]. Note that you need to use the "Framework" build of PyMOL [http://delsci.com/frameworkpymol/ FrameWorkPyMol].

===Windows XP (Roger Dodd)===
1. Download and install python (to the default location - C:\Python24)

[http://www.python.org/ftp/python/2.4.1/python-2.4.1.msi Python-2.4.1]

1a. If you want to use the draw_symops.py or draw_symops_cctbx.py
scripts you also need to install numarray after installing python

[http://prdownloads.sourceforge.net/numpy/numarray-1.3.3.win32-py2.4.exe?download Numarray-1.3.3]

2. Download cctbx *without* python included and unpack into
C:\cctbx_build and C:\cctbx_sources (i.e. execute the file in C:\)

[http://cci.lbl.gov/cctbx_build/ cctbx]

3. Download pymol built against python 2.4 (but not including its own
python) and install in the default location

[http://delsci.com/rel/098/pymol-0_98rc5-bin-win32-py24.zip pymol-0_98rc5]

(You cannot use the latest beta versions which include their own version
of python to the best of my knowledge)

4. Create 2 files (use notepad or wordpad or any other text editor) and
save in the C:\Program Files\Delano Scientific\PyMOL directory:

a) pymol.cmd

@python -x "%~f0" %* & exit /b
import cctbx
import pymol

b) run.cmd

CALL C:\cctbx_build\setpaths_all.bat
CALL "C:\Program Files\Delano Scientific\PyMOL\pymol.cmd"

5. It's important to have python in your path variable (which you can access by going to control panel|system|advanced|environment variables), just add C:\python24 to the end of the path variable, separated by a semi-colon.

===Linux (Robert Campbell)===
When you run the setpaths.sh script, it adds the cctbx_build/bin directory to the *front* of your $PATH. In that directory is a shell script called "python" that sets the environment necessary to import cctbx. So, to get cctbx to work, you have to call python without prefixing a directory path. If you were like me and had:
/usr/bin/python $PYMOL_PATH/modules/launch_pymol.py $*
in your pymol.com file, then it would not run that cctbx_build/bin/python script. So you need to either change the above line to:
python $PYMOL_PATH/modules/launch_pymol.py $*
(assuming you've already run the setpaths.sh script) or you need to copy the cctbx_build/bin/python contents (without the actual "python" command) into your pymol.com file or some other file that you source before pymol.com.

Within pymol, type the command:
print sys.path
and you should now see the cctbx directories show up.

[[Category:PyMol_Integration|cctbx]]

CCTBX

2005-09-20T10:21:22Z

Rogerdodd:

=Computational Crystallography Toolbox=
[http://cctbx.sourceforge.net cctbx]

==Using With PyMol==

===On a Mac===
There is a page on the cctbx with special instructions for using it on the Mac [http://cci.lbl.gov/cctbx_build/mac_os_x_notes.html cctbx On Mac]. Note that you need to use the "Framework" build of PyMOL [http://delsci.com/frameworkpymol/ FrameWorkPyMol].

===Windows XP (Roger Dodd)===
1. Download and install python (to the default location - C:\Python24)

[http://www.python.org/ftp/python/2.4.1/python-2.4.1.msi Python-2.4.1]

1a. If you want to use the draw_symops.py or draw_symops_cctbx.py
scripts you also need to install numarray after installing python

[http://prdownloads.sourceforge.net/numpy/numarray-1.3.3.win32-py2.4.exe?download Numarray-1.3.3]

2. Download cctbx *without* python included and unpack into
C:\cctbx_build and C:\cctbx_sources (i.e. execute the file in C:\)

[http://cci.lbl.gov/cctbx_build/results/2005_08_18_0201/cctbx_win_xp_py24_pre.exe cctbx]

3. Download pymol built against python 2.4 (but not including its own
python) and install in the default location

[http://delsci.com/rel/0_98/pymol-0_98rc5-bin-win32-py24.zip pymol-0_98rc5]

(You cannot use the latest beta versions which include their own version
of python to the best of my knowledge)

4. Create 2 files (use notepad or wordpad or any other text editor) and
save in the C:\Program Files\Delano Scientific\PyMOL directory:

a) pymol.cmd

@python -x "%~f0" %* & exit /b
import cctbx
import pymol

b) run.cmd

CALL C:\cctbx_build\setpaths_all.bat
CALL "C:\Program Files\Delano Scientific\PyMOL\pymol.cmd"

5. It's important to have python in your path variable (which you can access by going to control panel|system|advanced|environment variables), just add C:\python24 to the end of the path variable, separated by a semi-colon.

===Linux (Robert Campbell)===
When you run the setpaths.sh script, it adds the cctbx_build/bin directory to the *front* of your $PATH. In that directory is a shell script called "python" that sets the environment necessary to import cctbx. So, to get cctbx to work, you have to call python without prefixing a directory path. If you were like me and had:
/usr/bin/python $PYMOL_PATH/modules/launch_pymol.py $*
in your pymol.com file, then it would not run that cctbx_build/bin/python script. So you need to either change the above line to:
python $PYMOL_PATH/modules/launch_pymol.py $*
(assuming you've already run the setpaths.sh script) or you need to copy the cctbx_build/bin/python contents (without the actual "python" command) into your pymol.com file or some other file that you source before pymol.com.

Within pymol, type the command:
print sys.path
and you should now see the cctbx directories show up.

[[Category:PyMol_Integration|cctbx]]

Category:PyMol Integration Arbitrary Graphics Objects

2005-09-20T10:19:36Z

Rogerdodd:

* [http://protlib.uchicago.edu/index.html PL: The Protein Library]

[[Category:PyMol_Integration|PL -- The Protein Library]]

CCTBX

2005-09-20T10:17:54Z

Rogerdodd:

=Computational Crystallography Toolbox=
[http://cctbx.sourceforge.net cctbx]

==Using With PyMol==

===On a Mac===
There is a page on the cctbx with special instructions for using it on the Mac [http://cci.lbl.gov/cctbx_build/mac_os_x_notes.html cctbx On Mac]. Note that you need to use the "Framework" build of PyMOL [http://delsci.com/frameworkpymol/ FrameWorkPyMol].

===Windows XP (Roger Dodd)===
1. Download and install python (to the default location - C:\Python24)

[http://www.python.org/ftp/python/2.4.1/python-2.4.1.msi Python-2.4.1]

1a. If you want to use the draw_symops.py or draw_symops_cctbx.py
scripts you also need to install numarray after installing python

[http://prdownloads.sourceforge.net/numpy/numarray-1.3.3.win32-py2.4.exe?download Numarray-1.3.3]

2. Download cctbx *without* python included and unpack into
C:\cctbx_build and C:\cctbx_sources (i.e. execute the file in C:\)

[http://cci.lbl.gov/cctbx_build/results/2005_08_18_0201/cctbx_win_xp_py24_pre.exe cctbx]

3. Download pymol built against python 2.4 (but not including its own
python) and install in the default location

[http://delsci.com/rel/0_98/pymol-0_98rc5-bin-win32-py24.zip pymol-0_98rc5]

(You cannot use the latest beta versions which include their own version
of python to the best of my knowledge)

4. Create 2 files (use notepad or wordpad or any other text editor) and
save in the C:\Program Files\Delano Scientific\PyMOL directory:

a) pymol.cmd

@python -x "%~f0" %* & exit /b
import cctbx
import pymol

b) run.cmd

CALL C:\cctbx_build\setpaths_all.bat
CALL "C:\Program Files\Delano Scientific\PyMOL\pymol.cmd"

5. It's important to have python in your path variable
(which you can access by going to control
panel|system|advanced|environment variables), just add C:\python24 to
the end of the path variable, separated by a semi-colon.

===Linux (Robert Campbell)===
When you run the setpaths.sh script, it adds the cctbx_build/bin directory to the *front* of your $PATH. In that directory is a shell script called "python" that sets the environment necessary to import cctbx. So, to get cctbx to work, you have to call python without prefixing a directory path. If you were like me and had:
/usr/bin/python $PYMOL_PATH/modules/launch_pymol.py $*
in your pymol.com file, then it would not run that cctbx_build/bin/python script. So you need to either change the above line to:
python $PYMOL_PATH/modules/launch_pymol.py $*
(assuming you've already run the setpaths.sh script) or you need to copy the cctbx_build/bin/python contents (without the actual "python" command) into your pymol.com file or some other file that you source before pymol.com.

Within pymol, type the command:
print sys.path
and you should now see the cctbx directories show up.

[[Category:PyMol_Integration|cctbx]]

CCTBX

2005-09-20T10:16:33Z

Rogerdodd:

=Computational Crystallography Toolbox=
[http://cctbx.sourceforge.net cctbx]

==Using With PyMol==

===On a Mac===
There is a page on the cctbx with special instructions for using it on the Mac [http://cci.lbl.gov/cctbx_build/mac_os_x_notes.html cctbx On Mac]. Note that you need to use the "Framework" build of PyMOL [http://delsci.com/frameworkpymol/ FrameWorkPyMol].

===Windows XP (Roger Dodd)===
1. Download and install python (to the default location - C:\Python24)

[http://www.python.org/ftp/python/2.4.1/python-2.4.1.msi Python-2.4.1]

1a. If you want to use the draw_symops.py or draw_symops_cctbx.py
scripts you also need to install numarray after installing python

[http://prdownloads.sourceforge.net/numpy/numarray-1.3.3.win32-py2.4.exe?download Numarray-1.3.3]

2. Download cctbx *without* python included and unpack into
C:\cctbx_build and C:\cctbx_sources (i.e. execute the file in C:\)

[http://cci.lbl.gov/cctbx_build/results/2005_08_18_0201/cctbx_win_xp_py24_pre.exe cctbx]

3. Download pymol built against python 2.4 (but not including its own
python) and install in the default location

[http://delsci.com/rel/0_98/pymol-0_98rc5-bin-win32-py24.zip pymol-0_98rc5]

(You cannot use the latest beta versions which include their own version
of python to the best of my knowledge)

4. Create 2 files (use notepad or wordpad or any other text editor) and
save in the C:\Program Files\Delano Scientific\PyMOL directory:

a) pymol.cmd

@python -x "%~f0" %* & exit /b
import cctbx
import pymol

b) run.cmd

CALL C:\cctbx_build\setpaths_all.bat
CALL "C:\Program Files\Delano Scientific\PyMOL\pymol.cmd"

5. One other thing, it's important to have python in your path variable
(which you can access by going to control
panel|system|advanced|environment variables), just add C:\python24 to
the end of the path variable, separated by a semi-colon.

===Linux (Robert Campbell)===
When you run the setpaths.sh script, it adds the cctbx_build/bin directory to the *front* of your $PATH. In that directory is a shell script called "python" that sets the environment necessary to import cctbx. So, to get cctbx to work, you have to call python without prefixing a directory path. If you were like me and had:
/usr/bin/python $PYMOL_PATH/modules/launch_pymol.py $*
in your pymol.com file, then it would not run that cctbx_build/bin/python script. So you need to either change the above line to:
python $PYMOL_PATH/modules/launch_pymol.py $*
(assuming you've already run the setpaths.sh script) or you need to copy the cctbx_build/bin/python contents (without the actual "python" command) into your pymol.com file or some other file that you source before pymol.com.

Within pymol, type the command:
print sys.path
and you should now see the cctbx directories show up.

[[Category:PyMol_Integration|cctbx]]

CCTBX

2005-09-20T10:15:43Z

Rogerdodd:

=Computational Crystallography Toolbox=
[http://cctbx.sourceforge.net cctbx]

==Using With PyMol==

===On a Mac===
There is a page on the cctbx with special instructions for using it on the Mac [http://cci.lbl.gov/cctbx_build/mac_os_x_notes.html cctbx On Mac]. Note that you need to use the "Framework" build of PyMOL [http://delsci.com/frameworkpymol/ FrameWorkPyMol].

===Windows XP (Roger Dodd)===
1. Download and install python (to the default location - C:\Python24)

[http://www.python.org/ftp/python/2.4.1/python-2.4.1.msi Python-2.4.1]

1a. If you want to use the draw_symops.py or draw_symops_cctbx.py
scripts you also need to install numarray after installing python

[http://prdownloads.sourceforge.net/numpy/numarray-1.3.3.win32-py2.4.exe?download Numarray-1.3.3]

2. Download cctbx *without* python included and unpack into
C:\cctbx_build and C:\cctbx_sources

[http://cci.lbl.gov/cctbx_build/results/2005_08_18_0201/cctbx_win_xp_py24_pre.exe cctbx]

3. Download pymol built against python 2.4 (but not including its own
python) and install in the default location

[http://delsci.com/rel/0_98/pymol-0_98rc5-bin-win32-py24.zip pymol-0_98rc5]

(You cannot use the latest beta versions which include their own version
of python to the best of my knowledge)

4. Create 2 files (use notepad or wordpad or any other text editor) and
save in the C:\Program Files\Delano Scientific\PyMOL directory:

a) pymol.cmd

@python -x "%~f0" %* & exit /b
import cctbx
import pymol

b) run.cmd

CALL C:\cctbx_build\setpaths_all.bat
CALL "C:\Program Files\Delano Scientific\PyMOL\pymol.cmd"

5. One other thing, it's important to have python in your path variable
(which you can access by going to control
panel|system|advanced|environment variables), just add C:\python24 to
the end of the path variable, separated by a semi-colon.

===Linux (Robert Campbell)===
When you run the setpaths.sh script, it adds the cctbx_build/bin directory to the *front* of your $PATH. In that directory is a shell script called "python" that sets the environment necessary to import cctbx. So, to get cctbx to work, you have to call python without prefixing a directory path. If you were like me and had:
/usr/bin/python $PYMOL_PATH/modules/launch_pymol.py $*
in your pymol.com file, then it would not run that cctbx_build/bin/python script. So you need to either change the above line to:
python $PYMOL_PATH/modules/launch_pymol.py $*
(assuming you've already run the setpaths.sh script) or you need to copy the cctbx_build/bin/python contents (without the actual "python" command) into your pymol.com file or some other file that you source before pymol.com.

Within pymol, type the command:
print sys.path
and you should now see the cctbx directories show up.

[[Category:PyMol_Integration|cctbx]]

CCTBX

2005-09-20T10:15:02Z

Rogerdodd:

=Note=
We need someone to make some edits to this page. I don't know anything about cctbx except what's shown here.

=Computational Crystallography Toolbox=
[http://cctbx.sourceforge.net cctbx]

==Using With PyMol==

===On a Mac===
There is a page on the cctbx with special instructions for using it on the Mac [http://cci.lbl.gov/cctbx_build/mac_os_x_notes.html cctbx On Mac]. Note that you need to use the "Framework" build of PyMOL [http://delsci.com/frameworkpymol/ FrameWorkPyMol].

===Windows XP (Roger Dodd)===
1. Download and install python (to the default location - C:\Python24)

[http://www.python.org/ftp/python/2.4.1/python-2.4.1.msi Python-2.4.1]

1a. If you want to use the draw_symops.py or draw_symops_cctbx.py
scripts you also need to install numarray after installing python

[http://prdownloads.sourceforge.net/numpy/numarray-1.3.3.win32-py2.4.exe?download Numarray-1.3.3]

2. Download cctbx *without* python included and unpack into
C:\cctbx_build and C:\cctbx_sources

[http://cci.lbl.gov/cctbx_build/results/2005_08_18_0201/cctbx_win_xp_py24_pre.exe cctbx]

3. Download pymol built against python 2.4 (but not including its own
python) and install in the default location

[http://delsci.com/rel/0_98/pymol-0_98rc5-bin-win32-py24.zip pymol-0_98rc5]

(You cannot use the latest beta versions which include their own version
of python to the best of my knowledge)

4. Create 2 files (use notepad or wordpad or any other text editor) and
save in the C:\Program Files\Delano Scientific\PyMOL directory:

a) pymol.cmd

@python -x "%~f0" %* & exit /b
import cctbx
import pymol

b) run.cmd

CALL C:\cctbx_build\setpaths_all.bat
CALL "C:\Program Files\Delano Scientific\PyMOL\pymol.cmd"

5. One other thing, it's important to have python in your path variable
(which you can access by going to control
panel|system|advanced|environment variables), just add C:\python24 to
the end of the path variable, separated by a semi-colon.

===Linux (Robert Campbell)===
When you run the setpaths.sh script, it adds the cctbx_build/bin directory to the *front* of your $PATH. In that directory is a shell script called "python" that sets the environment necessary to import cctbx. So, to get cctbx to work, you have to call python without prefixing a directory path. If you were like me and had:
/usr/bin/python $PYMOL_PATH/modules/launch_pymol.py $*
in your pymol.com file, then it would not run that cctbx_build/bin/python script. So you need to either change the above line to:
python $PYMOL_PATH/modules/launch_pymol.py $*
(assuming you've already run the setpaths.sh script) or you need to copy the cctbx_build/bin/python contents (without the actual "python" command) into your pymol.com file or some other file that you source before pymol.com.

Within pymol, type the command:
print sys.path
and you should now see the cctbx directories show up.

I hope this is clear enough!

[[Category:PyMol_Integration|cctbx]]

CCTBX

2005-09-20T10:13:55Z

Rogerdodd:

Older News

2005-08-17T11:01:52Z

Rogerdodd:

= Older News=
* How to create multiple [[Distance]] objects.
* [[Nuccyl]]'s address changed.

* PyMol gets some new features. PyMol 0.99beta07 added these commands for testing, check out the new
# [[Draw]] command and,
# [[Spheres]] Shader Spheres represenation
* Also, [[Ray]] and [[Draw]] now show oversized images scaled into the viewport.