https://pymolwiki.org/api.php?action=feedcontributions&user=Rogerdodd&feedformat=atomPyMOLWiki - User contributions [en]2024-03-28T08:56:42ZUser contributionsMediaWiki 1.35.7https://pymolwiki.org/index.php?title=CCTBX&diff=3274CCTBX2006-10-27T23:36:48Z<p>Rogerdodd: </p>
<hr />
<div>=Computational Crystallography Toolbox=<br />
[http://cctbx.sourceforge.net cctbx]<br />
<br />
==Using With PyMol==<br />
<br />
===On a Mac===<br />
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].<br />
<br />
===Windows XP (Roger Dodd)===<br />
1. Download and install python (to the default location - C:\Python24)<br />
<br />
[http://www.python.org/ftp/python/2.4.1/python-2.4.1.msi Python-2.4.1]<br />
<br />
1a. If you want to use the draw_symops.py or draw_symops_cctbx.py<br />
scripts you also need to install numarray after installing python<br />
<br />
[http://prdownloads.sourceforge.net/numpy/numarray-1.3.3.win32-py2.4.exe?download Numarray-1.3.3]<br />
<br />
2. Download cctbx *without* python included and unpack into<br />
C:\cctbx_build and C:\cctbx_sources (i.e. execute the file in C:\)<br />
<br />
[http://cci.lbl.gov/cctbx_build/ cctbx]<br />
<br />
3. Download pymol built against python 2.4 (but not including its own<br />
python) and install in the default location<br />
<br />
[http://delsci.com/rel/098/pymol-0_98rc5-bin-win32-py24.zip pymol-0_98rc5]<br />
<br />
(Newer versions of PyMOL linked against an external python are available from Delano Scientific on request for holders of a valid subscription.)<br />
<br />
4. Create 2 files (use notepad or wordpad or any other text editor) and<br />
save in the C:\Program Files\Delano Scientific\PyMOL directory:<br />
<br />
a) pymol.cmd<br />
<br />
@cctbx.python -x "%~f0" %* & exit /b<br />
import cctbx<br />
import pymol<br />
<br />
b) run.cmd<br />
<br />
CALL C:\cctbx_build\setpaths_all.bat<br />
CALL "C:\Program Files\Delano Scientific\PyMOL\pymol.cmd"<br />
<br />
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.<br />
<br />
===Linux (Robert Campbell)===<br />
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:<br />
/usr/bin/python $PYMOL_PATH/modules/launch_pymol.py $*<br />
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:<br />
python $PYMOL_PATH/modules/launch_pymol.py $*<br />
(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.<br />
<br />
Within pymol, type the command:<br />
print sys.path<br />
and you should now see the cctbx directories show up.<br />
<br />
[[Category:PyMol_Integration|cctbx]]</div>Rogerdoddhttps://pymolwiki.org/index.php?title=CCTBX&diff=1733CCTBX2006-10-27T23:35:37Z<p>Rogerdodd: </p>
<hr />
<div>=Computational Crystallography Toolbox=<br />
[http://cctbx.sourceforge.net cctbx]<br />
<br />
==Using With PyMol==<br />
<br />
===On a Mac===<br />
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].<br />
<br />
===Windows XP (Roger Dodd)===<br />
1. Download and install python (to the default location - C:\Python24)<br />
<br />
[http://www.python.org/ftp/python/2.4.1/python-2.4.1.msi Python-2.4.1]<br />
<br />
1a. If you want to use the draw_symops.py or draw_symops_cctbx.py<br />
scripts you also need to install numarray after installing python<br />
<br />
[http://prdownloads.sourceforge.net/numpy/numarray-1.3.3.win32-py2.4.exe?download Numarray-1.3.3]<br />
<br />
2. Download cctbx *without* python included and unpack into<br />
C:\cctbx_build and C:\cctbx_sources (i.e. execute the file in C:\)<br />
<br />
[http://cci.lbl.gov/cctbx_build/ cctbx]<br />
<br />
3. Download pymol built against python 2.4 (but not including its own<br />
python) and install in the default location<br />
<br />
[http://delsci.com/rel/098/pymol-0_98rc5-bin-win32-py24.zip pymol-0_98rc5]<br />
<br />
(Newer versions of PyMOL linked against an external python are available from Delano Scientific on request for holders of a valid description.)<br />
<br />
4. Create 2 files (use notepad or wordpad or any other text editor) and<br />
save in the C:\Program Files\Delano Scientific\PyMOL directory:<br />
<br />
a) pymol.cmd<br />
<br />
@cctbx.python -x "%~f0" %* & exit /b<br />
import cctbx<br />
import pymol<br />
<br />
b) run.cmd<br />
<br />
CALL C:\cctbx_build\setpaths_all.bat<br />
CALL "C:\Program Files\Delano Scientific\PyMOL\pymol.cmd"<br />
<br />
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.<br />
<br />
===Linux (Robert Campbell)===<br />
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:<br />
/usr/bin/python $PYMOL_PATH/modules/launch_pymol.py $*<br />
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:<br />
python $PYMOL_PATH/modules/launch_pymol.py $*<br />
(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.<br />
<br />
Within pymol, type the command:<br />
print sys.path<br />
and you should now see the cctbx directories show up.<br />
<br />
[[Category:PyMol_Integration|cctbx]]</div>Rogerdoddhttps://pymolwiki.org/index.php?title=CCTBX&diff=1732CCTBX2006-10-27T23:32:44Z<p>Rogerdodd: </p>
<hr />
<div>=Computational Crystallography Toolbox=<br />
[http://cctbx.sourceforge.net cctbx]<br />
<br />
==Using With PyMol==<br />
<br />
===On a Mac===<br />
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].<br />
<br />
===Windows XP (Roger Dodd)===<br />
1. Download and install python (to the default location - C:\Python24)<br />
<br />
[http://www.python.org/ftp/python/2.4.1/python-2.4.1.msi Python-2.4.1]<br />
<br />
1a. If you want to use the draw_symops.py or draw_symops_cctbx.py<br />
scripts you also need to install numarray after installing python<br />
<br />
[http://prdownloads.sourceforge.net/numpy/numarray-1.3.3.win32-py2.4.exe?download Numarray-1.3.3]<br />
<br />
2. Download cctbx *without* python included and unpack into<br />
C:\cctbx_build and C:\cctbx_sources (i.e. execute the file in C:\)<br />
<br />
[http://cci.lbl.gov/cctbx_build/ cctbx]<br />
<br />
3. Download pymol built against python 2.4 (but not including its own<br />
python) and install in the default location<br />
<br />
[http://delsci.com/rel/098/pymol-0_98rc5-bin-win32-py24.zip pymol-0_98rc5]<br />
<br />
(You cannot use the latest beta versions which include their own version<br />
of python to the best of my knowledge)<br />
<br />
4. Create 2 files (use notepad or wordpad or any other text editor) and<br />
save in the C:\Program Files\Delano Scientific\PyMOL directory:<br />
<br />
a) pymol.cmd<br />
<br />
@python -x "%~f0" %* & exit /b<br />
import cctbx<br />
import pymol<br />
<br />
b) run.cmd<br />
<br />
CALL C:\cctbx_build\setpaths_all.bat<br />
CALL "C:\Program Files\Delano Scientific\PyMOL\pymol.cmd"<br />
<br />
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.<br />
<br />
===Linux (Robert Campbell)===<br />
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:<br />
/usr/bin/python $PYMOL_PATH/modules/launch_pymol.py $*<br />
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:<br />
python $PYMOL_PATH/modules/launch_pymol.py $*<br />
(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.<br />
<br />
Within pymol, type the command:<br />
print sys.path<br />
and you should now see the cctbx directories show up.<br />
<br />
[[Category:PyMol_Integration|cctbx]]</div>Rogerdoddhttps://pymolwiki.org/index.php?title=CCTBX&diff=1553CCTBX2005-09-20T10:21:22Z<p>Rogerdodd: </p>
<hr />
<div>=Computational Crystallography Toolbox=<br />
[http://cctbx.sourceforge.net cctbx]<br />
<br />
==Using With PyMol==<br />
<br />
===On a Mac===<br />
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].<br />
<br />
===Windows XP (Roger Dodd)===<br />
1. Download and install python (to the default location - C:\Python24)<br />
<br />
[http://www.python.org/ftp/python/2.4.1/python-2.4.1.msi Python-2.4.1]<br />
<br />
1a. If you want to use the draw_symops.py or draw_symops_cctbx.py<br />
scripts you also need to install numarray after installing python<br />
<br />
[http://prdownloads.sourceforge.net/numpy/numarray-1.3.3.win32-py2.4.exe?download Numarray-1.3.3]<br />
<br />
2. Download cctbx *without* python included and unpack into<br />
C:\cctbx_build and C:\cctbx_sources (i.e. execute the file in C:\)<br />
<br />
[http://cci.lbl.gov/cctbx_build/results/2005_08_18_0201/cctbx_win_xp_py24_pre.exe cctbx]<br />
<br />
3. Download pymol built against python 2.4 (but not including its own<br />
python) and install in the default location<br />
<br />
[http://delsci.com/rel/0_98/pymol-0_98rc5-bin-win32-py24.zip pymol-0_98rc5]<br />
<br />
(You cannot use the latest beta versions which include their own version<br />
of python to the best of my knowledge)<br />
<br />
4. Create 2 files (use notepad or wordpad or any other text editor) and<br />
save in the C:\Program Files\Delano Scientific\PyMOL directory:<br />
<br />
a) pymol.cmd<br />
<br />
@python -x "%~f0" %* & exit /b<br />
import cctbx<br />
import pymol<br />
<br />
b) run.cmd<br />
<br />
CALL C:\cctbx_build\setpaths_all.bat<br />
CALL "C:\Program Files\Delano Scientific\PyMOL\pymol.cmd"<br />
<br />
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.<br />
<br />
===Linux (Robert Campbell)===<br />
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:<br />
/usr/bin/python $PYMOL_PATH/modules/launch_pymol.py $*<br />
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:<br />
python $PYMOL_PATH/modules/launch_pymol.py $*<br />
(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.<br />
<br />
Within pymol, type the command:<br />
print sys.path<br />
and you should now see the cctbx directories show up.<br />
<br />
[[Category:PyMol_Integration|cctbx]]</div>Rogerdoddhttps://pymolwiki.org/index.php?title=Category:PyMol_Integration_Arbitrary_Graphics_Objects&diff=3154Category:PyMol Integration Arbitrary Graphics Objects2005-09-20T10:19:36Z<p>Rogerdodd: </p>
<hr />
<div>* [http://protlib.uchicago.edu/index.html PL: The Protein Library]<br />
<br />
[[Category:PyMol_Integration|PL -- The Protein Library]]</div>Rogerdoddhttps://pymolwiki.org/index.php?title=CCTBX&diff=1088CCTBX2005-09-20T10:17:54Z<p>Rogerdodd: </p>
<hr />
<div>=Computational Crystallography Toolbox=<br />
[http://cctbx.sourceforge.net cctbx]<br />
<br />
==Using With PyMol==<br />
<br />
===On a Mac===<br />
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].<br />
<br />
===Windows XP (Roger Dodd)===<br />
1. Download and install python (to the default location - C:\Python24)<br />
<br />
[http://www.python.org/ftp/python/2.4.1/python-2.4.1.msi Python-2.4.1]<br />
<br />
1a. If you want to use the draw_symops.py or draw_symops_cctbx.py<br />
scripts you also need to install numarray after installing python<br />
<br />
[http://prdownloads.sourceforge.net/numpy/numarray-1.3.3.win32-py2.4.exe?download Numarray-1.3.3]<br />
<br />
2. Download cctbx *without* python included and unpack into<br />
C:\cctbx_build and C:\cctbx_sources (i.e. execute the file in C:\)<br />
<br />
[http://cci.lbl.gov/cctbx_build/results/2005_08_18_0201/cctbx_win_xp_py24_pre.exe cctbx]<br />
<br />
3. Download pymol built against python 2.4 (but not including its own<br />
python) and install in the default location<br />
<br />
[http://delsci.com/rel/0_98/pymol-0_98rc5-bin-win32-py24.zip pymol-0_98rc5]<br />
<br />
(You cannot use the latest beta versions which include their own version<br />
of python to the best of my knowledge)<br />
<br />
4. Create 2 files (use notepad or wordpad or any other text editor) and<br />
save in the C:\Program Files\Delano Scientific\PyMOL directory:<br />
<br />
a) pymol.cmd<br />
<br />
@python -x "%~f0" %* & exit /b<br />
import cctbx<br />
import pymol<br />
<br />
b) run.cmd<br />
<br />
CALL C:\cctbx_build\setpaths_all.bat<br />
CALL "C:\Program Files\Delano Scientific\PyMOL\pymol.cmd"<br />
<br />
5. It's important to have python in your path variable<br />
(which you can access by going to control<br />
panel|system|advanced|environment variables), just add C:\python24 to<br />
the end of the path variable, separated by a semi-colon.<br />
<br />
===Linux (Robert Campbell)===<br />
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:<br />
/usr/bin/python $PYMOL_PATH/modules/launch_pymol.py $*<br />
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:<br />
python $PYMOL_PATH/modules/launch_pymol.py $*<br />
(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.<br />
<br />
Within pymol, type the command:<br />
print sys.path<br />
and you should now see the cctbx directories show up.<br />
<br />
[[Category:PyMol_Integration|cctbx]]</div>Rogerdoddhttps://pymolwiki.org/index.php?title=CCTBX&diff=1086CCTBX2005-09-20T10:16:33Z<p>Rogerdodd: </p>
<hr />
<div>=Computational Crystallography Toolbox=<br />
[http://cctbx.sourceforge.net cctbx]<br />
<br />
==Using With PyMol==<br />
<br />
===On a Mac===<br />
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].<br />
<br />
===Windows XP (Roger Dodd)===<br />
1. Download and install python (to the default location - C:\Python24)<br />
<br />
[http://www.python.org/ftp/python/2.4.1/python-2.4.1.msi Python-2.4.1]<br />
<br />
1a. If you want to use the draw_symops.py or draw_symops_cctbx.py<br />
scripts you also need to install numarray after installing python<br />
<br />
[http://prdownloads.sourceforge.net/numpy/numarray-1.3.3.win32-py2.4.exe?download Numarray-1.3.3]<br />
<br />
2. Download cctbx *without* python included and unpack into<br />
C:\cctbx_build and C:\cctbx_sources (i.e. execute the file in C:\)<br />
<br />
[http://cci.lbl.gov/cctbx_build/results/2005_08_18_0201/cctbx_win_xp_py24_pre.exe cctbx]<br />
<br />
3. Download pymol built against python 2.4 (but not including its own<br />
python) and install in the default location<br />
<br />
[http://delsci.com/rel/0_98/pymol-0_98rc5-bin-win32-py24.zip pymol-0_98rc5]<br />
<br />
(You cannot use the latest beta versions which include their own version<br />
of python to the best of my knowledge)<br />
<br />
4. Create 2 files (use notepad or wordpad or any other text editor) and<br />
save in the C:\Program Files\Delano Scientific\PyMOL directory:<br />
<br />
a) pymol.cmd<br />
<br />
@python -x "%~f0" %* & exit /b<br />
import cctbx<br />
import pymol<br />
<br />
b) run.cmd<br />
<br />
CALL C:\cctbx_build\setpaths_all.bat<br />
CALL "C:\Program Files\Delano Scientific\PyMOL\pymol.cmd"<br />
<br />
5. One other thing, it's important to have python in your path variable<br />
(which you can access by going to control<br />
panel|system|advanced|environment variables), just add C:\python24 to<br />
the end of the path variable, separated by a semi-colon.<br />
<br />
===Linux (Robert Campbell)===<br />
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:<br />
/usr/bin/python $PYMOL_PATH/modules/launch_pymol.py $*<br />
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:<br />
python $PYMOL_PATH/modules/launch_pymol.py $*<br />
(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.<br />
<br />
Within pymol, type the command:<br />
print sys.path<br />
and you should now see the cctbx directories show up.<br />
<br />
[[Category:PyMol_Integration|cctbx]]</div>Rogerdoddhttps://pymolwiki.org/index.php?title=CCTBX&diff=1085CCTBX2005-09-20T10:15:43Z<p>Rogerdodd: </p>
<hr />
<div>=Computational Crystallography Toolbox=<br />
[http://cctbx.sourceforge.net cctbx]<br />
<br />
==Using With PyMol==<br />
<br />
===On a Mac===<br />
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].<br />
<br />
===Windows XP (Roger Dodd)===<br />
1. Download and install python (to the default location - C:\Python24)<br />
<br />
[http://www.python.org/ftp/python/2.4.1/python-2.4.1.msi Python-2.4.1]<br />
<br />
1a. If you want to use the draw_symops.py or draw_symops_cctbx.py<br />
scripts you also need to install numarray after installing python<br />
<br />
[http://prdownloads.sourceforge.net/numpy/numarray-1.3.3.win32-py2.4.exe?download Numarray-1.3.3]<br />
<br />
2. Download cctbx *without* python included and unpack into<br />
C:\cctbx_build and C:\cctbx_sources<br />
<br />
[http://cci.lbl.gov/cctbx_build/results/2005_08_18_0201/cctbx_win_xp_py24_pre.exe cctbx]<br />
<br />
3. Download pymol built against python 2.4 (but not including its own<br />
python) and install in the default location<br />
<br />
[http://delsci.com/rel/0_98/pymol-0_98rc5-bin-win32-py24.zip pymol-0_98rc5]<br />
<br />
(You cannot use the latest beta versions which include their own version<br />
of python to the best of my knowledge)<br />
<br />
4. Create 2 files (use notepad or wordpad or any other text editor) and<br />
save in the C:\Program Files\Delano Scientific\PyMOL directory:<br />
<br />
a) pymol.cmd<br />
<br />
@python -x "%~f0" %* & exit /b<br />
import cctbx<br />
import pymol<br />
<br />
b) run.cmd<br />
<br />
CALL C:\cctbx_build\setpaths_all.bat<br />
CALL "C:\Program Files\Delano Scientific\PyMOL\pymol.cmd"<br />
<br />
5. One other thing, it's important to have python in your path variable<br />
(which you can access by going to control<br />
panel|system|advanced|environment variables), just add C:\python24 to<br />
the end of the path variable, separated by a semi-colon.<br />
<br />
===Linux (Robert Campbell)===<br />
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:<br />
/usr/bin/python $PYMOL_PATH/modules/launch_pymol.py $*<br />
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:<br />
python $PYMOL_PATH/modules/launch_pymol.py $*<br />
(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.<br />
<br />
Within pymol, type the command:<br />
print sys.path<br />
and you should now see the cctbx directories show up.<br />
<br />
[[Category:PyMol_Integration|cctbx]]</div>Rogerdoddhttps://pymolwiki.org/index.php?title=CCTBX&diff=1084CCTBX2005-09-20T10:15:02Z<p>Rogerdodd: </p>
<hr />
<div>=Note=<br />
We need someone to make some edits to this page. I don't know anything about cctbx except what's shown here.<br />
<br />
=Computational Crystallography Toolbox=<br />
[http://cctbx.sourceforge.net cctbx]<br />
<br />
==Using With PyMol==<br />
<br />
===On a Mac===<br />
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].<br />
<br />
===Windows XP (Roger Dodd)===<br />
1. Download and install python (to the default location - C:\Python24)<br />
<br />
[http://www.python.org/ftp/python/2.4.1/python-2.4.1.msi Python-2.4.1]<br />
<br />
1a. If you want to use the draw_symops.py or draw_symops_cctbx.py<br />
scripts you also need to install numarray after installing python<br />
<br />
[http://prdownloads.sourceforge.net/numpy/numarray-1.3.3.win32-py2.4.exe?download Numarray-1.3.3]<br />
<br />
2. Download cctbx *without* python included and unpack into<br />
C:\cctbx_build and C:\cctbx_sources<br />
<br />
[http://cci.lbl.gov/cctbx_build/results/2005_08_18_0201/cctbx_win_xp_py24_pre.exe cctbx]<br />
<br />
3. Download pymol built against python 2.4 (but not including its own<br />
python) and install in the default location<br />
<br />
[http://delsci.com/rel/0_98/pymol-0_98rc5-bin-win32-py24.zip pymol-0_98rc5]<br />
<br />
(You cannot use the latest beta versions which include their own version<br />
of python to the best of my knowledge)<br />
<br />
4. Create 2 files (use notepad or wordpad or any other text editor) and<br />
save in the C:\Program Files\Delano Scientific\PyMOL directory:<br />
<br />
a) pymol.cmd<br />
<br />
@python -x "%~f0" %* & exit /b<br />
import cctbx<br />
import pymol<br />
<br />
b) run.cmd<br />
<br />
CALL C:\cctbx_build\setpaths_all.bat<br />
CALL "C:\Program Files\Delano Scientific\PyMOL\pymol.cmd"<br />
<br />
5. One other thing, it's important to have python in your path variable<br />
(which you can access by going to control<br />
panel|system|advanced|environment variables), just add C:\python24 to<br />
the end of the path variable, separated by a semi-colon.<br />
<br />
===Linux (Robert Campbell)===<br />
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:<br />
/usr/bin/python $PYMOL_PATH/modules/launch_pymol.py $*<br />
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:<br />
python $PYMOL_PATH/modules/launch_pymol.py $*<br />
(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.<br />
<br />
Within pymol, type the command:<br />
print sys.path<br />
and you should now see the cctbx directories show up.<br />
<br />
<br />
I hope this is clear enough!<br />
<br />
<br />
<br />
[[Category:PyMol_Integration|cctbx]]</div>Rogerdoddhttps://pymolwiki.org/index.php?title=CCTBX&diff=1083CCTBX2005-09-20T10:13:55Z<p>Rogerdodd: </p>
<hr />
<div>=Note=<br />
We need someone to make some edits to this page. I don't know anything about cctbx except what's shown here.<br />
<br />
=Computational Crystallography Toolbox=<br />
[http://cctbx.sourceforge.net cctbx]<br />
<br />
==Using With PyMol==<br />
<br />
===On a Mac===<br />
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].<br />
<br />
===Windows XP (Roger Dodd)===<br />
1. Download and install python (to the default location - C:\Python24)<br />
<br />
[http://www.python.org/ftp/python/2.4.1/python-2.4.1.msi Python-2.4.1]<br />
<br />
1a. If you want to use the draw_symops.py or draw_symops_cctbx.py<br />
scripts you also need to install numarray after installing python<br />
<br />
[http://prdownloads.sourceforge.net/numpy/numarray-1.3.3.win32-py2.4.exe?download Numarray-1.3.3]<br />
<br />
2. Download cctbx *without* python included and unpack into<br />
C:\cctbx_build and C:\cctbx_sources<br />
<br />
[http://cci.lbl.gov/cctbx_build/results/2005_08_18_0201/cctbx_win_xp_py24_pre.exe cctbx]<br />
<br />
3. Download pymol built against python 2.4 (but not including its own<br />
python) and install in the default location<br />
<br />
[http://delsci.com/rel/0_98/pymol-0_98rc5-bin-win32-py24.zip pymol-0_98rc5]<br />
<br />
(You cannot use the latest beta versions which include their own version<br />
of python to the best of my knowledge)<br />
<br />
4. Create 2 files (use notepad or wordpad or any other text editor) and<br />
save in the C:\Program Files\Delano Scientific\PyMOL directory:<br />
<br />
a) pymol.cmd<br />
<br />
@python -x "%~f0" %* & exit /b<br />
import cctbx<br />
import pymol<br />
<br />
b) run.cmd<br />
<br />
CALL C:\cctbx_build\setpaths_all.bat<br />
CALL "C:\Program Files\Delano Scientific\PyMOL\pymol.cmd"<br />
<br />
5. One other thing, it's important to have python in your path variable<br />
(which you can access by going to control<br />
panel|system|advanced|environment variables), just add C:\python24 to<br />
the end of the path variable, separated by a semi-colon.<br />
<br />
===Linux (Robert Campbell)===<br />
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:<br />
/usr/bin/python $PYMOL_PATH/modules/launch_pymol.py $*<br />
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:<br />
python $PYMOL_PATH/modules/launch_pymol.py $*<br />
(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.<br />
<br />
Within pymol, type the command:<br />
print sys.path<br />
and you should now see the cctbx directories show up.<br />
<br />
<br />
I hope this is clear enough!<br />
<br />
<br />
<br />
[[Category:PyMol_Integration|CCTBX]]</div>Rogerdoddhttps://pymolwiki.org/index.php?title=Older_News&diff=1201Older News2005-08-17T11:01:52Z<p>Rogerdodd: </p>
<hr />
<div>= Older News=<br />
* How to create multiple [[Distance]] objects.<br />
* [[Nuccyl]]'s address changed.<br />
<br />
* PyMol gets some new features. PyMol 0.99beta07 added these commands for testing, check out the new <br />
# [[Draw]] command and,<br />
# [[Spheres]] Shader Spheres represenation<br />
* Also, [[Ray]] and [[Draw]] now show oversized images scaled into the viewport.</div>Rogerdodd