TABLE OF CONTENT
  1. ANONYMOUS ACCESS TO OUR CVS REPOSITORY:
  2. SUBMIT A BUG REPORT
  3. GETTING HELP
  4. DOWNLOAD PROBLEMS:
  5. INSTALLATION PROBLEMS:
  6. KNOWN BUGS
  7. CVS UPDATING PACKAGES
  8. Problems While Running MGLTools
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I- ANONYMOUS ACCESS TO OUR CVS REPOSITORY:

If you have a CVS client installed on your machine, our CVS repository can be checked out through anonymous (pserver) CVS with the following instruction set. The module you wish to check out must be specified as the modulename. When prompted for a password for anonymous, simply press the Enter key.
% cvs -d:pserver:anonymous@moses.scripps.edu:/export/cvs login
% cvs -z3 -d:pserver:anonymous@moses.scripps.edu:/export/cvs co modulename

For more information on CVS please visit CVS reference Manual If you have any problem contact Alex Gillet
II- SUBMIT A BUG REPORT:
If you cannot find an answer to your problem in the following please send an email to the MGLTools support (mgllab)mgltools@scripps.edu. In order to better help you we need to following information: Thank you very much.

III-DOWNLOAD PROBLEMS:

The browser tries to display either the archive or the cgi as plain text
If the browser tries to display wither the archive or the cgi as text rather than saving it to disk, try cancelling the operation. Instead, do shift-Click, or right-click on the link to get a menu. Similar tricks (a right-click?) will probably get you a menu in Internet Explorer, with which to save the file.
IV-INSTALLATION PROBLEMS:

glNewTraceMESA Error running pmv or adt version 1.3alpha1 under linux
If you are getting the following error message while running PMV or ADT version 1.3alpha1 under linux:
Run PMV from /home/computation/ADT/share/lib/python2.3/site-packages/Pmv
Traceback (most recent call last):
File "/home/computation/ADT/share/lib/python2.3/site-packages/Pmv/bin/runPmv.py", line 54, in ? from Pmv.moleculeViewer import MoleculeViewer
File "/home/computation/ADT/share/lib/python2.3/site-packages/Pmv/moleculeViewer.py", line 18, in ? from DejaVu.Geom import Geom
File "/home/computation/ADT/share/lib/python2.3/site-packages/DejaVu/__init__.py", line 92, in ? from Viewer import Viewer
File "/home/computation/ADT/share/lib/python2.3/site-packages/DejaVu/Viewer.py", line 18, in ? from opengltk.OpenGL import GL
File "/home/computation/ADT/i86Linux2/lib/python2.3/site-packages/opengltk/OpenGL/GL.py", line 7, in ? from opengltk.extent._gllib import *
ImportError:
/home/computation/ADT/i86Linux2/lib/python2.3/site-packages/opengltk/extent/_gllib.so: undefined symbol: glNewTraceMESA
hit enter to continue
Please do the following:
1- If you have an NVIDIA graphics card, please check if the header files for OpenGL are the ones provided by Nvidia:
/usr/include/GL/glext.h gl.h glx.h glxtokens.h
are the same than:
/usr/share/doc/NVIDIA_GLX-1.0/include/GL/glext.h gl.h glx.h glxtokens.h
If not:
- Backup the files glext.h gl.h glx.h glxtokens.h located in /usr/include/GL
- Copy the ones located in /usr/share/doc/NVIDIA_GLX-1.0/include/GL/
cp /usr/share/doc/NVIDIA_GLX-1.0/include/GL/* /usr/include/GL
2- Recompile the opengltk package:
In the following $MGL_ROOT refers to the directory where you installed the MGLTools
% cd $MGL_ROOT
% source initPython.csh # this sets up environmental variable needed to the compilation step.
% setenv PYTHONHOME $MGL_ROOT/share:$MGL_ROOT/$MGL_ARCHOSV
% cd $MGL_ROOT/MGLPACKS/opengltk-1.0
% rm -rf build
% rm -rf $MGL_ROOT/i86Linux2/lib/python2.3/opengltk
% $MGL_ROOT/i86Linux2/bin/python2.3 setup.py install
3- Try to run pmv, adt again. Please contact the MGLTools support (mgltools@scripps.edu) if either you don't have a NVIDIA graphics card or if this doesn't work.
Nothing happens when starting PMV, ADT on windows (rel1-2beta1, 08-06-04)
If nothing happens when double clicking on the runPmv or runADT icon please do the following:
  1. Start the python interpreter by double clicking on python.exe in C:\Python23
  2. In the python shell type the following:
    from Pmv.moleculeViewer import MoleculeViewer
    mv = MoleculeViewer()
  3. Send an email to MGLTools support (mgltools@scripps.edu) with the error message
glAsyncMarkerSGIX Error message(rel.1.2beta1, 03-19-04)
The following error message, when trying to run the PMV or ADT on a SGI
...
ImportError:
11031:/usr/freeware/mglTools/rel.1.2beta/sgi4DIRIX6/bin/python2.3: rld:
Fatal Error: unresolvable symbol in
/usr/freeware/mglTools/rel.1.2beta/sgi4DIRIX6/lib/python2.3/site-packages/opengltk/extent/gllib.so: glAsyncMarkerSGIX
hit enter to continue
may mean that the version of the OS running on your machine is too old. The MGLTools have been compiled on a SGI machine running 6.5.13.
To get the OS version running on your machine use the 'uname -R' command.
Where do I get AutoDock and AutoGrid (02-17-04)
AutoDock and AutoGrid are not distributed with the MGLTools. Please go to the 'Obtaining AutoDock' web page for more information on how to download AutoDock and AutoGrid (http://www.scripps.edu/pub/olson-web/people/gmm/autodock/obtaining.html). If you have any questions please contact Garrett Morris (garrett@scripps.edu)
ImportError "The _imaging C module is not installed" (rel.1.2beta1, 02-04-04)
If you get the following error when trying to run ADT/PMV or VIPER version 1.2beta1 on a sgi machine:
packages/PIL/Image.py, line 39, in __getattr__
raise ImportError("The _imaging C module is not installed")
ImportError: The _imaging C module is not installed
hit enter to continue
Exception exceptions.AttributeError: "PhotoImage instance
has no attribute '_PhotoImage__photo'" in PhotoImage.__del__ of > ignored
import _tkinter # If this fails your Python may not be configured for Tk
This might be caused by python2.3 not being able to load the PIL/_imaging library. To check if this is the problem please do the following:
  1. cd to the directory where you installed the MGLTools.
  2. start the python2.3 interpreter coming with the MGLTools. % ./sgi4DIRIX646/bin/python2.3
    >>>import _imaging

    If you get the following error:
    dlopen("/users/chestud/ken318/mglTools/sgi4DIRIX646/lib/python2.3/site-packages/PIL/_imaging.so", 2); Traceback (most recent call last): File "", line 1, in ? ImportError: 14430:python2.3: rld: Fatal Error: Cannot find object libjpeg.so with version 62.0 in any of the filenames /mgl/prog/sgi4DIRIX646/lib/libjpeg.so:/mgl/prog/sgi4DIRIX646//lib/libjpeg.so:/oc/lib/libjpeg.so:/users/chestud/ken318/mglTools/sgi4DIRIX646/lib/libjpeg.so:/users/chestud/ken318/mglTools/sgi4DIRIX646/extralibs/libjpeg.so:/usr/lib32/libjpeg.so:/usr/lib32/internal/libjpeg.so:/lib32/libjpeg.so:/opt/lib32/libjpeg.so:
The problem comes from the fact that libjpeg is not installed on your machine and that PIL requires that library.
You can either:
  • Download the source from ftp://ftp.uu.net/graphics/jpeg/jpegsrc.v6b.tar.gz compile it and install it on your machine. This probably would be the best option.
  • Download libjpeg.tar.gz containing our libjpeg.so for sgi in the directory where you installed the MGLTools.
    Then to install the library:
    - cd to the directory where you installed the MGLTools.
    - gunzip libjpeg.tar.gz
    - tar zf libjpeg.tag
    - in the sgi4DIRIX646/extralibs you should now have libjpeg.so and libjpeg.so.62.0.0
You should now be able to start ADT, PMV or VIPER.

If this doesn't solve your problem please go to http://effbot.org/zone/pil-imaging-not-installed.htm and send me mgltools@scripps.edu the result of each steps.
GLIBC2.3 Problem with linux installation (rel.1.2beta1, 01-13-04)
If you get the following error when trying to run ADT/PMV or VIPER version 1.2beta1 on a linux machine:
import _tkinter # If this fails your Python may not be configured for Tk
ImportError: /lib/libc.so.6: version `GLIBC_2.3' not found (required by $MGL_ROOT/i86Linux2/extralibs/libtk8.4
where $MGL_ROOT is the directory where you installed the MGLTools.

Please do the following:
  1. Download the proper libtk8.4.so and libtcl8.4.so HERE
  2. Backup the old extralibs directory:
  3. mv $MGL_ROOT/i86Linux2/extralibs $MGL_ROOT/i86Linux2/extralibsOld
    where $MGL_ROOT refers to the directory where you installed the MGLTools version 1.2beta1.
  4. Untar the linuxextralibs.tar.gz in the directory where you installed the MGLTools cd $MGL_ROOT
    gunzip linuxextralibs.tar.gz
    tar xf linuxextralibs.tar.gz
  5. You should be now able to run ADT, PMV or VIPER.
Mac OS 10.3 installation problems (rel.1.1, 01-13-2004)
If you are trying to install the MGLTools version 1.1 on a MacOSX version 10.3.x and you get the following error when sourcing install.csh or install.bash
tcsh: python2.0: Command not found.
You need to do the following:
  1. In a terminal shell go to the directory where you installed the MGLTools or ADT
  2. create a symbolic link ppcDarwin7 pointing to ppcDarwin6
  3. ln -s ./ppcDarwin6 ppcDarwin7
  4. Run the install script again
If you get
tcsh: Python2.0: Command not found.
You also need to edit your install.csh or install.bash script and replace Python2.0 by python2.0.
Install.bash error when creating the initPythonBash
The install.py coming with the distribution has a bug when used with bash shell.
Please download the install.py
  1. Replace the install.py located in MglTools/rel.1.1/Tools/ by the one you just downloaded.
  2. Remove the following line from your .bashrc
    source $ROOT/MglTools/rel.1.1/$ARCHOSV/bin/initPythonBash
    where $ROOT is the directory where you install the MGLTOOLS and $ARCHOSV can be i86Linux2, sgi4DIRIX646 or sun4sunOS5
  3. delete the MglTools/rel.1.1/$ARCHOSV/bin/initPythonBash
  4. source the install.bash again
  5. cd MglTools/rel.1.1/

    source ./install.bash
libglut problems running the MGLTools
If you get the following error message when trying to run the MGLTools on Redhat9.0:
Traceback (innermost last):
  File "/usr/local/rel.1.1/i86Linux2/bin//pmv", line 53, in ?
    from Pmv.moleculeViewer import MoleculeViewer
  File
"/usr/local/rel.1.1/share/lib/python1.5/site-packages/Pmv/moleculeViewer.py",
line 17, in ?
    from DejaVu.Geom import Geom
  File
"/usr/local/rel.1.1/share/lib/python1.5/site-packages/DejaVu/__init__.py",
line 50, in ?
    from Viewer import Viewer
  File
"/usr/local/rel.1.1/share/lib/python1.5/site-packages/DejaVu/Viewer.py",
line 14, in ?
    from OpenGL import GL
  File
"/usr/local/rel.1.1/i86Linux2/lib/python1.5/site-packages/OpenGL/GL/__init__.py",
line 5, in ?
    from openglutil_num import *
ImportError: /usr/lib/libglut.so.3: undefined symbol:
glXBindChannelToWindowSGIX
Run PMV from  /usr/local/rel.1.1/share/lib/python1.5/site-packages/Pmv
hit enter to continue

Please download the libglut.tar containing the libglut.so.3 library at: http://www.scripps.edu/~sanner/python/download/misc/libglut.tar
After extracting the tar file in a temp directory copy the libglut.so.3 in /usr/lib.

If you wish to copy this file to another location add the path to the LD_LIBRARY_PATH in order for python to find it.

openglutil_num import error under linux
If you get the following error message when trying to run Adt or pmv under linux:
Traceback (innermost last):
File '', line 1, in ?
File '/mgl/home/sophiec/links/pkgs/share/lib/python1.5/site-packages/OpenGL/GL/__init__.py', line 4, in ? from _opengl_num import *
ImportError: No module named _opengl_num
Try the following:
%python
>>> import sys
>>> sys.platform
'name of the platform'
quit Python
cd $ROOT/rel.1.1beta/share/lib/python1.5/site-packages/OpenGL/shared
Create a link :
ln -s $ROOT/rel.1.1alpha/share/lib/python1.5/site-packages/OpenGL/shared/linux2 'name of the platform'

The name of the platform is the string that returned by sys.platform.

Then try again and it should work !
glutsolidshpere import error when starting PMV, ADT or ViPEr on windows.
If you get the following error message when trying to run ADT, PMV or ViPEr under windows
>importerror: cannot import name glutsolidshpere...
or any error message related to glut.
Try the following:
if you are running windows 98 or XP:
copy C:\PYTHON20\extra\glut32.dll in C:\WINDOWS\SYSTEM32
if you are running windows 2000 or NT:
copy C:\PYTHON20\extra\glut32.dll in C:\WINNT\SYSTEM32


GLX extension not found when running pmv adt or viper after upgrading redhat7.1 to redhat7.3

If you get the following message when trying to run either ADT, Pmv or viper after upgrading your linux box from redhat 7.1 to redhat 7.3:
$ pmv
Run PMV from /bronze/xtal1/carrell/MglTools/rel.1.1beta/share/lib/python1.5/site-packages/Pmv
Traceback (innermost last):
File "/bronze/xtal1/carrell/MglTools/rel.1.1beta/i86Linux2/bin/pmv",
line 55, in ?
libraries=libraries)
File
"/bronze/xtal1/carrell/MglTools/rel.1.1beta/share/lib/python1.5/site-packages/Pmv/moleculeViewer.py",
line 209, in __init__
guiVisible=guiVisible)
File
"/bronze/xtal1/carrell/MglTools/rel.1.1beta/share/lib/python1.5/site-packages/ViewerFramework/VF.py",
line 264, in __init__
root = master)
File
"/bronze/xtal1/carrell/MglTools/rel.1.1beta/share/lib/python1.5/site-packages/ViewerFramework/VFGUI.py",
line 130, in __init__
self.VIEWER = viewerClass(self.vwrCanvas, 1)
File
"/bronze/xtal1/carrell/MglTools/rel.1.1beta/share/lib/python1.5/site-packages/DejaVu/Viewer.py",
line 170, in __init__
c = apply(Viewer.AddCamera, (self, master, screenName), kw)
File
"/bronze/xtal1/carrell/MglTools/rel.1.1beta/share/lib/python1.5/site-packages/DejaVu/Viewer.py",
line 63, in AddCamera
c = apply( Camera, (master, screenName, self, len(self.cameras)), kw)
File
"/bronze/xtal1/carrell/MglTools/rel.1.1beta/share/lib/python1.5/site-packages/DejaVu/Camera.py",
line 519, in __init__
Tkinter.Widget.__init__(self, self.frame, 'togl', cnf, kw)
File
"/bronze/xtal1/carrell/MglTools/rel.1.1beta/share/lib/python1.5/lib-tk/Tkinter.py",
line 1084, in __init__
self.tk.call(
TclError: Togl: X server has no OpenGL GLX extension
hit enter to continue
You need to install the libglx library.
python1.5:Command not found after sourcing install.csh on sgi
Try to create a link ./MglTools/rel.1.1beta/sgi4DIRIX6 pointing to the ./MglTools/rel.1.1beta/sgi4DIRIX646 directory
cd ./MglTools/rel.1.1beta/
ln -s ./sgi4DIRIX646 ./sgi4DIRIX6
...Trace/BPT trap under MACOSX
Users who installed Apple's first release of X11 have this problem. Just upgrade to Apple's latest (0.2 or higher) X11, even though it is in beta release.
http://www.apple.com/macosx/x11/download/
Idlelib problem locale.error,'module' object has no attribute 'error' while running pmv or adt under SGI (rel-1-3alpha2 binary)
Users who installed on SGI,if you get this error,move idlelib to idlelibold and download new idlelib below ,
/homedir/share/lib/python2.3/idlelib/IOBinding.py",line 32, in ?
except (ImportError, locale.error):
AttributeError: 'module' object has no attribute 'error'

click here to download the idlelib tar file

install it in the same location where idlelib was present.
gunzip idlelib-0.9b1.tar.gz
tar xf idlelib-0.9b1.tar
Installtion problem ImportError: No module named time ,error raised when right python is not used by installation script
when i run install script , I get the following error:

Traceback (most recent call last):
File "Tools/install.py", line 11, in ?
import tarfile
File
"homedir/share/lib/python2.3/tarfile.py",
line 50, in ?
import time
ImportError: No module named time

Solution to this problem is,editing install.bash.
In Tools/initPython.bash, there is a line ,
export PATH="$MGL_ROOT/$MGL_ARCHOSV/bin:$PATH"
copy this line in install.bash before 3rd line(i.e,python2.3 Tools/install.py bash $argv) save the file.
Now try running install.bash
Error:When PQR radii is used to compute MSMS surface
The radii used in APBS caluculation often make atoms (in particular hydrogen) to be completely inside other atom which is not good for MSMS.MSMS needs a set of spheres representing atoms for which no sphere is completely inside another sphere.The radii of the PQR sphere often have this situation, read the PQR file but then overwrite the radii with Pmv radii in Pmv.

Edit--> Atoms--> AssignRadii

In the gui check "Overwrite radii" to force replacing the pqr radii and check or uncheck the united checkbutton based on the presence or absence of hydrogens.After doing this you can compute molecular surface
CVS updating Packages
Updating platform independent packages:
To update packages under sys.prefix,
%cd sys.prefix/python2.3/site-packages
%cvs -d:pserver:anonymous@moses.scripps.edu: /export/cvs login
%cvs -z3 -d:pserver:anonymous@moses.scripps.edu:/export/cvs update packname
(for eg:packnames like DejaVu,Pmv,AutoDockTools,Vision etc)

Updating platform dependent packages:
To update packages under sys.exec_prefix you have to cvs checkout packnameDIST as given below,
%cvs -d:pserver:anonymous@moses.scripps.edu: /export/cvs login
%cvs -z3 -d:pserver:anonymous@moses.scripps.edu:/export/cvs co packnameDIST
(for eg: packnames like opengltk,sff,mslib,stride etc)
And build and install them by yourself,
%cd packnameDIST
%python2.3 setup.py build
%python2.3 setup.py install --install-purelib="puredir" --install-platlib="platdir"
puredir="sys.prefix/python2.3/site-packages"
platdir="sys.exec_prefix/python2.3/site-packages"

MAC OS X 10.4 installation problem
Error:python2.3 not found or ImportError: No module named time

1.3alpha2 release is done for MAC OSX 10.3.
Tiger (Mac OS X 10.4) corresponds to a new version of Darwin, version 8 so,
If you look in the "/Applications/MGLTools" directory, you will see directory called "ppcDarwin7". All you need to do is create a symbolic link from the ppcDarwin7 directory to a new directory called ppcDarwin8.

%ln -s /Applications/MGLTools/ppcDarwin7 /Applications/MGLTools/ ppcDarwin8

create one more link,

%ln -s /Applications/MGLTools/MGLPACKS/Applications/MGLTools/ppcDarwin7 /Applications/MGLTools/MGLPACKS/Applications/MGLTools/ppcDarwin8

Now source install.bash
Unable to adjust a number of gridpoints and option of choosing rotatable bonds by picking does not work.
Updating mglutil/gui/BasiWidgtes/Tk/thumbwheel.py will solve your problems.
Click here to download thumbwheel.py file

%gunzip thumbwheel.tar.gz
%tar xf thumbwheel.tar

OR
cvs update thumbwheel.py

III-AVAILABLE PATCHES

Go to our download site (http://www.scripps.edu/~sanner/python/packager.html to see the patches available for the version of the mgl tools you are using. If you don't see a patch for the problem you are experiencing please send a bug report. Click here to see how to submit a bug report.