Content-Type: multipart/alternative; boundary="------------090203050700000706040703" --------------090203050700000706040703 Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit hi Michael et al., I'm still unable to visualize DX-formatted electrostatics maps in PyMOL, as described in my earlier email (attached). I've tried various scenarios to get this to work, including the following: (1) fresh, clean install of the pymol-0.95-1.rh90.py22 RPM, downloading the various electrostatics.py, dx.py, etc. modules from your website and then using the load_dx() function with DX maps already calculated in a standalone APBS run... (2) rebuilding PyMOL 0.95 from CVS version, incorporating the new and modified source such as ObjectMap.{h,c}, PMGApp.py, etc. exactly as described on your website (the recompiled PyMOL works fine)... (3) both of the above steps with either a pre-calculated dx map or for one generated on-the-fly in PyMOL via the apbs_tools wizard, for both a small protein and a large one Based on the ~60-sec delay and increased processor usage after issuing a PyMOL command like 'load_dx("some_file.dx","mapa")', I think the DX file is actually being read. However, the process invariably dies with the following error stream: > PyMOL>load_dx some_file.dx > Traceback (most recent call last): > File "modules/pymol/parser.py", line 139, in parse > result=apply(kw[nest][0],args[nest],kw_args[nest]) > File "/usr/lib/python2.2/site-packages/pymol/modules/pymol/dx.py", > line 1034, in load_dx > importing.load_object(importing.loadable.DX, thing, mapName) > AttributeError: class loadable has no attribute 'DX' The "line 139" parser.py error sometimes shows up as line 255, and this error behavior also results if I perform more explicit function calls such as 'load_dx("some_file.dx","mapa")'. If anyone has any ideas about solving this problem, please let me know.... Thanks, Cameron PS. This is all on a Red Hat 9 Linux PC utilizing the following Python packages: > CHEMCCA35:NFkB[8] rpm -qa | egrep -i python > python-2.2.2-26 > python-optik-1.4-2 > rpm-python-4.2-1 > python-devel-2.2.2-26 > gnome-python2-canvas-1.99.14-5 > gnome-python2-gtkhtml2-1.99.14-5 > gnome-python2-bonobo-1.99.14-5 > python-numeric-devel-22.0-2mdk > libxml2-python-2.5.4-3.rh9 > gnome-python2-1.99.14-5 > python-numeric-22.0-2mdk === Michael George Lerner wrote (on 05/13/2004 09:55 AM): === >Hi, > >My code should work again. The parsing errors were probably caused by the >fact that my code was out of date with respect to the current CVS version >of PyMOL. Please let me know if it doesn't work! > >Thanks, > >-michael > > > >>Has anyone had luck with loading DX format electrostatic potential maps >>that were generated by APBS? I tried to use the electrostatics wizard and >>load_dx function created by Michael Lerner >>(http://www-personal.umich.edu/~mlerner/Pymol/) but I get parsing errors >>when I try to load a map calculated by standalone APBS. The maps are very >>large (small grid spacing and a very large molecule) - could that be the >>problem? Please help. >> >>Ken >> >> >> >>------------------------------------------------------- >>This SF.Net email is sponsored by Sleepycat Software >>Learn developer strategies Cisco, Motorola, Ericsson & Lucent use to deliver >>higher performing products faster, at low TCO. >>http://www.sleepycat.com/telcomwpreg.php?From=osdnemail3 >>_______________________________________________ >>PyMOL-users mailing list >>PyMOL-users@lists.sourceforge.net >>https://lists.sourceforge.net/lists/listinfo/pymol-users >> >> >> > > >------------------------------------------------------- >This SF.Net email is sponsored by: SourceForge.net Broadband >Sign-up now for SourceForge Broadband and get the fastest >6.0/768 connection for only $19.95/mo for the first 3 months! >http://ads.osdn.com/?ad_id=2562&alloc_id=6184&op=click >_______________________________________________ >PyMOL-users mailing list >PyMOL-users@lists.sourceforge.net >https://lists.sourceforge.net/lists/listinfo/pymol-users > > > -- Cameron Mura UCSD --------------090203050700000706040703 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit hi Michael et al.,

I'm still unable to visualize DX-formatted electrostatics maps in PyMOL, as described in my earlier email (attached).  I've tried various scenarios to get this to work, including the following:

(1) fresh, clean install of the pymol-0.95-1.rh90.py22 RPM, downloading the various electrostatics.py, dx.py, etc. modules from your website and then using the load_dx() function with DX maps already calculated in a standalone APBS run...

(2) rebuilding PyMOL 0.95 from CVS version, incorporating the new and modified source such as ObjectMap.{h,c}, PMGApp.py, etc. exactly as described on your website (the recompiled PyMOL works fine)...

(3) both of the above steps with either a pre-calculated dx map or for one generated on-the-fly in PyMOL via the apbs_tools wizard, for both a small protein and a large one

Based on the ~60-sec delay and increased processor usage after issuing a PyMOL command like 'load_dx("some_file.dx","mapa")', I think the DX file is actually being read.  However, the process invariably dies with the following error stream:

PyMOL>load_dx some_file.dx
Traceback (most recent call last):
  File "modules/pymol/parser.py", line 139, in parse
    result=apply(kw[nest][0],args[nest],kw_args[nest])
  File "/usr/lib/python2.2/site-packages/pymol/modules/pymol/dx.py", line 1034, in load_dx
    importing.load_object(importing.loadable.DX, thing, mapName)
AttributeError: class loadable has no attribute 'DX'
The "line 139" parser.py error sometimes shows up as line 255, and this error behavior also results if I perform more explicit function calls such as 'load_dx("some_file.dx","mapa")'. 

If anyone has any ideas about solving this problem, please let me know....

Thanks,

        Cameron


PS.  This is all on a Red Hat 9 Linux PC utilizing the following Python packages:
CHEMCCA35:NFkB[8] rpm -qa | egrep -i python
python-2.2.2-26
python-optik-1.4-2
rpm-python-4.2-1
python-devel-2.2.2-26
gnome-python2-canvas-1.99.14-5
gnome-python2-gtkhtml2-1.99.14-5
gnome-python2-bonobo-1.99.14-5
python-numeric-devel-22.0-2mdk
libxml2-python-2.5.4-3.rh9
gnome-python2-1.99.14-5
python-numeric-22.0-2mdk


=== Michael George Lerner wrote (on 05/13/2004 09:55 AM): ===
Hi,

My code should work again.  The parsing errors were probably caused by the
fact that my code was out of date with respect to the current CVS version
of PyMOL.  Please let me know if it doesn't work!

Thanks,

-michael

  
Has anyone had luck with loading DX format electrostatic potential maps
that were generated by APBS? I tried to use the electrostatics wizard and
load_dx function created by Michael Lerner
(http://www-personal.umich.edu/~mlerner/Pymol/) but I get parsing errors
when I try to load a map calculated by standalone APBS.  The maps are very
large (small grid spacing and a very large molecule) - could that be the
problem? Please help.

Ken



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-- 
Cameron Mura
UCSD
--------------090203050700000706040703--