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[modeller_usage] complete_pdb.py


Now the scripts are working. Log files are being generated successfully.

I am trying to use complete_pdb.py to add missing atoms to my pdbfile.

Here is the command i am using

mod9v5 complete_pdb.py (ChainA.pdb)

The following log file is being generated

MODELLER 9v5, 2008/10/07, r6498


                     Copyright(c) 1989-2008 Andrej Sali
                            All Rights Reserved

                             Written by A. Sali
                               with help from
           B. Webb, M.S. Madhusudhan, M-Y. Shen, M.A. Marti-Renom,
                N. Eswar, F. Alber, M. Topf, B. Oliva, A. Fiser,
                    R. Sanchez, B. Yerkovich, A. Badretdinov,
                      F. Melo, J.P. Overington, E. Feyfant
                 University of California, San Francisco, USA
                    Rockefeller University, New York, USA
                      Harvard University, Cambridge, USA
                   Imperial Cancer Research Fund, London, UK
              Birkbeck College, University of London, London, UK

Kind, OS, HostName, Kernel, Processor: 4, Windows Vista build 6001 Service Pack 1, EINSTEIN, SMP, x86 Family 6 Model 14 Stepping 12

Date and time of compilation         : 2008/10/07 16:19:49
MODELLER executable type             : i386-w32
Job starting time (YY/MM/DD HH:MM:SS): 2009/01/08 00:07:19

Total CPU time [seconds]                                 :       0.22

I have been using the following link http://salilab.org/modeller/manual/node403.html

Am i missing something.

Please help me how to use it.


On Wed, Jan 7, 2009 at 4:28 PM, Modeller Caretaker <">> wrote:
Sarath Chandra wrote:
> I am Sarath and i am an intern in Max Planck Institute of Biophysical
> Chemistry Gottingen. I am working on Molecular Dynamic simulations of
> Photosystem II a membrane protein which has 17 subunits and all of these
> subunits has all together 200 atoms missing.
> I am trying to use complete_pdb.py  and i am facing an error "import
> site failed;"
> Any suggestions on a the problem and how to use the script

See #2 at http://salilab.org/modeller/release.html#issues

The script should still run fine, despite that warning.

       Ben Webb, Modeller Caretaker
">             http://www.salilab.org/modeller/
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage