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Checked in Greg Cipriano's change in Rev. 904.
2009-12-22 16:57:09 UTC by yhuang01
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yhuang01 committed revision 904 to the PDB2PQR SVN repository, changing 2 files.
2009-12-21 16:46:10 UTC by yhuang01
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yhuang01 committed revision 903 to the PDB2PQR SVN repository, changing 2 files.
2009-12-18 22:05:07 UTC by yhuang01
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So says Greg Cipriano:
Hello. I believe I found a bug in pdb2pqr:
When running it on the pdb 1B8A, it seems to get into an infinite loop in analyzeConnectivity() in utilities.py
As far as I can tell, it's possible that there are cycles in the map, in which case, the same key gets added to the list over and over.
Here's my fix (note that the only change is in the indentation of the...
2009-12-16 15:45:41 UTC by yhuang01
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"TER" added to the end of every chain as of Rev. 902.
2009-12-04 15:35:21 UTC by yhuang01
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yhuang01 committed revision 902 to the PDB2PQR SVN repository, changing 5 files.
2009-12-03 16:17:02 UTC by yhuang01
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So says Danny in pdb2pqr-users mailing list:
'But after each chain of a PDB file there is a line that
begins with or that only contains "TER", indicating the end of the
chain. When using pdb2pqr this lines are not printed in the output and i
need them 'cause i'll do energy calculations.'
It will be good to have an option (e.g., --ter) to keep the TER records.
2009-12-02 15:22:27 UTC by yhuang01
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yhuang01 committed revision 901 to the PDB2PQR SVN repository, changing 1 files.
2009-11-24 21:01:08 UTC by yhuang01
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yhuang01 committed revision 900 to the PDB2PQR SVN repository, changing 1 files.
2009-11-23 19:32:16 UTC by yhuang01
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For example, one line saying "APBS calculation on x.pqr with default values provided by PDB2PQR:", then a "Submit" button. Below the Submit button there is another line saying "If you prefer to run APBS with your own configurations, click here: ", then another button "Custom-defined parameters". Only when this button is clicked do we see those selections, parameters, etc.
2009-11-20 21:46:09 UTC by yhuang01
