1RQW: Difference between revisions

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=== automatic structure solution using Auto-Rickshaw (http://www.embl-hamburg.de/Auto-Rickshaw/) ===
=== automatic structure solution using Auto-Rickshaw (http://www.embl-hamburg.de/Auto-Rickshaw/) ===


This uses Santosh Panjikar's script DPS2AR.csh:
This uses Santosh Panjikar's script DPS2AR.csh version XX:
  DPS2AR.csh datafile1 thau-peak-I.mtz keeps world ver completeversion nres 207 nsm 20 masu 1 meth SAD SG P41212 \
  DPS2AR.csh datafile1 thau-peak-I.mtz keeps world ver completeversion nres 207 nsm 20 masu 1 meth SAD SG P41212 \
             email kay.diederichs@uni-konstanz.de sequencefile 1rqw.seq
             email kay.diederichs@uni-konstanz.de sequencefile 1rqw.seq
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  FSYVLDKPTT VTCPGSSNYR VTFCPTA
  FSYVLDKPTT VTCPGSSNYR VTFCPTA


The result of this is a model that only lacks residues 1, 82, 83, 207, and which has a "core RMS" (from coot's SSM superpose) of 0.14 Å against 1rqw (which is a 1.05 Å structure).
The result of this (see logfile at http://webapps.embl-hamburg.de/lresult/421317/LOG/viewlog/result.html) is a model that only lacks residues 1, 82, 83, 207, and which has a "core RMS" (from coot's SSM superpose) of 0.14 Å against 1rqw (which is a 1.05 Å structure).


It couldn't be simpler than that. Thanks, Santosh!
It couldn't be simpler than that. Thanks, Santosh!
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=== automatic structure solution using Auto-Rickshaw (http://www.embl-hamburg.de/Auto-Rickshaw/) ===
=== automatic structure solution using Auto-Rickshaw (http://www.embl-hamburg.de/Auto-Rickshaw/) ===


In the same way as with the peak data, Auto-Rickshaw was started. The structure could be solved but the process was laborious - take a look at the [[1rqw_arp_warp_log|Arp/Warp logfile]]! The final model lacks residues 1, 85, 205, 206, 207 and the "core RMS" of SSM superpose, against 1rqw, is 0.15 Å (better than I would expect).
In the same way as with the peak data, Auto-Rickshaw was started. Please see the Auto-Rickshaw logfile at http://webapps.embl-hamburg.de/lresult/542521/LOG/viewlog/result.html (it will be kept on the server).  


It should be noted that the structure can ''not'' be solved when searching for 15 or 28 sites - rather, 20 appears to be the magic number.
The structure could be solved but Arp/Warp had a difficult start - take a look at the [[1rqw_arp_warp_log|Arp/Warp logfile]]! The final model lacks residues 1, 85, 205, 206, 207 and the "core RMS" of SSM superpose, against 1rqw, is 0.15 Å (better than I would expect).
 
It should also be noted that the structure can ''not'' be solved when searching for 15 or 28 sites - rather, 20 appears to be the magic number.


Once again, great job, Santosh (and of course those people who wrote the programs that Auto-Rickshaw uses)!
Once again, great job, Santosh (and of course those people who wrote the programs that Auto-Rickshaw uses)!
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