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Questions and answers => General discussions (Q&As) => Topic started by: bala on April 09, 2007, 10:53:23 am

Title: extracting best representative from NMR
Post by: bala on April 09, 2007, 10:53:23 am: Hello,

I want to extract the best structure from a NMR ensemble. When i run the command as below,

ex_str -nmrb qd_nmr.pdb best.pdb

I got the following message
------------------------------------------------------------------------------------------
No best representative conformer assigned: set to 1
Model selected #1
------------------------------------------------------------------------------------------

I think the program selects model 1 by default if it cant find a best representative. Kindly write 1) what may be wrong 2) What is the criteria based on which this program selects the best representative.

thanks in advance,
Bala
Title:
Post by: xiangjun on April 09, 2007, 11:38:36 pm: Hi,

The following is taken directly from the C-source code comment:

Code: [Select]
/* Best representative NMR conformer, use #1 if not assigned in REMARK 210. * Typical cases: * BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL [pdb28sp] * BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 [pdb2bj2] * BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 3 [pdb2lef] * BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 5 [pdb3php] * * For structures pdb1qby, pdb1djd & pdb1bjd, the REMARK 210 says the * best representative conformer is #12 or #13, but the data file * actually does not has that model. Reset inum to 1 for such cases. */
HTH,

Xiang-Jun
Title:
Post by: bala on April 13, 2007, 01:17:47 am: Hi, Xiang-Jun

Thank You. But I am not getting how i should extract it or why i am getting the message "NO BEST REPRESENTATIVE ASSIGNED".

Bala
Title:
Post by: xiangjun on April 13, 2007, 10:02:55 pm: Hi,

Please check carefully the PDB file format (http://http://www.rcsb.org/pdb/static.do?p=file_formats/pdb/index.html). As I understand it, REMARK 210 contains info about which one is the best representative structure in an NMR ensemble, which is used by "ex_str". If no such info is available, or the PDB is somehow inconsistent for certain entry, the first structure is extracted. That's exactly what my previous message is about. It also contains some example PDB entries that you can verify. These were the samples I tested when adding such functionality in "ex_str".

A better understanding of the PDB format would certainly help. In any event, you can always check the PDB file itself to see what's in there -- it is a text file anyway.

Hope this clarifies the issue a little bit.

Xiang-Jun