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Questions and answers => General discussions (Q&As) => Topic started by: mfb on June 25, 2010, 10:55:37 am

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Title: Suggestions
Post by: mfb on June 25, 2010, 10:55:37 am
Could find_pair be modified to recognize explicit ribonucleotide abreviations (RG,RA,RC,RU,RG5,...,RC3,...)?  These are used by AMBER's ptraj and have to be substituted with single-letter base desigations before find_pair recognizes them.

Is it intended that when you enter "find_pair -h" the previous set of files from a find_pair analysis are erased?

Mike Bruist
Title: Re: Suggestions
Post by: xiangjun on June 25, 2010, 08:15:19 pm
Quote from: "Mike Bruist"
Could find_pair be modified to recognize explicit ribonucleotide abreviations (RG,RA,RC,RU,RG5,...,RC3,...)? These are used by AMBER's ptraj and have to be substituted with single-letter base desigations before find_pair recognizes them.
I am not familiar with AMBER, but I guess RG is for G, RA is for A etc. So they fall into the FAQ entry How to handle modified (uncommon) bases? (http://http://3dna.rutgers.edu/x3dna/faqs#baselist). Specifically, add the following into file baselist.dat:
Code: [Select]
RA    A
RG    G
RC    C
RU    U
RG5   G
RC3   CPlease verify.

Quote from: "Mike Bruist"
Is it intended that when you enter "find_pair -h" the previous set of files from a find_pair analysis are erased?
Not necessarily "intended", but just the way it is: the file clean-up operation is performed before parsing the command line options. You are the first to raise this question; it indeed makes more logical sense to just show help information with the "-h" option and I will consider change this behavior in future version of 3DNA.

Thanks for making suggestions; please keep coming -- the more, the better.

Xiang-Jun
Title: Re: Suggestions
Post by: mfb on June 26, 2010, 06:48:44 pm
Your suggestion works very well.  I have added all of the deoxyribose, ribose and terminus specific nucleotide desigantions.  I can now read the AMBER ptraj pdb files without running them through a tailor.

Thanks

Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids

Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University