Suggestions

[mfb]

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

[xiangjun]

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?. Specifically, add the following into file baselist.dat:

Code: [Select]

RA    A
RG    G
RC    C
RU    U
RG5   G
RC3   CPlease verify.

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

[mfb]

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