3DNA Forum

Questions and answers => MD simulations => Topic started by: souviksur on April 17, 2012, 10:04:31 am

Netiquette · Download · News · Gallery · Homepage · DSSR · Web-DSSR · DSSR Manual · G-quadruplexes · DSSR-Jmol · DSSR-PyMOL

Title: Analysis of PDB file:query
Post by: souviksur on April 17, 2012, 10:04:31 am
Dear all,

I am using 3DNA for analysis of data, but I found the output files were not proper, are the pdb files not appropriate or something else, please suggest me, I am attaching two pdb files with this mail, please find those in attachments and suggest me.

Souvik 
Title: Re: Analysis of PDB file:query
Post by: xiangjun on April 17, 2012, 11:04:14 am
Quote
I found the output files were not proper
What do you mean "not proper"? What would you expect the output to be? I tried your attached PDB files, and found 3DNA is doing its job.

Xiang-Jun
Title: Re: Analysis of PDB file:query
Post by: souviksur on April 18, 2012, 12:36:09 am
there are 15 no.s of base pairs in each pdb, but I found in one case 9 and in another case 10 out of 15 pairs.
Title: Re: Analysis of PDB file:query
Post by: xiangjun on April 18, 2012, 09:33:32 am
Okay, let's check step-by-step how find_pair is working for your two attached structures.

In my experience, whenever a user suspects the output from find_pair as "improper", it is more than likely that the structure itself is "weird" -- if in doubt, always check your structure using a molecular graphics visualization program (Jmol/PyMOL/RasMol etc). Of course, I am consistently on the watch to refine find_pair, especially for the edge cases.

Xiang-Jun
Title: Re: Analysis of PDB file:query
Post by: souviksur on April 19, 2012, 08:44:40 am
I modified the pds and now got 14 nos. of base pairs out of 15 ( I found there was some spacing problem in pdbs), thanks a lot, I am attaching the files.
Title: Re: Analysis of PDB file:query
Post by: xiangjun on April 19, 2012, 12:18:08 pm
Quote
now got 14 nos. of base pairs out of 15
There must be something special with the missing base pair. If you visualize the structure graphically using Jmol/PyMOL etc, I believe you won't take it as a "base pair" either. Checking the details why it is "missed" by find_pair would be an interesting exercise for those who want to understand 3DNA better.

Xiang-Jun

Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.