Netiquette · Download · News · Gallery · Homepage · DSSR Manual · G-quadruplexes · DSSR-Jmol · DSSR-PyMOL · DSSR Licensing · Video Overview· RNA Covers

Author Topic: 'find_pair' and 'analyze' with pdb files of unbound base pairs  (Read 7524 times)

Offline ry54451

  • non-commercial
  • with-posts
  • *
  • Posts: 16
    • View Profile
Good afternoon.
I'm needing to generate ref_frame and/or .par files from a series of pdb files sent to me by a collaborator. These pdb files are from MD work (from 'ptraj'). Upon inspection of the pdb file, they lack CONECT information at the bottom and the final letter code column on the far right.

However, I have been able to generate my desired files from most of these pdb files. There are a few, however, that the number of base pairs and the number of bases do not match. I'm expecting 336 base pairs and I only get data for 335, 334, or 332. PYMOL use shows that these trajectories do not have base pairing, some bases ninety-degrees from its complement. However, my 3DNA files do not give me 672 base info, only 335*2, 334*2, or 332*2.

Here's my question: Is there a way using 3DNA that even if the bases are not bound, I should get values for them so that every 'find_pair' and 'analyze' output file is made up of 336*2 bases? I've attached two files in particular that are of frustration.

Offline xiangjun

  • Administrator
  • with-posts
  • *****
  • Posts: 1642
    • View Profile
    • 3DNA homepage
Re: 'find_pair' and 'analyze' with pdb files of unbound base pairs
« Reply #1 on: April 23, 2018, 10:44:48 pm »
The issues you experienced with "find_pair" have been reported many times (searching the Forum should give you some hints). The source of the missing or mis-assigned pairs is due to the irregularity of the structure under consideration. Some of the 'assumed' pairs are simply too distorted to be taken as a pair. Using your attached 'plus2.MD.traj.09.pdb' as an example, DA86 and DT587 certainly do not form a pair in any (canonical) sense -- see the attached fragment with DA86 and DT587 embedded.

In such cases, if you insist that nucleotides such as DA86 and DT587 should be taken as a pair, you can manually edit the output from "find_pair" as desired. You can think of the scenario where "find_pair" does not exist, and you have to prepare an input file with pairing info by hand.

The "analyze" program will follow strictly the pairing info as provided in the input file.



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