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

Author Topic: Baselist.dat  (Read 6416 times)

Offline auffinger

  • with-posts
  • *
  • Posts: 108
    • View Profile
Baselist.dat
« on: April 08, 2008, 11:45:41 am »
Dear Xiang-Jun,

We recently experienced a pb with the file baselist.dat. This file contains all the name exceptions that are contained in a PDB file. If a residue name for a modified base is not present in this file, the entire nucleic acid structure is skipped by 3DNA. Hence, we added residue names by hand to this file (see attached baselist1.dat) and it worked  up to a certain point. Lately, we tried with the (attached) file baselist2.dat and the program crashed giving a "too many arguments" message. Are there too many residue names in this file or did something else go wrong ?

Thanks for your answer,

and kind regards,

Pascal
pascal auffinger
ibmc-cnrs
15, rue rené descartes
67084 strasbourg cedex
france

web sites:
http://www-ibmc.u-strasbg.fr/arn/Westho ... er_pub.HTM
http://www-ibmc.u-

Offline xiangjun

  • Administrator
  • with-posts
  • *****
  • Posts: 1640
    • View Profile
    • 3DNA homepage
Re: Baselist.dat
« Reply #1 on: April 09, 2008, 10:01:47 pm »
Hi Pascal,

Glad you noticed the size limitation of base list. In v1.5, which is the one currently being used, the upper limit was set to 512, and that explains the differences with the two baselist.dat files your attached. Back in around year 2000, I thought 512 would be large enough when I processed all the NDB entries. Indeed you are the first user to uncover this limit!

As far as so many unrecognized base residues as in your case, it is normal and intended. In principle, one could auto-detect the uncommon residues to keep 3DNA running without bothering with the baselist.dat file. However, as a design guideline, I have put several "check-points" in the 3DNA pipeline so users have more control, and can know what's going on. You could write a utility program to facilitate your job. If you do go that way, you might want to contribute back your work so others can benefit from your effort.

In the coming release of 3DNA v2.0, I have an up to date baselist.dat file for all the NDB entries up to March 2008, and of course, the 512 upper limit is gone. Sorry, No specified release date yet!

HTH,

Xiang-Jun

Offline auffinger

  • with-posts
  • *
  • Posts: 108
    • View Profile
Re: Baselist.dat
« Reply #2 on: April 10, 2008, 12:16:27 pm »
Thanks Xiang-Jun,

Of course, we could wait for the new release but, in the mean time, do you think you could manage to send us a linux version without this size limitation ?

Pascal
pascal auffinger
ibmc-cnrs
15, rue rené descartes
67084 strasbourg cedex
france

web sites:
http://www-ibmc.u-strasbg.fr/arn/Westho ... er_pub.HTM
http://www-ibmc.u-

 

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.