3DNA Forum

Questions and answers => General discussions (Q&As) => Topic started by: ijimenez on February 13, 2013, 11:23:40 am

Title: pdf files to use with spdbv and Curves+
Post by: ijimenez on February 13, 2013, 11:23:40 am: I have used w3DNA to generate pdb files of dsDNA 157bp long but I haven't been able to use those files with spdbv or Curves+. I was wondering if there is anything I can do to make the pdf files work with these software.
Title: Re: pdf files to use with spdbv and Curves+
Post by: xiangjun on February 13, 2013, 12:11:28 pm: It certainly would help if you've included specifics as to how w3DNA-generated PDB files cannot be used with spdbv or Curves+. I guess the issue is due to PDB v2.x atom names used by w3DNA which is still not updated to v2.1 yet. In the current 3DNA release, PDB v3.x atom names are used by default, which should make "spdbv or Curves+" happy.

Please download and install 3DNA v2.1, and report back if that helps. See also the thread "Missing atoms (http://forum.x3dna.org/web-3dna/missing-atoms)".

HTH,

Xiang-Jun