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

Author Topic: Analysis of PDB file  (Read 4701 times)

Offline souviksur

  • with-posts
  • *
  • Posts: 8
    • View Profile
Analysis of PDB file
« on: April 07, 2012, 03:35:08 am »
Hello Every one,

I tried to run "manalyze" using my pdb, but it was running, can you please suggest is there any problem in my pdb file, and I also want to generate the .out file. Please suggest me, I am attaching the pdb file.

regards & thanks,
SOUVIK

Offline xiangjun

  • Administrator
  • with-posts
  • *****
  • Posts: 1524
    • View Profile
    • 3DNA homepage
Re: Analysis of PDB file
« Reply #1 on: April 07, 2012, 09:21:16 am »
Hi,

The simple Perl script manalyze was introduced around v1.5 for the analysis of "multiple" structures. Over the years, I've not been aware of its usage: your question is the first one. As of v2.1beta, I am migrating from Perl to Ruby as the scripting language for 3DNA. Now manalyze and most other not widely used Perl scripts are moved out the $X3DNA/bin/ directory into $X3DNA/perl_scripts/ -- they are obsolete, but kept there for the record.

As of 3DNA v2.1, the Ruby script "x3dna_ensemble" should be used for the analysis of NMR ensembles or MD simulation trajectories. Type -h for detailed info, and run the examples to get familiar with its usage/functionality.

Your attached PDB file contains only one model, so you can use the find_pair/analyze combination to calculate 3DNA parameters. Note, however, your structure has poor geometry, as shown in the image below. As a rule, one should always perform "sanity" check to ensure sensible results.

HTH,

Xiang-Jun
« Last Edit: April 08, 2012, 08:49:39 am by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

* Click "NOTIFY" to receive email notifications
* Original Poster, please provide a summary
* DSSR 2.0 has superseded the 3DNA v2.4 suite

 

Created and maintained by Dr. Xiang-Jun Lu [律祥俊], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.