Netiquette · Download · News · Gallery · Homepage · DSSR · Web-DSSR · DSSR Manual · Reproduce DSSR · DSSR-Jmol · DSSR-PyMOL · Web-SNAP

Author Topic: Problems using 'Analyze'  (Read 59 times)

Offline Ellaliv

  • regular
  • *
  • Posts: 1
    • View Profile
Problems using 'Analyze'
« on: December 23, 2017, 06:09:55 am »
Hello,

I've downloaded and installed 3DNA and "played" with it a while to understand the basic commands and functions, using the manual given in the forum. I didn't encounter any problems.
In the past days the 'analyze' command has not been working as it used to for me.
I thought it was something wrong with my PDB input files but when I tried it on one of the PDB's from the examples directory I got the same error-

......Processing structure #1: <..\examples\analyze_rebuild\355d.pdb>......
cannot read strand information

What can I do to fix it and make it work again?

Thanks a lot in advance,
Ella.

Offline xiangjun

  • Administrator
  • regular
  • *****
  • Posts: 1232
    • View Profile
    • 3DNA homepage
Re: Problems using 'Analyze'
« Reply #1 on: December 23, 2017, 09:42:01 am »
Hi Ellia,

You need to run "find_pair" first to prepare pairing info for "analyze" to work out the parameters, as shown in the command-line help message:

Code: [Select]
INPUT
        given a PDB file "sample.pdb", the input to analyze can be most
        conveniently generated with the utility program find_pair:
        find_pair sample.pdb sample.inp
        an explicit input file (including 'stdin') must be specified.
EXAMPLES
        analyze sample.inp
        analyze sample1.inp sample2.inp sample3.inp
        find_pair sample.pdb stdout | analyze stdin
        find_pair sample.pdb stdout | analyze -c stdin

In other words, this is a two-step process. Using 355d as an example, you need to do the following:

Code: [Select]
find_pair 355d.pdb 355d.inp
analyze 355d.inp

HTH,

Xiang-Jun
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

 

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.