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Questions and answers => General discussions (Q&As) => Topic started by: Ellaliv on December 23, 2017, 06:09:55 am

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Title: Problems using 'Analyze'
Post by: Ellaliv 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.
Title: Re: Problems using 'Analyze'
Post by: xiangjun 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
Title: Re: Problems using 'Analyze'
Post by: Ellaliv on February 13, 2018, 07:30:08 am
Thank you!

Ella

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.