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Questions and answers => General discussions (Q&As) => Topic started by: yangxi on February 04, 2009, 10:04:26 pm

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Title: unknown step values
Post by: yangxi on February 04, 2009, 10:04:26 pm

Hi,all

  I'm currently dealing with nucleosome structures.My problem is some dimer steps in the.out file have no values

E.G. dimer steps like "21 CC/GG"  

    step            Shift     Slide      Rise       Tilt        Roll     Twist

  20 TC/GA     -0.04      0.59      2.61      7.59     12.27     18.30
  21 CC/GG      ----         ----      ----        ----       ----       ----
  22 CC/GG      1.22      0.53      1.78     24.42     3.72     32.21

I want to know the reason, and how can I handle step values like this?


Yangxi

Title: Re: unknown step values
Post by: xiangjun on February 05, 2009, 12:48:48 am

Things would have been much clearer if you have provided a reproducible example, as requested.

Lacking that info, I would guess there are some missing bps as identified directly by 'find_pair'.

You might also try '-c' option with 'analyze'.

HTH,

Xiang-Jun

Title: Re: unknown step values
Post by: yangxi on February 05, 2009, 10:10:51 pm

Hi, Xiang-jun

I do as you suggest,trying '-c' option with 'analyze', and it really works. Now all the dimer steps have values.I also compare current values with previous ones and find that they remain the same (except the previously unknown ones, of course)  
Thanks a lot for your reply!


sincerely
yangxi

Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids

Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University