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Problems using fiber in version 2.1 -- 2012
mauricio esguerra:
Hi Xiang-Jun,
Thanks.
Problem fixed with fiber-2 :-)
Here's the verbatim copy of running both commands:
--- Code: ---fiber-1 -a -seq="aattgg" fa-1.pdb
Fiber data in directory: /Users/esguerra/Software/X3DNA2.1/fiber/
...... /Users/esguerra/Software/X3DNA2.1/config/ ......
...... reading file: misc_3dna.par ......
Structure #1; Twist: 32.7 (degrees); Rise: 2.548 (Angstrom)
fiber dir: str01/
structure: str01/A.rpt
open_file <str01/A.rpt> failed: No such file or directory
--- End code ---
And for the working version I get the fa-2.pdb output as expected.
--- Code: ---=>fiber-2 -a -seq="aattgg" fa-2.pdb
Fiber data in directory: /Users/esguerra/Software/X3DNA2.1/fiber/
...... /Users/esguerra/Software/X3DNA2.1/config/ ......
...... reading file: misc_3dna.par ......
Structure #1; Twist: 32.7 (degrees); Rise: 2.548 (Angstrom)
--- End code ---
Thank you very much,
Mauricio
xiangjun:
Hi Mauricio,
--- Quote ---Problem fixed with fiber-2
--- End quote ---
Thanks for your feedback -- I am glad to hear that the problem has been solved. You are so great :) in helping me identify and fix this very subtle bug that can be traced back to v1.5! The tricky part is that it normally does not show up -- not on CentOS 5, Scientific Linux 6, Debian 5, Debian 6, Ubuntu 10.10 and OpenSuSE 11.3. Even if I compile 3DNA directly on Fedora 14 64bit, everything runs smoothly.
This is an excellent example to show that a software program can never be claimed bug-free, and why user's feedback is always appreciated in my support of 3DNA. Please do not be shy to report back any issue you experience that can potentially help made 3DNA better.
As a side note with the fiber application, it's an old dog with new tricks in 3DAN v2.1. For example, to generate a single stranded RNA with sequence "aaauuuggc", it can now be conveniently done as below:
--- Code: ---fiber -s -r -seq="aaauuuggc" rna_model.pdb
--- End code ---
Thanks again for your help in fixing this bug!
Xiang-Jun
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Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.
