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Problems using fiber in version 2.1 -- 2012
mauricio esguerra:
Dear Xiang-Jun,
First of all, thanks for 3DNA V2.1.
The new website and forum are looking great.
I just downloaded and set-up 3DNA V 2.1. and I'm running into the following error when running:
fiber -a ADNA.pdb
open_file <str01/A.rpt> failed: No such file or directory
I have checked my environment variables and they are right.
Thanks once more,
Mauricio
xiangjun:
--- Quote ---open_file <str01/A.rpt> failed: No such file or directory
--- End quote ---
Weird -- that certainly should not happen! What do the following output?
--- Code: ---echo $X3DNA
ls $X3DNA/fiber
--- End code ---
I've just tried on my machine. As the screen output shows below, the program is working as expected:
--- Code: ---tmp [510] fiber -a ADNA.pdb
Fiber data in directory: /Users/xiangjun/X3DNA/x3dna-v2.1beta/fiber/
...... /Users/xiangjun/X3DNA/x3dna-v2.1beta/config/ ......
...... reading file: misc_3dna.par ......
Structure #1; Twist: 32.7 (degrees); Rise: 2.548 (Angstrom)
Input your base sequence with only ACGT:
1. From a data file (complete sequence)
2. From keyboard (enter only the repeating sequence)
Your choice (1 or 2, Dft: 2):
Repeating unit (Dft: A):
Repeating unit: A
Number of repeats (Dft: 10):
--- End code ---
Xiang-Jun
mauricio esguerra:
Hi Xiang-Jun,
Here's the output I get from the commands you suggest:
--- Code: ---echo $3DNA
/Users/esguerra/Software/X3DNA2.1
--- End code ---
--- Code: ---ls $X3DNA/fiber
data str05 str11 str17 str23 str29 str35 str41 str47 str53
README str06 str12 str18 str24 str30 str36 str42 str48 str54
str01 str07 str13 str19 str25 str31 str37 str43 str49 str55
str02 str08 str14 str20 str26 str32 str38 str44 str50 str901
str03 str09 str15 str21 str27 str33 str39 str45 str51
str04 str10 str16 str22 str28 str34 str40 str46 str52
--- End code ---
I have fedora 14 64bit version.
xiangjun:
Hi Mauricio,
Thanks for providing further information. I'll dig the issue further to see if I can reproduce the problem in machines I have access to, and then get back to you ...
Best regards,
Xiang-Jun
xiangjun:
Hi Mauricio,
You may have helped trace a subtle bug that only shows up in specific OS (here, fedora 14 64bit). Download the following two modified versions of fiber, named fiber-1 and fiber-2. Copy them into $X3DNA/bin, and then run the following, and report back verbatim what you see from screen (as I did in my first reply).
--- Code: ---fiber-1 -a -seq="aattgg" fa-1.pdb
fiber-2 -a -seq="aattgg" fa-2.pdb
--- End code ---
If I have fixed the bug, then the second version (fiber-2) should run successfully, and fiber-1 should provide further information about the source of the bug.
Please let me know how it goes.
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.
