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Welcome => Bug reports => Topic started by: mauricio esguerra on February 22, 2012, 08:03:52 am

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Title: Problems using fiber in version 2.1 -- 2012
Post by: mauricio esguerra on February 22, 2012, 08:03:52 am
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
Title: Re: Problems using fiber in version 2.1 -- 2012
Post by: xiangjun on February 22, 2012, 08:12:27 am
Quote
open_file <str01/A.rpt> failed: No such file or directory
Weird -- that certainly should not happen! What do the following output?

Code: [Select]
echo $X3DNA
ls $X3DNA/fiber

I've just tried on my machine. As the screen output shows below, the program is working as expected:
Code: [Select]
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):

Xiang-Jun
Title: Re: Problems using fiber in version 2.1 -- 2012
Post by: mauricio esguerra on February 22, 2012, 08:32:45 am
Hi Xiang-Jun,

Here's the output I get from the commands you suggest:

Code: [Select]
echo $3DNA
/Users/esguerra/Software/X3DNA2.1

Code: [Select]
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

I have fedora 14 64bit version.
Title: Re: Problems using fiber in version 2.1 -- 2012
Post by: xiangjun on February 22, 2012, 10:29:55 am
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
Title: Re: Problems using fiber in version 2.1 -- 2012
Post by: xiangjun on February 22, 2012, 08:18:22 pm
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 (http://x3dna.bio.columbia.edu/downloads/miscs/fiber-1) and fiber-2 (http://x3dna.bio.columbia.edu/downloads/miscs/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: [Select]
fiber-1 -a -seq="aattgg" fa-1.pdb
fiber-2 -a -seq="aattgg" fa-2.pdb
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
Title: Re: Problems using fiber in version 2.1 -- 2012
Post by: mauricio esguerra on February 23, 2012, 03:54:34 am
Hi Xiang-Jun,

Thanks.
Problem fixed with fiber-2  :-)

Here's the verbatim copy of running both commands:

Code: [Select]
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

And for the working version I get the  fa-2.pdb output as expected.

Code: [Select]
=>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)

Thank you very much,

Mauricio
Title: Re: Problems using fiber in version 2.1 -- 2012
Post by: xiangjun on February 23, 2012, 03:42:32 pm
Hi Mauricio,

Quote
Problem fixed with fiber-2

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: [Select]
fiber -s -r -seq="aaauuuggc" rna_model.pdb
Thanks again for your help in fixing this bug!

Xiang-Jun

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