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Author Topic: open_file <./Atomic.g.pdb> failed: No such file or directory  (Read 3126 times)

Offline mauricio esguerra

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open_file <./Atomic.g.pdb> failed: No such file or directory
« on: October 24, 2012, 05:48:15 am »
Hi Xiang-Jun,

I have just downloaded the latest version of 3DNA dated October 16 for Intel Mac.

I have OS X 10.8.2 (Lion) on a MacBookPro 9.2.

When running find_pair i get the following output:

Code: [Select]
find_pair 1ehz.pdb 1ehz.inp                       ──(Wed,Oct24)─┘

handling file <1ehz.pdb>
uncommon residue 2MG   10  on chain A [#10] assigned to: g
uncommon residue H2U   16  on chain A [#16] assigned to: u
uncommon residue H2U   17  on chain A [#17] assigned to: u
uncommon residue M2G   26  on chain A [#26] assigned to: g
uncommon residue OMC   32  on chain A [#32] assigned to: c
uncommon residue OMG   34  on chain A [#34] assigned to: g
uncommon residue YYG   37  on chain A [#37] assigned to: g
uncommon residue PSU   39  on chain A [#39] assigned to: P
uncommon residue 5MC   40  on chain A [#40] assigned to: c
uncommon residue 7MG   46  on chain A [#46] assigned to: g
uncommon residue 5MC   49  on chain A [#49] assigned to: c
uncommon residue 5MU   54  on chain A [#54] assigned to: u
uncommon residue PSU   55  on chain A [#55] assigned to: P
uncommon residue 1MA   58  on chain A [#58] assigned to: a
open_file <./Atomic.g.pdb> failed: No such file or directory

I thought this was a problem related to not including config in the path and added $X3DNA/config to the path, unsuccessfully.

So 1ehz.inp, with the base-pairing results is not produced as output.

Other commands such as, get_part, work well.

Thanks once more,

Mauricio

Offline xiangjun

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Re: open_file <./Atomic.g.pdb> failed: No such file or directory
« Reply #1 on: October 24, 2012, 11:11:33 am »
Hi Mauricio,

Thanks for your report. I can reproduce the 'problem'; it has nothing to do with including $X3DNA/config in the environment settings.

The error message:
Code: [Select]
open_file <./Atomic.g.pdb> failed: No such file or directorymeans 3DNA (find_pair) is trying to locate the file in your current working directory (CWD), instead of the default system setting $X3DNA/config where the file Atomic.g.pdb is available, among other Atomic*.pdb files.

If file Atomic_A.pdb exists in your CWD, 3DNA assumes all other Atomic*.pdb files there as well. That's normally true if you run, e.g.:
Code: [Select]
x3dna_utils cp_std bdna
For your case, you must have Atomic_A.pdb and possibly several other canonical base Atomic_[CGTU].pdb files in your CWD, but not the modified version (in lower case, prefixed with a dot instead of underscore). So simply run the following command in you CWD will do the trick:

Code: [Select]
cp -f $X3DNA/config/Atomic.*.pdb .
Alternatively, you can delete all the Atomic*pdb files from your CWD, and find_pair will work as expected:

Code: [Select]
rm -f Atomic*.pdb
find_pair 1ehz.pdb stdout

Please have a try and report back how it goes.

I may consider to refine 3DNA to check for each Atomic*.pdb file separately, but that would complicate the code. You are actually the first to notice this 'limitation'. Practically, knowing what's happening behind the scene, you can easily work around it, as suggested above.

HTH,

Xiang-Jun

« Last Edit: October 24, 2012, 01:12:35 pm by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline mauricio esguerra

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Re: open_file <./Atomic.g.pdb> failed: No such file or directory
« Reply #2 on: October 24, 2012, 03:52:30 pm »
Hi Xiang-Jun,

That was exactly the problem.  :)
Thanks
I deleted the canonical bases Atomic_[CGTU].pdb, and it works with no problem.
Or also by just running the new:
Code: [Select]

x3dna_utils cp_std BDNA
Beforehand.


Mauricio

Offline xiangjun

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Re: open_file <./Atomic.g.pdb> failed: No such file or directory
« Reply #3 on: October 26, 2012, 01:46:07 pm »
As a follow up, as of 3DNA v2.1 2012oct26, your initial problem has been solved. Now you can have for example only Atomic_A.pdb in your current working directory, and 3DNA will use that file; for the Atomic*.pdb files not found in the current directory, 3DNA will use the default in $X3DNA/config. Overall, this revision allows 3DNA users greater flexibility in choosing the standard base-reference-frame files for analysis and rebuilding.

Xiang-Jun
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

 

Created and maintained by Dr. Xiang-Jun Lu[律祥俊]· Supported by the NIH grant R01GM096889 · Dr. Lu is currently a member of the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University. The project is in collabration with the Olson Laborarory at Rutgers where 3DNA got started.