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Author Topic: Unable to generate .out file by using analyze command  (Read 3432 times)

Offline Anju Sharma

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Unable to generate .out file by using analyze command
« on: May 16, 2007, 01:57:52 am »
Hello

Please ignore the queries posted by me earlier to this. After reading similar prblms in d forum nd solutions provided to them i am able to convert my .pdb file to .inp file

But again m struck at next step, while trying to analyze my DNA seq using command:
# analyze atc.inp

no main parameter output file is generated (.out). where is the fault please do let me know.

files that are being generated are:
atc.inp                 bp_order.dat                   col_helices.scr                ref_frames.dat
auxiliary.par        bp_step.par                    hel_regions.pdb               stacking.pdb
bestpairs.pdb      cf_7methods.par            hstacking.pdb                
bp_helical.par      col_chains.scr               poc_haxis.r3d
Anju Sharma,
Project Fellow,
NIT, Hamirpur,
Himachal Pradesh (India)

Offline xiangjun

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« Reply #1 on: May 16, 2007, 10:34:04 pm »
Thanks for using 3DNA! I am glad that you solved your two previous problems by browsing the forum -- that's exactly why the forum was created in the fist place.

While 3DNA is not a point-and-click package, setting it up should be straightforward and requires minimum effort, i.e., by setting the environment variable X3DNA and put $X3DNA/bin into your command line search path. To make life even easier for inexperienced Linux/Unix users, I have created a Perl script (setup_x3dna) to detect the SHELL and set up these two items automatically -- it will be included in the coming new release.

Now come to your question. The main output file name is derived from your PDB file by changing to (or appending) the ".out" extension. It will be in the same directory as your PDB structure file. Have a look at .inp file -- the 2nd line will tell you where the .out resides. Now I notice a bit of inconsistency here -- all other files are written in the current working directory (CWD), but this .out file is not. Maybe it is more logical to put the .out file in the CWD as well. I will make this change into the new release of 3DNA.

HTH,

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], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.