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Author Topic: analysis outputs  (Read 2181 times)

Offline ghzheng

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analysis outputs
« on: December 28, 2008, 09:26:40 pm »
Hi Xiangjun,

I begin to write documents on the webpage, such as description of output files, tutorials, etc.

Could you please advise which of following output files one would be interested to checking out?


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1WD1.inp  auxiliary.par   bp_order.dat     col_chains.scr   hstacking.pdb
1WD1.out  bestpairs.pdb   bp_step.par      col_helices.scr  ref_frames.dat
1WD1.pdb  bp_helical.par  cf_7methods.par  hel_regions.pdb  stacking.pdb
1WD1.outs
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And could you please write a description for each of the output files, including purpose, description for each column if possible, criteria, etc? I don't really understand all of these. Later on, I will place your descriptions right under the output files on the web and in the tutorial page.

Thanks for your help. It would be nice if you can have them ready as soon as possible.

Guohui

Offline xiangjun

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Re: analysis outputs
« Reply #1 on: December 28, 2008, 10:30:15 pm »
Hi Guohui,

Code: [Select]
1WD1.inp auxiliary.par bp_order.dat col_chains.scr hstacking.pdb
1WD1.out bestpairs.pdb bp_step.par col_helices.scr ref_frames.dat
1WD1.pdb bp_helical.par cf_7methods.par hel_regions.pdb stacking.pdb
1WD1.outs
A brief description of nine relevant files for double helical structure analysis is at URL: http://rutchem.rutgers.edu/~xiangjun/3DNA/examples.html

You do/should not need to put too much information in w3DNA -- that would cause more confusions than clarify issues. There are many auxiliary files generated with 3DNA, depending on which program or option is used. In my experience, I have not received that many questions regarding the various non-out files. For simplicity, only the .out file should be linked, at least at this stage. Key parameters are presented in tables, as you have already done.

Given below is a brief description of the files in your list, but not mentioned in the 3DNA examples link:
[ol:19tgzkup][li:19tgzkup]bp_order.dat -- an intermediate file related to base-pair and helical region finding algorithm.[/li:19tgzkup]
[li:19tgzkup]chains.scr -- rasmol script to color each chain separately.[/li:19tgzkup]
[li:19tgzkup]bestpairs.pdb -- multiple base-pairs coordinates in PDB format, each expressed in its reference frame, as identified in double helical regions; corresponding to bps in the .inp file from 'find_pair'.[/li:19tgzkup]
[li:19tgzkup]col_helices.scr -- rasmol script to color each helical region separately.[/li:19tgzkup]
[li:19tgzkup]hel_regions.pdb -- multiple helical regions in PDB format, as identified by 'find_pair'.[/li:19tgzkup]
[li:19tgzkup]1WD1.outs -- similar to .out file, but corresponding to 'find_pair -s' option. As we discussed before, we should always run 'find_pair -s ... | analyze' to collect backbone torsion angles and sugar conformational parameters in tables.[/li:19tgzkup][/ol:19tgzkup]

For w3DNA, the major focus should be a robust and efficient web-interface to commonly used 3DNA functionality, targeted at the general audience. There are so many technical details that are hard to explain to non-experts, to some extent, even to the experts in nucleic acid structures. Along this line, I feel it would be helpful to separate 'Fiber model' as a main category and set it as default of w3DNA.

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]· 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.