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Author Topic: Rebuilding part  (Read 3932 times)

Offline ghzheng

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Rebuilding part
« on: December 01, 2008, 01:26:22 pm »
Hi Xiangjun,

I am working on the Rebuilding part as you suggested:

[hr:oont1n9o][/hr:oont1n9o][li:oont1n9o]Rebuilding: put fiber model-building part first since this is the most-useful part to the general community; add sequence-specific building funcationality next: do not forget with sugar-phosphate backbone in various conformation, and the simplified Calladine-Drew style in Alchemy format. The download page should also be linked to Jmol/RasMol for online view.[/li:oont1n9o][hr:oont1n9o][/hr:oont1n9o]

Now, I have a question here:

For the fiber model-building part, I am trying to use the program "fiber", am I right? This program requires parameter inputs from the screen/keyboard, to provide the sequence information. However, if we want to execute it from the web, this could be a trouble, since we won't be able to type it those information. Is it possible that you can adjust the program a little bit such that all parameters (maybe data files) could be included in just a command line, such as "fiber -s sequence.txt -a fiber_a.pdb"? Or do you have any other ways to solve this? Can I use "rebuild"  function as an alternative? How? Thanks.

Best,
Guohui

Offline xiangjun

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Re: Rebuilding part
« Reply #1 on: December 01, 2008, 01:45:18 pm »
Quote from: "guohui"
For the fiber model-building part, I am trying to use the program "fiber", am I right? This program requires parameter inputs from the screen/keyboard, to provide the sequence information. However, if we want to execute it from the web, this could be a trouble, since we won't be able to type it those information. Is it possible that you can adjust the program a little bit such that all parameters (maybe data files) could be included in just a command line, such as "fiber -s sequence.txt -a fiber_a.pdb"?

Right. User needs to first select a model, which can be provided via a HTML form selection list. Depending on the model selected, the sequence could be fixed, where user just needs to select the number of repeating unit (form input field with type="text"), or user need to input a sequence. The sequence could be from a file which is to be uploaded to the server, or through textarea tag. All such info is collected from a web-based form, and then passed to fiber. The program needs not to be changed, by taking advantage of Unix file indirection, e.g., '<' or '>'. Please play around in command-line first to get it right before you are able to implemented a web-interface to it.

Quote from: "guohui"
Or do you have any other ways to solve this? Can I use "rebuild" function as an alternative? How?

The rebuild program is for a different purpose, thus it is not a substitute for fiber. Let's get fiber functionality done first: itself would be of great value to a large audience.

HTH,

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

Offline ghzheng

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Re: Rebuilding part
« Reply #2 on: December 01, 2008, 04:16:46 pm »
Hi Xiangjun,

Thanks for your prompt response.

I did the exact thing as you mentioned. I allow users to type in the sequence (by textarea) or use the repeating unit. Multiple choices are provided to users through a web form.

I did try the indirection '<' before asking you, but I didn't work it out. But now, I got it:

>> fiber -b fiber_b.pdb < par.txt > log

[hr:1jxh7qj1][/hr:1jxh7qj1]
par.txt:

1
seq.txt
[hr:1jxh7qj1][/hr:1jxh7qj1]
seq.txt:

AAACCCGGGTTTAAA
[hr:1jxh7qj1][/hr:1jxh7qj1]

The par.txt file tells the fiber program the input options (line 1: 1 for sequence file), and the sequence file (line 2: seq.txt). It works very well. Thanks.

Guohui

 

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.