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Author Topic: side_view.dat rotate_mol NO rotation  (Read 5243 times)

Offline ilibarra

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side_view.dat rotate_mol NO rotation
« on: June 29, 2012, 06:38:49 pm »
Hello,

I am using the following command (as detailed in the Recipe 01 of the Nature 3DNA paper)

"rotate_mol -r=side_view.dat propeller_mg.alc propeller_sv.alc"

side_view.dat has the following text written, in two lines

"
by rotation y –30
by rotation x 20
"

I receive as output:
"wrong <by rotation> format"

I have checked many things (tabs, spaces number) with the same results. Also writing "byrotation" or just "rotation" as keyword gives me an output file but with no rotations. I obtain the message "NO rotation applied to the structure", and the final of the recipe (.fig) is not rotated as it is explained in expected results.

I would like to know if there is something that I am doing wrong with this file. I have everything else until that step working properly

Cheers,
Ignacio
« Last Edit: June 29, 2012, 06:41:53 pm by ilibarra »

Offline ilibarra

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Re: side_view.dat rotate_mol NO rotation
« Reply #1 on: June 29, 2012, 06:58:23 pm »
Using the Recipe 02, I see that the command works. I will check in details the recipe 01 to see what is different. In the meantime, I leave the input files that I am using for that particular command

Offline ilibarra

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Re: side_view.dat rotate_mol NO rotation
« Reply #2 on: June 29, 2012, 07:11:29 pm »
Okay.

With side_view.dat file it seems to be working. My problem is solved  :D.

Anyway, I can't recognize differences between both side_view.dat files. In this file, I have typed all the characters, while in the first one I copied the texts from the .pdf paper. I think that is the reason of the difference during execution.

Cheers,
Ignacio

Offline xiangjun

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Re: side_view.dat rotate_mol NO rotation
« Reply #3 on: June 29, 2012, 07:27:30 pm »
Hi Ignacio,

I am glad to hear that your problem has been solved  :).

The reason: what you copied from .pdf file has hidden characters in it. On my MacBook Air running OS X 10.7.4 (Lion), I have the following:
Quote
more side_view.dat
by rotation y <96>30
by rotation x 20

Notice the extra characters <96>? Program vi shows the same info, while emacs displays \226. I do not know what the chars mean exactly, but 'rotate_mol' certainly do not like them, and outputs sensible error message:
Quote
wrong <by rotation> format

Thanks for using 3DNA. Keeping asking if anything is unclear or needs to be improved -- it's an ever-learning experience for all of us; through the process, we make 3DNA a better tool to serve the community.

HTH,

Xiang-Jun
« Last Edit: June 29, 2012, 07:35:02 pm by xiangjun »

 

Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.