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#356 - 01/11/08 10:30 AM Re: rmsf-residue.str [Re: lennart]
irina Offline
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Registered: 03/14/06
Posts: 2
Thank you! I fixed the problem. It was Gly.

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#357 - 05/16/08 04:05 AM Re: rmsf-residue.str [Re: lennart]
joseph Offline
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Registered: 02/25/08
Posts: 3
Dear Lennart,

I watched the script carefully as well as the scalar doc but I don't understand something.

What does the WMAIN variable contain?
The Scalar doc says it's the main coordinate weight, yet I don't understand how the rmsf is calculated using these weights.

Is there something I'm missing in the script or the doc? What do WMAIN, X, Y and Z variables contain?

Thank you for your script

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#358 - 05/16/08 04:58 AM Re: rmsf-residue.str [Re: joseph]
lennart Online   content

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Registered: 09/25/03
Posts: 4741
Loc: ~ 59N, 15E
coor dyna puts the fluctuations into wmain (and the averages of x,y,z in x,y,z)
_________________________
Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

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#359 - 05/16/08 05:09 AM Re: rmsf-residue.str [Re: lennart]
joseph Offline
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Registered: 02/25/08
Posts: 3
Thank you for your quick answer.

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#29246 - 02/02/12 01:36 PM Re: rmsf-residue.str [Re: joseph]
karan Offline
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Registered: 07/02/11
Posts: 66
Hi Prof. Nilsson,
I went through your script rmsf-residue.str . Inside the loop you have selected only CA and CB atom types. so I could not understand how it gives the rmsf for the whole backbone and sidechain.

Karan

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#29253 - 02/02/12 05:06 PM Re: rmsf-residue.str [Re: karan]
lennart Online   content

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Registered: 09/25/03
Posts: 4741
Loc: ~ 59N, 15E
The averaging is done for all the relevant atoms, no mention of CA or CB there. CA and CB are selected just for the output (hint: one of them is a backbone atom, the other a sidechain atom).
_________________________
Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

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#29286 - 02/07/12 05:53 PM Re: rmsf-residue.str [Re: lennart]
karan Offline
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Registered: 07/02/11
Posts: 66
Thank you
I got it.

karan

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#34259 - 08/11/14 03:38 AM Re: rmsf-residue.str [Re: lennart]
Yong Mao Offline
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Registered: 08/04/13
Posts: 41
Thanks,
I want to know whatis the function of "stream rmsf-residue.str" ? rmsf-residue.str is the input file.

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#34262 - 08/11/14 10:16 AM Re: rmsf-residue.str [Re: lennart]
lennart Online   content

Forum Member

Registered: 09/25/03
Posts: 4741
Loc: ~ 59N, 15E
did you look at the contents of rmsf-residue.str? If you wonder about the stream command it is described in doc/miscom.doc
_________________________
Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

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