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Re: rmsf-residue.str
lennart #356 01/11/08 03:30 PM
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Thank you! I fixed the problem. It was Gly.

Re: rmsf-residue.str
lennart #357 05/16/08 08:05 AM
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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

Re: rmsf-residue.str
joseph #358 05/16/08 08:58 AM
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lennart Online Content OP
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coor dyna puts the fluctuations into wmain (and the averages of x,y,z in x,y,z)


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Re: rmsf-residue.str
lennart #359 05/16/08 09:09 AM
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Thank you for your quick answer.

Re: rmsf-residue.str
joseph #29246 02/02/12 06:36 PM
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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

Re: rmsf-residue.str
karan #29253 02/02/12 10:06 PM
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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
Re: rmsf-residue.str
lennart #29286 02/07/12 10:53 PM
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Thank you
I got it.

karan

Re: rmsf-residue.str
lennart #34259 08/11/14 07:38 AM
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Thanks,
I want to know whatis the function of "stream rmsf-residue.str" ? rmsf-residue.str is the input file.

Re: rmsf-residue.str
lennart #34262 08/11/14 02:16 PM
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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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