VMD-L Mailing List

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Mon Jun 30 2014 - 02:48:45 CDT

 

Von: sunyeping [mailto:sunyeping_at_aliyun.com]
Gesendet: Montag, 30. Juni 2014 09:11
An: vmd-l
Cc: norman.geist; mbelkin
Betreff: RE：vmd-l: select all residues in a molecule

 

Thank you, Dr. Belkin and Dr. Geist.

Acutually I mean to select all the ca atoms and calculate their individual rmsf.

 

set cas [atomselect top „protein and name CA“]

set rmsf [measure rmsf $cas]

puts $rmsf

$cas delete

 

I don't know the "measure rmsf" command is proper for the purpose. In my opinion, to calcualte rmsf, we should get an average structure of the trajectory and align each frame to this average structure and then calculate rmsf of the selected atoms.

 

Alignment might be needed. See VMD Main->Extension->Analysis->RMSD Trajectory Tool

 

I don't know if the "measure rmsf" command calculates a an average structure, but obviously it doesn't do the alignment. Could anyone give me a complete script to calculate rmsf?

 

Average structure over whole trajectories might be garbage, be careful. See “avgpos”

 

Thanks.

Yeping

------------------------------------------------------------------
发件人：Maxim Belkin <mbelkin_at_ks.uiuc.edu>
发送时间：2014年6月29日(星期日) 12:58
收件人：孙业平 <sunyeping_at_aliyun.com>
抄　送：vmd-l <vmd-l_at_ks.uiuc.edu>
主　题：Re: vmd-l: select all residues in a molecule

Hi Yeping,

It is not clear what you want to do (select residues in VMD or run some analysis script). If you want to run a per-residue analysis, you can do something like:

 

set all [atomselect top all]

set residues [lsort -unique [$all get residue]]

$all delete

 

foreach residue $residues {

    ... your per-residue analysis code goes here ..

}

 

 

 

 

On Jun 28, 2014, at 9:45 PM, sunyeping <sunyeping_at_aliyun.com> wrote:

 

Dear all,

 

Could you tell me how to select all residues in a molecule in VMD so that I can operate them one by one?

 

Yeping Sun

 

 

  

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