VMD-L Mailing List

From: Wang Yi (dexterwy_at_gmail.com)
Date: Fri Aug 10 2012 - 09:26:39 CDT

Flavio,

"measure fit" (http://www.ks.uiuc.edu/Research/vmd/vmd-1.9/ug/node135.html) and "move by" can help you do the alignment.

Your atom selection selected all the C-alpha atoms as a whole. That's why you get one column of numbers. If you need numbers of each C-alpha atom, you need to select them separately.
___________________________

Yi (Yves) Wang
Duke University

On 2012-8-10, at 上午10:17, flavio seixas wrote:

> Hi Axel and Yves,
> Thank you for your suggestion.
>
> My intention is to observe which residues are more flexible within the last 1000ps of dynamics (equilibrated stage).
>
> To do that, I am trying to create a *.dat file in order to generate a plot of B-factor (or rmsf) at Y coordinates against residue number (at X coordinates).
>
> Searching vmd-list, i found this script:
>
> set outfile [open rmsf.dat w]
> set sel [atomselect top "name CA"]
> puts $outfile "[measure rmsf $sel first 4021 last 5020 step 1]"
> close $outfile
>
> My questions are:
>
> 1) The output of the above script displays a single column with 100 numbers. My protein has 233 residues, and I was expecting 233 numbers in the output file. Obviously I assume that the output file does not contain my desired information! What is missing?
>
> 2) I am not an expert in tcl script, but I wonder if I need to align the protein with the trajectory first? If it is correct, how is the command line(s) that I must put in the script?
>
> 3) Or, may I firstly align the protein using "RMSD Trajectory Tool" and then run the script?
>
> Thanks for any help.
>
> Flavio
>
>
>
>
>
> --- On Thu, 8/9/12, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
>
>> From: Axel Kohlmeyer <akohlmey_at_gmail.com>
>> Subject: Re: vmd-l: B-factor plugin
>> To: "Wang Yi" <dexterwy_at_gmail.com>
>> Cc: "flavio seixas" <oivalf_nix_at_yahoo.com>, "VMD List" <vmd-l_at_ks.uiuc.edu>
>> Date: Thursday, August 9, 2012, 9:50 PM
>> On Thu, Aug 9, 2012 at 10:00 PM, Wang
>> Yi <dexterwy_at_gmail.com>
>> wrote:
>>> set allatoms [atomselect top all]
>>> $allatoms get beta
>>>
>>> You need to read the online manual for VMD keywords.
>>> By the way, why extracting B-factors from trajectory?
>> Is there any thing
>>> during your simulation will change the B-factor?
>>
>> i suppose the question would work the other way around:
>> provided you do an MD of a crystal, can you measure
>> the mobility of atoms around their centers and translate
>> that into an approximation of the beta factor?
>>
>> i don't know of anything that would be a direct
>> translation,
>> but the calculation of RMSF values with "measure rmsf"
>> might be a starting point.
>>
>> cheers,
>> axel.
>>
>>>
>>> ___________________________
>>>
>>> Yi (Yves) Wang
>>> Duke University
>>>
>>>
>>>
>>>
>>>
>>> On 2012-8-9, at 下午3:13, flavio seixas wrote:
>>>
>>> Hi all,
>>>
>>> Anyone knows a tcl script to extract the B-factors
>> values of protein
>>> residues (or atoms) from namd trajectory file?
>>>
>>> I´ll be thankful for any help.
>>>
>>> regards,
>>>
>>> flavio
>>>
>>>
>>>
>>
>>
>>
>> --
>> Dr. Axel Kohlmeyer akohlmey_at_gmail.com
>> http://goo.gl/1wk0
>> International Centre for Theoretical Physics, Trieste.
>> Italy.
>>
>>