From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Fri Aug 10 2012 - 12:48:17 CDT

Actually, I think "measure rmsf" returns a per-atom list. So if you only get 100 numbers, you should try to figure out why only 100 atoms are named CA, apparently. You'll have to be a little more willing to play around to figure out what's up, rather than just trying to find bits of random code snippets here and there and hoping they work.

On Aug 10, 2012, at 9:26 AM, Wang Yi wrote:

> 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.
>>>
>>>
>