VMD-L Mailing List

From: Wang Yi (dexterwy_at_gmail.com)
Date: Fri Aug 10 2012 - 12:53:48 CDT

Oh, it's RMSF, not RMSD. Right...
___________________________

Yi (Yves) Wang
Duke University

On 2012-8-10, at 下午1:48, JC Gumbart wrote:

> 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.
>>>>
>>>>
>>
>