[gmx-users] Average Structure outputted from g_rmsf

[Erik Marklund]

If you want a structure representative for your trajectory, rather  
than the average, I suggest using g_cluster to cluster your frames  
and take the cluster center from the largest cluster.

/Erik

20 sep 2007 kl. 17.18 skrev Arneh Babakhani:

> Great, got it, thanks for the suggestion, appreciate the input,
>
> Arneh
>
>> Arneh Babakhani wrote:
>>> Hi,
>>>
>>> When outputting the average structure from g_rmsf using the -ox  
>>> option,
>>> some of my residues in that average structure pdb have awkward
>>> coordinates
>>> (when you visualize it in VMD, it looks very strange).  Sometimes  
>>> atoms
>>> are placed very close to each other, with really bad bond angles.  I
>>> suppose this is a facet of the averaging scheme in g_rmsf.
>>
>> Yes. If you ask for an not-necessarily-physical result, you  
>> usually get
>> one... see http://wiki.gromacs.org/index.php/Average_Structure
>>
>>> Is there a way to correct for this, and to obtain an
>>> averagestructure.pdb
>>> that looks more reasonable coordinates and bond angles? (I ask b/ 
>>> c I'd
>>> like to use this averagestructure.pdb in further studies, such as
>>> docking.)
>>
>> "Correcting for" is not quite the right phrasing here... :-) It's
>> already correct according to the algorithm you used... it's not the
>> algorithm's fault you actually wanted a physical structure. One  
>> approach
>> you can use is to select the structure with the smallest RMSD from  
>> the
>> average, kind of like selecting the median as the central measure  
>> rather
>> than the mean of a numerical data set. Or you can take the  
>> nonphysical
>> structure and do EM on it... One needs to apply brain, of course!
>>
>> Mark
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>
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_______________________________________________
Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,	75124 Uppsala, Sweden
phone:	+46 18 471 4537		fax: +46 18 511 755
erikm at xray.bmc.uu.se	http://xray.bmc.uu.se/molbiophys