[MMTK] pb with nma overlap

Nathalie Reuter nathalie.reuter at bccs.uib.no
Sun Jul 9 14:00:25 CEST 2006


Hi,

Konrad is right, webnma uses the Calpha force-field and we calculate 
squared overlaps.
Otherwise, you should check that the number of modes you calculate is 
the same as in webnma if you wish to compare overlaps obtained with both 
MMTK and webnma....

Please do not hesitate to contact us at contact at bioinfo.no if you have 
more questions.

Best regards,
Nathalie Reuter

hinsen at cnrs-orleans.fr wrote:

> On 06.07.2006, at 14:36, Gaelle Debret wrote:
>
>> I use NMA overlap to find which modes better describe transition  
>> between two conformations of a protein. Results I get are strange  
>> and different from those obtained with webnm@ :
>
>
> ...
>
>> Here is the script I use :
>> (NB: structures have already been fitted with profit)
>>
>> from MMTK import *
>> from MMTK.Proteins import Protein
>> from MMTK.ForceFields import DeformationForceField
>
>
> If I remember correctly, WebNMA uses CalphaForceField instead of  
> DeformationForceField. For C-alpha models, CalphaForceField gives  
> better results than DeformationForceField, so I suggest you do the same.
>
>> for i in range(len(modes)):
>>     m = modes[i]
>>     o = m.dotProduct(vec) / \
>>     sqrt(m.dotProduct(m)) / \
>>     sqrt(vec.dotProduct(vec))
>>     overlap.append(abs(o))
>
>
> It's also worth checking if WebNMA overlaps are the same as yours -  
> they might be the squares, as it is the squares that add up to one.
>
> Otherwise your script looks fine!
>
> Konrad.
> -- 
> ---------------------------------------------------------------------
> Konrad Hinsen
> Centre de Biophysique Moléculaire, CNRS Orléans
> Synchrotron Soleil - Division Expériences
> Saint Aubin - BP 48
> 91192 Gif sur Yvette Cedex, France
> Tel. +33-1 69 35 97 15
> E-Mail: hinsen at cnrs-orleans.fr
> ---------------------------------------------------------------------
>
>
>
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