[gmx-users] CRY-ED question

[Bert de Groot]

Ruben Martinez Buey wrote:
>> Hi all,
> 
> I would like to compare my MD/ED simulations with a CRY-ED analysis of 
> my protein, but I only have two crystal structures. Can I correctly 
> deduce the essential dynamics from only two experimental conformations?
> 

Only partially. Obviously, from a PCA in this case you'll get only one (meaningful) eigenvector:
the difference vector between the two conformations.
But this can still be used in e.g. a comparison to a simulation.

Bert

____________________________________________________________________________
Dr. Bert de Groot

Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
37077 Goettingen, Germany

tel: +49-551-2012308, fax: +49-551-2012302

email: bgroot at gwdg.de
http://www.mpibpc.gwdg.de/abteilungen/073
____________________________________________________________________________