Hi German - 

I’m not sure I follow exactly what you’re asking, but `align` does its superimposition based on sequence alignment, which isn’t really meaningful for small molecule ligands.  I would suggest using `fit`, `super`, or `cealign` instead, which all use just the coordinates, although it’s possible these also won’t work.

For a more sophisticated approach, maybe check out LigAlign, which comes with a tutorial: http://www.pymolwiki.org/index.php/LigAlign.

Cheers,
Jared

--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/






On Aug 5, 2014, at 10:04 AM, German Erlenkamp <Erlenkamp@uni-duesseldorf.de> wrote:

Hi all,

I have two sets of ligands, the first are the crystal structures, the second
one are the same compounds, but aligned by a flexible ligand alignment, where
I used one of the crystal structures as a template. Unfortunately the
coordinates of the templates changed during the alignment.
Now I want to calculate the RMSD-values between these structures, and for this
I want to superpose the group of aligned ligands to the template ligand.
I started with 'align Aligned_1, Start_1' but after this command, all atoms of
'Aligned_1' vanished and I can only represent this as a sphere. This will be
Ok for me, because the RMSD between 'Aligned_1' and 'Start_1' is 0.
But after this I want to move 'Aligned_2' the same way as I moved 'Aligned_1'.
I thought 'matrix_copy Alinged_1, Start_1' should do the job, but after this
all atoms of 'Aligned_2' are gone. I still have this object, but nothing more.

My questions are: Am I using the correct commands for this task, or not? And, if
I am using the right commands, what is going wrong? And - for the case my way
is not correct - what would be the proper way to solve my problem?

Thanks in advance,

German
--
German Erlenkamp

Computational Pharmaceutical Chemistry
and Molecular Bioinformatics

Heinrich-Heine-Universität Düsseldorf
Institut für Pharmazeutische und Medizinische Chemie
Universitätsstr. 1
40225 Düsseldorf
Germany

Tel:    +49-211-81-13829
E-Mail: erlenkamp@uni-duesseldorf.de
URL:    http://cpclab.uni-duesseldorf.de


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