Hi Jared,
I've also tried the 'super' command, but this gives me only this error
message: super aligned_1, cryst_1
ExecutiveAlign: invalid selections for alignment.
And I'll have a closer look at LigAlign, but on the first sight it seems, that
I'll need the binding site for this approach.
Cheers,
German
Am Dienstag, den 05 Aug 2014 schrieb Sampson, Jared:
> 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
> <erlenk...@uni-duesseldorf.de<mailto:erlenk...@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: erlenk...@uni-duesseldorf.de<mailto:erlenk...@uni-duesseldorf.de>
> URL: http://cpclab.uni-duesseldorf.de
>
>
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--
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: erlenk...@uni-duesseldorf.de
URL: http://cpclab.uni-duesseldorf.de
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