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 URL: http://cpclab.uni-duesseldorf.de ------------------------------------------------------------------------------ Infragistics Professional Build stunning WinForms apps today! Reboot your WinForms applications with our WinForms controls. Build a bridge from your legacy apps to the future. http://pubads.g.doubleclick.net/gampad/clk?id=153845071&iu=/4140/ostg.clktrk _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
