Dear Amjad,
Thank you for your reply. Following your suggestion, I prepared a PDB file consisting of 1fas and 2ctx structures (from modeller examples) and submitted it to structuropedia.org. It does seem to work, reporting modeller calculated alignment with RMSD CA of 1.32A (http://dalton.med.miami.edu/4ki/models/modXX.txt). While it does not report how many pairs were used for RMSD calculation, both the number and visualization seem correct. So now I know that I am doing it wrong :-) but still I am at loss, why? I would be grateful for any hint to get it straight. What I am after is an automated/batch solution for comparing multiple structures. The modeller salign function seemed promising but I was stopped at the simplest attempt and I try to understand how I should use it correctly. The function does calculate the sequence alignment for me and I am able to use this alignment object to superimpose structures, but:
With gratitude,
|
begin:vcard fn;quoted-printable:Pawe=C5=82 K=C4=99dzierski n;quoted-printable;quoted-printable:K=C4=99dzierski;Pawe=C5=82 org;quoted-printable:Wroc=C5=82aw University of Technology, Faculty of Chemistry;Advanced Materials Engineering and Modelling Group adr;quoted-printable;quoted-printable;quoted-printable;quoted-printable:Wyb. Wyspia=C5=84skiego 27;;Politechnika Wroc=C5=82awska, Wydzia=C5=82 Chemiczny;Wroc=C5=82aw;dolno=C5=9Bl=C4=85skie;50-370;Poland email;internet: tel;work:+48 71 3203200 tel;fax:+48 71 3203364 version:2.1 end:vcard