On 10/21/16 8:15 PM, Evelyne Deplazes wrote: > I have previosly used align2d (see script align2d_old.py below) to > prepare homology models. but the current sequences are very long (a > pentamer with 573 aa per chain) and align2d was taking a very long time > (hours). so I wanted to use salign.
You probably want to adjust the value of max_gap_length; see https://salilab.org/modeller/9.17/manual/node309.html 573 residues is not that long and shouldn't take more than a few seconds to align.
You can certainly use SALIGN if you want, but the underlying algorithm is the same.
> - what is the sequence of scripts / commands to use? do I first use > salign to prepare an alignment and then align2d (or salign that emulates > align2d).
You can perform your alignments in any order you like. Often we find that a structural alignment (align3d()) does better if it's given a reasonable alignment (e.g. that from align()) as an initial starting guess.
> - in the previous scripts of align2d the .pdb file was used as an input. > in the new scripts that I used the .pdb file does not seem to be used. > so how is the known structure of the template taken in to consideration > for the alignment?
In every case you give the alignment function an alignment object ('aln' in your scripts), not structures. This contains the sequences you want to align. Functions that also need structural information will automatically read in the PDB file when needed using the header information in the PIR file.
Ben Webb, Modeller Caretaker