Just Launched: You can now import projects and releases from Google Code onto SourceForge
We are excited to release new functionality to enable a 1-click import from Google Code onto the Allura platform on SourceForge. You can import tickets, wikis, source, releases, and more with a few simple steps. Read More
So I'm trying to make a .pml script where I generate "rotamers" of
protein A around protein B using "rotate axis, degree, object" and
creating new object of rotated protein A - this generates a number of
rotamers, but they basically form a sphere until you align them, and so,
the last step is that I align all the rotamers I've generated either on
N- or C- term of protein A (i.e. the Ca atom of first/last residue),
depending on my choosing
So, at the moment, I manually renumbering whatever protein I'm
generating the rotamers for and setting it to some obscure number (like
5000) that is unlikely to be used by most pdb files
Manually, I do this by using=20
alter structure1, resi=3Dstr(int(resi) + 4999) ; rebuild
- this takes the object structure1, which starts at 1 as the
first amino acid residue and changes it to be 5000, so in case of my
alignments, aligning my rotamers with structure1 doesn't accidentally
align any other object in the pdb file...
doing this manually is a pain, especially since a number of pdb files
don't start with residue number 1 and I have to keep manually
renumbering the proteins...
is there a way to easily set the first residue to be 5000 or last
residue to be 5000? Regardless of what the object?
for example to do the following (i.e. what code might I use to do the
create object, sele
if the first residue number in object is not numbered "1", get value of
first residue number , calculate the difference between 5000 and value
of first residue number and add that difference to all residue numbers?
i.e. if my peptide starts at residue 23 and I want that to be 5000...
Similarly, if the last residue number of the object is not 5000, get
value of last residue number, calculate the difference between 5000 and
the value of last residue number and add/subtract this difference to all
residue numbers? i.e. if my peptide ends on residue 38 and I want that
residue to be 5000
I'd like this to be a "general" code, so that I can renumber and object,
regardless of whether the first residue is numbered 3, 600 or 2100, etc
Anyone familiar with how to do this?
I would greatly appreciate it