Dear Andrew,
Since I don't have the time to learn python fully and because there is
not too many of examples of python scripting available for Coot, thus I
use my expertise of VB to help me write the correct syntax for python script.
then paste it into notepad and run it as a python script from Coot's GUI.
For example I will paste an amino acid sequence of homologous proteins
from ClustalW into an excel spreadsheet, then using VB to write a program
that will put each amino acid into it's own spreadsheet cell as separate
objects with some fancy colors ( as color codes) to make it pretty. Now, I
can do all sorts of analyses of these sequences, like find the ones that are
non-homologous between two proteins, put them in a table, let VB write the
python syntax for "goto" and "mutate_autofit " of all these specific amino
acids, paste it into notepad and "wala !" i have automation. That is ,I
can goto (thus observe visually the mutational changes for oddballs) and
mutate_autofit about 300 amino acids in about 10 min, rather than spending
hours doing it manually.
Wes
In a message dated 1/19/2010 10:56:53 A.M. Central Standard Time,
and...@mrc-lmb.cam.ac.uk writes:
Having worked with O for many years I am only now getting serious with
COOT. There are a couple of things that I would like to do that don't
seem to be available (as far as I can tell), but which may well be
possible using Macros.
Unfortunately a quick Google has not revealed anything about how to
use macros in COOT, but a colleague suggested they need to be written
in Python or another language that I had not heard of before.
So my first question is where can I find a low level description of
how to write macros with some examples (I know nothing about Python,
except that it is fashionable) ?
There are specifically two things I want to be able to do:
1. Do an LSQ superposition using specified residues in multiple chains
(superposing one oligomer on another).
2. To do a LSQ superposition of a homologous structure onto my working
structure using +/- N residues about the current position, where N is
a variable (not essential, could be fixed) and the current position is
the last residue that I clicked on.
Thanks
Andrew
