Goodness, sounds like fun.
Coot does have an align&mutate function of course, but you don't get to
fiddle with the sequence alignment - Coot uses its own alignment [1].
My understanding is that should be fine for ~70% sequence identity or
better. My feeling though is that it is not widely used. So my question
to the community is: Is there a need to be able to use an alignment
rather than simply a target sequence?
Thanks,
Paul.
[1] courtesy of mmdb
Wes Ozarowski wrote:
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,
[email protected] 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
