Is my understanding correct that what Wes describes can be accomplished
in the following three steps:
1. Apply CHAINSAW using sequence alignment
2. fill-partial-residues
3. fit-protein (optional)
Seems to me that moving chainsaw step into coot will not save much time
(if at all).
Cheers,
Ed.
On Thu, 2010-01-28 at 10:10 +0000, Paul Emsley wrote:
> 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,
> > [log in to unmask] 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
> >
--
Edwin Pozharski, PhD, Assistant Professor
University of Maryland, Baltimore
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When the Way is forgotten duty and justice appear;
Then knowledge and wisdom are born along with hypocrisy.
When harmonious relationships dissolve then respect and devotion arise;
When a nation falls to chaos then loyalty and patriotism are born.
------------------------------ / Lao Tse /
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