Re: [ccp4bb]: Re: your mail

["Gerard \"DVD\" Kleywegt" <gerard@xray.bmc.uu.se>]

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> > > >  I am wondering if there is way to automatically walk through a
> > > protein
> > > > structure from N-terminal to C-terminal, so to have a better sense of
> > > 
> > > > chain trace than the ramp painting?
> > > 
> > > isn't this what you do when you rebuild your protein ? you can use OOPS2
> > > to
> > > generate O macros to take you from one residue to the next; see the
> > > manual at
> > > http://xray.bmc.uu.se/usf/oops2_man.html
> 
> If you'd prefer to use a robust scripting language like Python instead of
> O macros, you can do the same kind of thing with PyMOL.  After loading a
> structure, run "walk.py" below to be able to walk the chain using the F1
> and F2 keys.  It could easily be customized to suit your needs.  

but on the other hand, if you think that python is a british comedy show and
you don't even want to know what a 'robust scripting language' is, you can
always simply put "ce_nex ;; CA" (centre_next) on your O menu - every time you
click it you go to the next residue (and centre_prev will take you back)

however, if you *are* interested in producing protein *models* that are robust
(e.g., in the sense that they won't show up as an entertaining example a paper
about validation or protein model quality), you might still want to check out
oops2, even though it's written in fortran and produces humble little O
macros.

oops2 enables you to do something rather more interesting than generating a
trivial walk through your model. it can instead be used (if you want) to
generate a residue-by-residue critique of your model (including such things as
ramachandran violations, poor real-space fit, what-if-generated errors, etc.).
you can choose to walk through your entire model or only visit the residues
that violate at least one criterion, and you can do it from first to last
residue or starting with the residue with the largest number of violations
(the latter is a convenient way for busy supervisors to check that the models
they are about to attach their name to and write a paper about are actually
supported by the experimental data and look protein-like ...). for every
residue visited, a macro or set of commands can be executed automatically
(e.g. contouring your maps, generating symmetry-related molecules, etc.).
oops2 can not only reduce the time you spend checking and rebuilding your
model, it also focusses your attention on those residues most likely to need
it.

--dvd

  (who hates to admit that he has actually written some java code recently)

******************************************************************
                        Gerard J.  Kleywegt
    [Research Fellow of the Royal  Swedish Academy of Sciences]
Dept. of Cell & Molecular Biology  University of Uppsala
                Biomedical Centre  Box 596
                SE-751 24 Uppsala  SWEDEN

    http://xray.bmc.uu.se/gerard/  mailto:gerard@xray.bmc.uu.se
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