Gerard DVD Kleywegt wrote:
> Thanks Stephen!
>
> I was going to suggest that, but I was afraid of the self-appointed
> CCP4BB Gestapo that has been seen goose-stepping in this neighbourhood
> recently (Tassos recently accused me of becoming mellow and diplomatic
> in my dotage, so I hope I've set the record straight now). However,
> since this solution is neither CCP4 nor Phenix, we may get away with
> this heinous act of bulletin-board heresy... On the other hand, I've
> learned that it is often more expedient to beg for forgiveness than to
> ask for permission.
>
> I would add that:
>
> - I assume that the sequences and numbering are identical
>
> - you should put the structures in one big PDB file and read it into
> LSQMAN
>
> - since LSQMAN doesn't do true multiple-structure alignment, you could
> pre-align them, e.g. with SSM/PDBeFold
>
> - if you didn't, you could indeed use the MCentral and MAlign commands
> to align them
>
> - my favourite plot would be the "CD plot" (but then again, it would,
> wouldn't it?) - see for instance:
> http://xray.bmc.uu.se/cgi-bin/gerard/image_page.pl?image=usf/pics/cdplot_1ldn.gif
> - which is also produced with the MPlot command -
> http://xray.bmc.uu.se/usf/lsqman_man.html#S82 - a normal MPlot would
> look like this:
> http://xray.bmc.uu.se/cgi-bin/gerard/image_page.pl?image=usf/pics/mplot_1ldn.gif
>
>
> - the output file of the normal MPlot command is in a form that can be
> quickly converted into an O datablock for those handy with an editor
> and familiar with O datablocks, and could then be used to ramp a model
> inside O
>
> - you may also want to consider showing how the (main-chain or
> side-chain) torsion angles differ between the structures, e.g. by
> plotting the circular variance of phi and psi - see for instance
> http://xray.bmc.uu.se/cgi-bin/gerard/image_page.pl?image=usf/pics/vmain_1ldn.gif
> - as described here: http://xray.bmc.uu.se/usf/lsqman_man.html#S83 -
> or a multiple-model Ramachandran plot like this
> http://xray.bmc.uu.se/cgi-bin/gerard/image_page.pl?image=usf/pics/mrama_1ldn.gif
> (with the MRama command). The advantage is that no superposition is
> required at all and that any domain movements won't debeautify your
> results
>
> --dvd
>
>
>
>
> On Tue, 23 Feb 2010, Stephen Graham wrote:
>
>> I am pretty sure you can do this using LSQMAN from Gerard (BluRay?)
>> Kleywegt.
>>
>> The pertinent commands are MCENTRAL to determine the 'most
>> representative structure' (i.e. the one to align upon and show in the
>> figure), MALIGN to do the alignment and then MPLOT to calculate a
>> 'multi-RMSD' for each residue (see manual for details - set the
>> 'cut-off for printing' to 0 to get all values).
>>
>> Regards depiction, I think pymol can also represent structures as
>> sausages based on their B values:
>> cartoon putty
>> show cartoon
>>
>> HTH,
>>
>> Stephen
>>
>> On 23 February 2010 01:31, Ethan Merritt <[log in to unmask]>
>> wrote:
>>> Hi all,
>>>
>>> I am comparing 4 very similar (<1.5A rmsd) large (750 residues)
>>> structures,
>>> but struggling to find a way to generate a figure that conveys where
>>> they
>>> are most alike and where they diverge.
>>>
>>> Simply drawing a superimposed set of backbone traces results in what
>>> looks
>>> like colored spaghetti. I don't think that's going to work.
>>>
>>> So I had the idea of drawing a single backbone trace, or ribbon
>>> diagram,
>>> and coloring by the RMSD of the four C-alphas at each residue position.
>>> But I can't find a program that will output this as a table of numbers
>>> I can use. All of the multiple structure superposition programs must
>>> have this information internally. After all, that's what they are
>>> minimizing.
>>> But do any of the programs provide an option to write it out?
>>>
>>> I can get pairwise per-residue deviations by doing SSM superposition
>>> in Coot,
>>> but that doesn't get me to an RMSD for all four structures jointly.
>>>
>>> Ethan
>>>
>>>
>>> --
>>> Ethan A Merritt
>>> Biomolecular Structure Center
>>> University of Washington, Seattle 98195-7742
>>>
>>
>>
>>
>> --
>> Dr Stephen Graham
>> 1851 Research Fellow
>> Cambridge Institute for Medical Research
>> Wellcome Trust/MRC Building
>> Addenbrooke's Hospital, Hills Road
>> Cambridge, CB2 0XY, UK
>> Phone: +44 1223 762 638
>>
>
>
> Best wishes,
>
> --Gerard
>
> ******************************************************************
> Gerard J. Kleywegt
> Dept. of Cell & Molecular Biology University of Uppsala
> Biomedical Centre Box 596
> SE-751 24 Uppsala SWEDEN
>
> http://xray.bmc.uu.se/gerard/ mailto:[log in to unmask]
> ******************************************************************
> The opinions in this message are fictional. Any similarity
> to actual opinions, living or dead, is purely coincidental.
> ******************************************************************
May be if you changed your name to BlueRay, you can get away with this
heresy.
Subbu
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