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CCP4BB  February 2010

CCP4BB February 2010

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Subject:

Re: Per-residue RMSD for multiple structures?

From:

Gerard DVD Kleywegt <[log in to unmask]>

Reply-To:

Gerard DVD Kleywegt <[log in to unmask]>

Date:

Tue, 23 Feb 2010 15:57:02 +0100

Content-Type:

MULTIPART/MIXED

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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.
******************************************************************

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