Dear all, I have just subscribed to the CCP4BB. The description for this BB is "The CCP4BB mailing list is for discussions on the use of the CCP4 suite, and macromolecular crystallography in general. "
So, please, give us all possible solutions to crystallographic problems, including protein expression, purification etc. For many of us the CCP4BB is our school of crystallography. As this is probably the biggest crystallographic forum, any relevant information is wellcome plus job postings. Maia ----- Original Message ----- From: "Gerard DVD Kleywegt" <ger...@xray.bmc.uu.se> To: <CCP4BB@JISCMAIL.AC.UK> Sent: Tuesday, February 23, 2010 7:57 AM Subject: Re: [ccp4bb] Per-residue RMSD for multiple structures? 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 <merr...@u.washington.edu> 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:ger...@xray.bmc.uu.se ****************************************************************** The opinions in this message are fictional. Any similarity to actual opinions, living or dead, is purely coincidental. ******************************************************************
