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,

Re: [ccp4bb] Per-residue RMSD for multiple structures?

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

Re: [ccp4bb] Per-residue RMSD for multiple structures

and a blessing cheers, Martyn Martyn Symmons MRC-MBU - Original Message From: Gerard DVD Kleywegt ger...@xray.bmc.uu.se To: CCP4BB@JISCMAIL.AC.UK Sent: Tuesday, 23 February, 2010 14:57:02 Subject: Re: [ccp4bb] Per-residue RMSD for multiple structures? Thanks Stephen! I was going

Re: [ccp4bb] Per-residue RMSD for multiple structures?+ CCP4BB Gestapo

@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

Re: [ccp4bb] Per-residue RMSD for multiple structures? [INTERIM REPORT]

Wow! Thanks for all the suggestions, many of them sent off-line. It's going to take me a while to work through all of them to see which are most suitable, but I will report back to the bulletin board with a summary and evaluation when I get to that point. A couple of thoughts, perhaps

[ccp4bb] Per-residue RMSD for multiple structures?

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

Re: [ccp4bb] Per-residue RMSD for multiple structures?

One possible representation is the sausage produced by MOLMOL. It is meant for NMR ensembles - the thickness of sausage is directly proportional to local RMSD. Take a look at this image: http://www.msg.ucsf.edu/local/programs/molmol/images/tutorial_ex3.gif MOLMOL can be downloaded from

Re: [ccp4bb] Per-residue RMSD for multiple structures?

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