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Whilst I wholeheartedly applaud the intention of Bernhard's letter, I don't agree that the RSCC is the best measure for achieving the desired goal. The problem with the CC is that it's scale- (and origin-) independent, and thus can lead to false-positive conclusions. For example, suppose by chance the observed and calculated densities for a ligand were near-identical apart from a big difference in the means, e.g. suppose the observed density was everywhere about 1/100 of the calculated. This would still give a near-perfect CC around 1, yet the density could hardly be worse! As a measure of fit of the data, the CC is useful when the relative scale and origin of two sets of data are unknown, but in this case clearly we know that the maps are on an absolute scale (and there's no question of a difference in the zero level). In such a situation the CC is a very poor measure relative to alternative measures that make the assumption that the scale and origin are known. The point is that you don't actually want to know whether the densities are correlated, you just want to know whether they're different! A much better measure would be the likelihood, which if we make the assumption of normally-distributed errors is equivalent to the Z-score (i.e. RMSD/SU). There still remains a problem: as pointed out in the letter the RSCC _can_ give an indication of the poorly-ordered regions, whereas the Z-score would most likely simply tell you that there was no significant difference between the obs & calc densities. However we do have another obvious indicator of poor local order: the B factor, and it's hard to see how authors could reasonably object to allowing referees to see tables of residue and ligand-averaged B factors (or even separate per-residue averages for main & side-chain atoms). -- Ian > -----Original Message----- > From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On > Behalf Of William Scott > Sent: 14 December 2006 16:39 > To: [email protected] > Cc: [EMAIL PROTECTED] > Subject: [ccp4bb]: Bernhard Rupp's correspondence in Nature (Dec 14) > > *** For details on how to be removed from this list visit the *** > *** CCP4 home page http://www.ccp4.ac.uk *** > > > Hi folks: > > Bernhard has an interesting letter in the correspondence section of > Nature today (I have to confess I was looking for the > mezasoic flying > mammal when I found this). > > http://www.nature.com/nature/journal/v444/n7121/full/444817b.html > > > I think this is a good idea, but I wonder if it might be worth > tanking one step further. The last three structure papers that I > wrote were submitted along with the experimental map as a > pymol saved > session so that the referees could take a look at the map we > actually > used to build the molecule, as well as a composite-omit map > generated > using the final refined structure. I have no idea whether this was > in fact used, but I thought it might be helpful. Seeing the actual > maps always makes the statistics more concrete, for me at least. > > Bill > > > > > Disclaimer This communication is confidential and may contain privileged information intended solely for the named addressee(s). It may not be used or disclosed except for the purpose for which it has been sent. If you are not the intended recipient you must not review, use, disclose, copy, distribute or take any action in reliance upon it. If you have received this communication in error, please notify Astex Therapeutics Ltd by emailing [EMAIL PROTECTED] and destroy all copies of the message and any attached documents. Astex Therapeutics Ltd monitors, controls and protects all its messaging traffic in compliance with its corporate email policy. The Company accepts no liability or responsibility for any onward transmission or use of emails and attachments having left the Astex Therapeutics domain. Unless expressly stated, opinions in this message are those of the individual sender and not of Astex Therapeutics Ltd. The recipient should check this email and any attachments for the presence of computer viruses. Astex Therapeutics Ltd accepts no liability for damage caused by any virus transmitted by this email. E-mail is susceptible to data corruption, interception, unauthorized amendment, and tampering, Astex Therapeutics Ltd only send and receive e-mails on the basis that the Company is not liable for any such alteration or any consequences thereof.
