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> > >The problem with the CC is that it's scale- (and origin-) independent > > That is a good thing, imho. If you plot the B-factor below it > (as my program > for example does, see link) the underoccupation will express > itself as > excessive B-factors. That being said, I have rarely seen > cases where absent > density has been divined so perfectly that the RSCC was good.... The relative scale & origin insensitivity of the CC when sample means and s.d.'s are used (as they normally are if the textbook formula for the CC is used) is clearly an advantage if you don't know their values a priori but actually a bad thing if you do! It implies that two additional variables per residue are being added (i.e. the relative scale and zero level of the density maps in the region of density around each residue). It also implies that the relative scale and zero level of the maps varies from one residue to the next which is clearly nonsense! If the known (and of course constant) population means and SU's were used instead that would be different. However I very much doubt that they are - certainly the sample values are used in the OVERLAPMAP program which I guess is what everyone uses for this. Maybe the solution to this is for CCP4 to just provide an additional option to use population means & SU's in OVERLAPMAP if they are known (and while they're at it add the Z-scores to the output). Addition of extra degrees of freedom inevitable reduces the power of any statistical test, and in this case it's totally unnecessary because the values of the 'unknowns' are actually known accurately beforehand! Effectively the redundant variables act as 'rubbish bins' in which the errors that you're trying to highlight are instead partially or completely hidden. So are you proposing that inclusion of tables of residue-averaged B factor as well as RSCC in the manuscript sent to referees should be mandatory? If so, that would go some way to addressing concerns about the usefulness of the RSCC plot as a validation tool (particularly for small ligands and solvent molecules). -- Ian 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.
