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> -----Original Message----- > From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On > Behalf Of P.R. Evans > Sent: Thursday, October 19, 2006 4:56 PM > To: [email protected] > Subject: Re: [ccp4bb]: maprot changing contour level? > > *** For details on how to be removed from this list visit the *** > *** CCP4 home page http://www.ccp4.ac.uk *** > > > > The basic thing I don't understand is why anyone would ever > want to set the > contour level of a Fo-type map (ie one which tries to > estimate the "best" > electron density representing the structure, eg 2mFo-DFc) in > terms of its > RMSD. It makes no sense and never has. There is no legitimate > expectation > of what the RMSD should be. Phil, you don't like my idea of setting sigma(2Fo-Fc map) = 2*sigma(Fo-Fc map)? (based of course on the old idea that unmodelled density in a Fo map appears at approx half height, so you have to double the contribution from the Fo-Fc map to get the true peak heights). For example a 2Fo-Fc and a Fo-Fc map I'm looking at right now have RMSDs 0.207 and 0.0367 resp. (copied from the FFT maps when I extended them using extends, not recalculated, of course). So the 'true' SU of the 2Fo-Fc map is actually more like 2*0.0367 = 0.0734. So a contour level of 1 RMSD for the 2Fo-Fc map (i.e. the value that in this case seems to show significant unmodelled features) is really 0.207/0.0734 = 2.82 times its SU. And it so happens that I routinely contour my Fo-Fc maps (for which of course the SU can be much more accurately estimated and doesn't need to be varied according to the solvent content) at 2.8 times its SU. So features that I'm looking at in both maps really appear at the same level of significance, precisely as one would expect. > In practice, in the end it isn't really important, as when > you are looking > at maps on the screen you set the contour level to whatever shows the > features that you are interested in. Then it doesn't matter > whether the > units of the map are in e/A^3, RMSD or elephants. This issue of course hits you most forcefully when you're trying to devise an automated method of analysing maps and you need a way of deciding what really is significant without seeing the map in its entirety. Then you don't have the luxury of manually adjusting the contour level until the density 'looks roughly like what you expected'. You can of course have the software tweak the contour level up or down until the peak volume becomes what you expected but this presumes that the density is actually contiguous and doesn't have other nearby spurious density peaks to mess things up. > ... but this thread does allow me to let off some steam. .. indeed! -- 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.
