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> -----Original Message----- > From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On > Behalf Of A Hibbert > Sent: 17 November 2005 20:48 > To: [email protected] > Subject: [ccp4bb]: More RFCORR/PHASER Questions > > *** For details on how to be removed from this list visit the *** > *** CCP4 home page http://www.ccp4.ac.uk *** > > > Sorry about all these questions, but I have a few more: > > 1) For general self-education, I tried out the RFCORR/AMORE > script in the RFCORR documentation. From what I understand, > the X-rotation function shouldn't need a .tab file (from > TABLING) as normalized SFs from the model are already > calculated (and a TABLING run isn't included in the example). > Furthermore, the GENERATE command isn't executed. However, > AMORE complains that I haven't included a .tab file. Does > anyone know why? I think Eleanor's right, the example scripts need updating to reflect changes in the software since the scripts were last tested - sorry about that! After I made the script (and it certainly worked then!), I think AMoRe was modified in such a way that it then expected to find a .tab file even if it didn't need it (because the GENERATE step was being skipped). I think what happened was that Eleanor devised a way of using E's within AMoRe that made my work-around script redundant. But it's a simple matter to generate a .tab and include it. > 2) Do you think it's more sensitive doing a LOCKED ROTATION > in AMORE, then doing a translational search in PHASER, or > doing everything in PHASER and then running RFCORR? In principle the locked RF should be more sensitive because you're searching for the 2 NCS-related molecules simultaneously and automatically eliminating solutions that are not consistent with the SRF. Note that the locked RF is not the same thing as an ordinary RF with a dimer model, which clearly you should try if you can construct a believable dimer (the difference is that the dimer RF includes in Fcalc inter-molecular vectors between the molecules of the dimer, whereas the locked RF doesn't, it only uses the intra-molecular vectors within both molecules). The RFCORR route should be reserved for cases where the SRF is not readily interpretable, e.g. where the rotation group is not closed. Having said that, it's undoubtedly true that Phaser's scoring function is superior to that in Amore, so it's hard to say which combination of methods will be more sensitive. The obvious solution is to try them all - but then in difficult cases I would do that anyway! Clearly what we need for this kind of problem (which does after all pop up quite frequently) is the best of both worlds - a locked RF using Phaser's scoring function (Randy?). -- 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.
