> -----Original Message----- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On Behalf Of Eleanor Dodson > Sent: 30 May 2007 10:16 > To: Schubert, Carsten [PRDUS] > Cc: [email protected] > Subject: Re: [ccp4bb] How to determine ligand binding from > diffraction pat tern? > > 2) There is a lot of unnecessary and confusing molecular > replacement done. > If your ligand data is reasonably isomorphous ( similar cell > and space > group) then the berst procedure is to start from your known structure > and do rigid body refinement first to correct for any small > changes of cell. > If you do a full blown MR run you are very likely to get a > solution on a > different origin - this is formally correct but makes it hard > to overlap > the maps!
Often, even with soaked ligands the cell dimension changes are not small, e.g. I've seen up to 10%, and in many cases RB refinement simply doesn't work, even if you cut the resolution to say 4 Ang (which you would hope should increase the radius of convergence). But it's indeed totally unnecessary, and for the reasons you mention actually undesirable to do a full MR search. With Phaser for example in 'Brute Force' mode you can do 'ROTATE AROUND EULER 0 0 0 RANGE r' and 'TRANSLATE AROUND ORTHOGONAL POINT 0 0 0 RANGE d' (e.g. r = 10 deg, d = 5 Ang should normally do the trick). This does a limited search around the origin (and is also much quicker than a full BF search!!). -- 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. Astex Therapeutics Ltd., Registered in England at 436 Cambridge Science Park, Cambridge CB4 0QA under number 3751674
