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Bernhard There's the related issue of how to optimally treat the *test set* reflections, i.e. perfectly good measurements but not used (in refinement that is). The various program authors seem to treat these quite differently, e.g. Refmac AFAICS treats them exactly like unobserved for the maps and sets FOM=0, FWT=DFC, DELFWT=0. Buster AFAICS assigns a FOM>0 and treats them just like normal reflections for the maps. I don't quite understand why Refmac can't assign a valid FOM in this case, since that's obtained from the calculated phase distribution, and AFAICS has nothing to do with whether or not the reflection is used in refinement. I've no idea what Phenix does in this situation. It would be nice to have some transparency/consensus on best practice! There's also the issue I highlighted in January on the BB where none of the programs I tested (Refmac, Buster) were using the correct formulae for FWT in the centric case, or DELFWT in one or other of the acentric or centric case (apologies to Garib if his latest version fixes this, I haven't had time to test it yet). Cheers -- Ian > -----Original Message----- > From: [log in to unmask] [mailto:[log in to unmask]] On > Behalf Of Bernhard Rupp > Sent: 18 March 2009 01:34 > To: [log in to unmask] > Subject: map coefficients for padded reflections Fobs=0 > > Dear All, > > > > during processing some mtz files I noted that some programs complete > > the reflection list by padding missing reflections. > > > > a) for Refmac (which did not pad reflections automatically) I read > that > > 1) for 2mFo-DFc: Fwt = DFc in case Fo=0 > > 2) for mfo-fc : Fwt=0 for Fo=0 > > > > b) how does PHENIX/refine handle the fobs = 0 reflections in either > case? > > > > c) Prime and switch maps also have padded reflections, but here I am > at a loss, > > because the maps seem to acquire very high positive density - > i.e. the distribution > > seems atypical when read into say Xtalview. Might be a result > of the density modification > > procedure? Can I get the observed reflections only from P&S? > > > > Could the program authors kindly shed some light or references on the > treatment of absent reflections in their > > respective programs? In most cases, the padded reflections have not much > effect, as expected from their weights. > > > > Thx, br > > > > Bernhard Rupp > 001 (925) 209-7429 > +43 (676) 571-0536 > [log in to unmask] > [log in to unmask] > http://www.ruppweb.org/ > ----------------------------------------------------------------- > People can be divided in three classes: > The few who make things happen > The many who watch things happen > And the overwhelming majority > who have no idea what is happening. > ----------------------------------------------------------------- > > 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 [log in to unmask] 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