The SIGMAA program has since it was written in the 80's (mainly by Randy of course, but also in part by Eleanor I believe?) used only 1 phase column (= PHIC) for the case where the phases of FWT & DELFWT are equal to PHIC: obviously if they are unequal (e.g. as a result of phase combination) then additional phase columns are needed. The FWT & DELFWT columns may be negative, and (to my knowledge) this has never caused a single problem. In fact when I wrote the original CCP4 interface to Lynn ten Eyck's FFT I specifically ensured that negative amplitudes did not cause any problems. Since programs such as Refmac were developed *after* Sigmaa it's hard to understand the basis of this irrational fear of negative numbers!
According to Wikipedia the ancient Greeks didn't accept the existence of negative numbers either, in fact to quote from: http://en.wikipedia.org/wiki/Negative_numbers#History "For a long time, negative solutions to problems were considered "false". In Hellenistic Egypt, Diophantus in the third century A.D. referred to an equation that was equivalent to 4x + 20 = 0 (which has a negative solution) in Arithmetica, saying that the equation was absurd.". Hopefully we've come a long way since then! Cheers -- Ian > -----Original Message----- > From: owner-ccp...@jiscmail.ac.uk [mailto:owner-ccp...@jiscmail.ac.uk] On > Behalf Of Eleanor Dodson > Sent: 18 June 2009 09:50 > To: Dirk Kostrewa > Cc: CCP4BB@jiscmail.ac.uk > Subject: Re: [ccp4bb] [COOT] Novel maps... > > Well, it makes for consistency between the output when there is not, and > is, exptl phase information - in the 2nd case the PHWT is a weighted > derivative of the two phase estimates. > > You could get away with just one of PHWT and PHDELWT since they can > only differ bu 180, but that would require writing mFO-DFC as a signed > number , and there were concerns about what programs would do with > negative "F" estimates at one point.. > Eleanor > > > > Dirk Kostrewa wrote: > > Dear Eleaonor and CCP4ers, > > > > I always wondered, why there are phase columns PHWT, PHDELWT (Refmac) > > or PH2FOFCWT, PHFOFCWT (phenix.refine) in addition to the PHIC column > > of the atomic model. In absence of other phase information, the phase > > should come from the atomic model, only. > > > > Best regards, > > > > Dirk. > > > > Am 18.06.2009 um 10:24 schrieb Eleanor Dodson: > > > >> It would be a cock-up map. Unless there is exptl phasing > >> > >> PHDELWT = PHIC when mFo-DFc is positive, and mFo-DFc is negative it > >> equals PHIC + 180 > >> > >> Eleanor > >> > >> > >> Simon Kolstoe wrote: > >>> Dear cootbb, > >>> > >>> When building into density I use a map generated from the FWT > >>> amplitudes column and PHWT phases columns which I think is my > >>> 2Fo-Fc, and a second map generated from DELFWT and PHDELWT which I > >>> think is my Fo-Fc. This keeps me happy and in known territory. > >>> However today someone in the lab asked what it means to generate a > >>> map using FWT and PHDELWT. Does anyone know what type of map this > >>> would be in the Fo Fc terminology? > >>> > >>> Thanks, > >>> > >>> Simon > >>> > >>> > > > > > > ******************************************************* > > Dirk Kostrewa > > Gene Center, A 5.07 > > Ludwig-Maximilians-University > > Feodor-Lynen-Str. 25 > > 81377 Munich > > Germany > > Phone: +49-89-2180-76845 > > Fax: +49-89-2180-76999 > > E-mail: kostr...@lmb.uni-muenchen.de > > ******************************************************* > > > > 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 i.tic...@astex-therapeutics.com 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
