Dear Thomas, At the moment, Phaser only deals fully automatically with 2-fold tNCS (i.e. one unique peak in the native Patterson), although we’re hoping to make it more general. With some tailored input, it can also deal with the case of several copies related by multiples of the same NCS translation. If there are independent NCS translations, then it can’t deal with that. However, you can override the automatic definition of the NCS translations and, for instance, provide the translation vector for the dominant one, or you can set the threshold for automatica detection of Patterson peaks to just pick one.
When you said Phaser went into an endless loop, do you mean that it was exploring a very large number of potential solutions with no signal to distinguish among them, or do you mean that it went into an infinite loop repeating the same thing? If the latter, that would be a bug and we’d want to see the log file! If you’d like, you could send the logfile off-line and I could tell you how I might approach dealing with tNCS in your case. Best wishes, Randy Read ----- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: +44 1223 336500 Wellcome Trust/MRC Building Fax: +44 1223 336827 Hills Road E-mail: [email protected] Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk On 30 Jul 2014, at 17:09, Thomas Krey <[email protected]> wrote: > Dear all, > > we are currently in the process of solving the structure of a Fab/peptide > complex. We have first determined the structure of the native Fab and refined > it to ~2A, so we have a decent MR model. The complex crystals that we are > working on right now diffract to ~3.2A and are unfortunately in P1 (a > different spacegroup than the native Fab) with the cell parameters a=70.72 > b=91.53 c=206.07 α=95.14 β=99.01 γ=90.83. This large AU contains > between 8 and 12 Fab molecules and unfortunaly these are related by pseudo > symmetry as suggested by the 4 non-origin distinct peaks detected in the > Patterson. Unfortunately this leads to Phaser turning off the > pseudotranslation correction and running into one of those endless loops that > I stopped eventually after 40 hours. > Is there anything we can do in order to get around these different > pseudotranslations ? > > Thank you so much for any help or suggestions. > > Best wishes > > Thomas > > > > > Dr. Thomas Krey > Institut Pasteur > Structural Virology Unit > 25-28 Rue du Docteur Roux > 75015 Paris > France > [email protected]
