Dear Bart and Howard, let's assume that the paper is novel. Without asking too much, however, I think it would be fair to ask why they used a homology model for molecular replacement, when they claimed successful structure solution two years ago.
Also, since they claim successful structure solution, I think it is not too far-fetched to ask them for a preliminary coordinate file for reviewing purposes. Let's give them the freedom of doubt, but let's watch how they respond to the obvious question. I do agree completely with the two of you that in its present form the paper is not acceptable. But if we reject it, they will submit it elsewhere. At least we have the chance of catching something if it is there. Cheers, Manfred. On Thu, 26 Feb 2009, Jan Abendroth wrote:
Thanks a lot, Garib, as always, there is a new version of refmac just out that fixes all the problems. Cheers Jan 2009/2/26 Garib Murshudov <[email protected]>I think we have fixed this problem just recently. The problem was related with refmac not being able to pick correct dataset from mtz. IF there was one dataset in mtz then there was no problem Please have a look: www.ysbl.york.ac.uk/refmac/latest_refmac.html Garib On 26 Feb 2009, at 21:52, Jan Abendroth wrote: Hi all, I am trying to follow good practices and keep my set of free reflections between data sets, eg. in this case between an in-house low resolution and a synchrotron high resolution data set. High resolution data from hkl2000 were imported through the ccp4i task, keeping the low resolution FreeRs. This mtz file contains both unit cells, see below. The refined data set contains only one unit cell description, unfortunately the one from the FreeR (refmac5.5.72 and refmac5.5.70). As the two unit cells are sufficiently different, coot displays the model towards the edge of the density, real space refinement pulls the model back in the middle, refmac then starts with really high Rs and pulls the model back "out". When using rather ancient refmac5.2.0019, the mtz file has the correct unit cell description. Btw. both refinements look about the same. The only difference is a rather annoying shift of the electron density that is displayed in coot based on different unit cell in the mtz file. Is there a way to tell refmac which of the two unit cells to put in the output mtz file? Intuitively, it should be the one from which the amplitudes originate? Cheers Jan *mtz file after import* 1 myprotein high_reso synchrotron 79.0610 79.0610 311.7950 90.0000 90.0000 90.0000 1.00000 2 myprotein low_resol rotating_anode 78.5860 78.5860 311.1900 90.0000 90.0000 90.0000 1.54180 *refmac5.5.0072* 2 myprotein low_reso rotating_anode 78.5860 78.5860 311.1900 90.0000 90.0000 90.0000 1.54180 *refmac5.2.0019:* 1 myprotein high_reso synchrotron 79.0610 79.0610 311.7950 90.0000 90.0000 90.0000 1.00000 -- -- Jan Abendroth deCODE biostructures Seattle / Bainbridge Island, WA, USA work: JAbendroth_at_decode.com home: Jan.Abendroth_at_gmail.com
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