-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Dear so-far-posters,
I do not know Tom Van den Bergh, nor do I know his background, nor the history of the data, nor the reasons why he may have sent it to this list (although I think he did it to ask for help), but I find these answers irritatingly disrespectful and nasty. No regards to the ones addressed, Tim On 03/27/2013 06:43 PM, Bosch, Juergen wrote: > Sorry it has been accepted already, see attachment, it will soon be > online see the date for that. > > Jürgen > > ...................... Jürgen Bosch Johns Hopkins University > Bloomberg School of Public Health Department of Biochemistry & > Molecular Biology Johns Hopkins Malaria Research Institute 615 > North Wolfe Street, W8708 Baltimore, MD 21205 Office: > +1-410-614-4742 Lab: +1-410-614-4894 Fax: > +1-410-955-2926 http://lupo.jhsph.edu > > [cid:[email protected]] On Mar > 27, 2013, at 1:30 PM, Steiner, Roberto wrote: > > we should all chip in a water molecule or two and the second author > becomes "the CCP4 community"…. > > On 27 Mar 2013, at 17:22, Antony Oliver > <[email protected]<mailto:[email protected]>> > wrote: > > At the risk of being somewhat cheeky - perhaps I could claim second > author? I too have successfully solved the structure - and I > totally concur with Phil. Placing a second molecule in the > asymmetric unit, essentially resolves the perceived R-factor > problem. > > A good thorough manual inspection and rebuilding is *ALWAYS* good > practice for newcomers to the field. > > Tony. > > > On 27 Mar 2013, at 17:14, Petr Leiman > <[email protected]<mailto:[email protected]>> wrote: > > Since this is now public domain knowledge and if this gets ever > published, Phil has my vote to be the first author! > > Petr > > > On Mar 27, 2013, at 6:09 PM, Phil Jeffrey wrote: > > That's quite brave - shipping your entire structure to people that > could be actual competitors. But it was fun to play at 1.4 > Angstrom over lunch. > > Practical points: > > * not everyone loves 12Mb of attachments in one email in their > inbox, so if you do this again please put the files on a webserver > and point us there > > Structural points: > > * the map looks pretty good, but I think the sequence is > misassigned in some regions (e.g. A118-A122 etc). Automation is a > good tool but a poor master, and extreme caution is required before > taking the results too literally. Usually you'd expect a 1.4 > Angstrom to be easy to autobuild but I recently had a sequence > misassignment at just that resolution. That map was trivial to > interpret with the correct sequence however - one of the joys of > working with Arp/wArp at 1.4 Angstrom. > > * the large number of positive difference density blobs and water > molecules clustered in what otherwise would be the solvent void > strongly suggest that there's a second molecule present. > > > If I take redfluorescentprotein_refine_10.pdb (waters removed) and > exptl_fobs_phases_freeR_flags.mtz and ask Phaser to look for two > molecules, it finds them quite successfully. (for the record an > LLG of 15111 using nominal sequence identity of 90%). I will send > this to you off-list. Please note that Phaser is using a different > origin for this molecular replacement solution so the coordinates > and your previous map do not overlap. > > This rather nicely explains why your structure had an R-factor in > the 40's despite being a half-way decent model. The new MR > solution has an R-free in the 30's in the phenix.refine job I'm > running right now. > > > Going forward I suggest you utilize the Arp/wArp program to > autobuild your structure for you, starting from the molecular > replacement solution (or, perhaps with it stripped to ALA). While > you could use Autobuild, this is the CCP4 list and so you should > use CCP4 programs. > > Phil Jeffrey Princeton > > > On 3/27/13 12:22 PM, Tom Van den Bergh wrote: Dear members of > ccp4bb, > > I need some help with the refinement of my structure of a variant > of mRFP (monomer red fluorescent protein, sequence in attachment). > I have done molecular replacement with phaser with model 2VAD of > protein database. Then i have done some model building > phenix.autobuild. (2 pdb's (overall...), freeR flags and log file > attached) When i refine with phenix.refine my structure i get a > R-value of 0,42 which is still way too high. (redfluorescent > protein.pdb, .mtz and logfile attached) When i look at the > structure in coot i find many unmodelled blobs and many outliers in > density analysis and rotamer analysis. The problem is that there > are so many problems with my structure, that i dont know where to > begin. Could you try some refinement for me, because this is first > structure that i need to solve as a student and i dont have too > many experience with it. > > Greetings, > > Tom > > > > Roberto A. Steiner Group Leader Randall Division of Cell and > Molecular Biophysics King's College London > [email protected]<mailto:[email protected]> > > Room 3.10A New Hunt's House Guy's Campus SE1 1UL London > > Phone 0044 20 78488216 Fax 0044 20 78486435 > > > > > - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFRUzKSUxlJ7aRr7hoRAoW6AJkBPhUJPYXTYxmyi2nGd8FyCCDh5QCfTpr2 mAkVKBLCgmcRfcIaHj3BniM= =RRt9 -----END PGP SIGNATURE-----
