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ncs in phenix.autobuild
by wang kaituo 07 Aug '08

07 Aug '08

Hi all, I failed in running phenix.autobuild. The end of the logfile said : ______________________________________________________ Build cycle 2 of 11 method:rebuild ...Using simple_ncs_from_pdb to find NCS Residues expected: [62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74] Residues found : [] ******************************************************************************** Failed to carry out AutoBuild_build_cycle: Did not find expected residues in get_xyz_list _____________________________________________________________ The two ncs chain sequence is not exactly same , some sidechain missing and some connectivity not well. But the residue 62-74 is there in both chains. Have the ncs group to be exactly same to find NCS? how can i fix this? ps: phenix.simple_ncs_from_map works well with my pdb. using the ncs_spec file also not works many thanks kaituo

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riding hydrogens
by Jianghai Zhu 07 Aug '08

07 Aug '08

Hi, I used phenix.reduce to add riding hydrogens. After phenix.refine, the structure got a good score from MolProbity. However, if I stripped the riding hydrogens from the structure and let MolProbity to add hydrogens before the analysis, I got a much worse score, especially the clash score. Does phenix.refine refine the hydrogen positions? -- Jianghai

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DNA restraints
by jens j birktoft 07 Aug '08

07 Aug '08

Hi, Is there a way to restrain selected hydrogen bonds between base pairs during the refinement of DNA structures ? CNS has something like DNA_RNA.def if I remember correctly and I am looking for something of that nature. Cheers Jens -- Jens J. Birktoft - e-mail: jens.knold(a)gmail.com slow-mail: 350 Central Park West, Suite 9F, New York, NY 10025 use 212-749-5057 for ALL phone calls

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Deborah Palestrant is out of the office.
by deborah.palestrant＠novartis.com 06 Aug '08

06 Aug '08

I will be out of the office starting 08/05/2008 and will not return until 08/11/2008.

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torsion angle dynamics simulated annealing?
by Bryan W. Lepore 05 Aug '08

05 Aug '08

i was wondering if someone could comment on any possibility of implementing torsion angle dynamics in phenix's simulated annealing procedure, in a future release of phenix? i.e. is that "in the works"? thanks! -bryan 1

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phenix.refine: Override 'Number of bonds with excessive lengths'
by Martin.Laurberg 05 Aug '08

05 Aug '08

Dear All, Is there a way to override the phenix.refine Setup Restraints Manager, preventing phenix.refine from terminating if the model features a lot of excessive bond lenghts? Thanks, /Martin ========================== Set up restraints manager ========================== .... Bonds with excessive lengths: Distance model: 50.2364 (ideal: 1.525) ATOM 1336 C3' DC B 20 12.611 28.560 12.463 1.00 42.81 C ATOM 1338 C2' DC B 20 -11.801 15.989 54.531 1.00 42.03 C .... Sorry: Number of bonds with excessive lengths: 71 -- Martin Laurberg, PhD Noller Laboratory 225 Sinsheimer Laboratories University of California at Santa Cruz CA-95064 Santa Cruz USA Tel +1 (831) 459 35 84 Fax +1 (831) 459 37 37

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Wishful thinking with AutoBuild?
by Francis E Reyes 05 Aug '08

05 Aug '08

Hello all Given a mediocre to bad experimental density map, what hopes does AutoBuild have of building a model? i.e. Should I be able to tell clear helicies and side chain density in the experimental density map before even attempting an autobuild? Thanks FR --------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

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GUI inactivity
by David Hoover 05 Aug '08

05 Aug '08

We have RedHat Enterprise Linux 5, and the Phenix installation went just fine. When I fired up the GUI, it looked ok, but the inset was blank. Many of the buttons seemed inactive as well. Is there any support for installation beyond that on the web page? David Hoover, Helix Systems Staff, CIT/NIH

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Ordered solvent - wish list
by Jendrek 04 Aug '08

04 Aug '08

Hi All, On the matter of ordered solvent I was just wondering if fixing specific waters (like ones close to metals) was implemented in the latest release. Also, it would be a nice touch if the water list was ordered according to some criteria. In my lab we prefer to have them in decreasing B factors - but that is just wishing... Regards, Andrzej -- Andrzej LYSKOWSKI, Ph.D. (andrzej[.]lyskowski[(a)]helsinki[.]fi) Institute of Biotechnology - Structural Biology & Biophysics P. O. Box 65 - Viikinkaari 1 Floor/Room: 4/4316 Mail: FIN-00014 University of HELSINKI, FINLAND Delivery: FIN-00710 University of HELSINKI, FINLAND TEL.: 358 9 191 58921 FAX : 358 9 191 59940

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ordered solvent - parameters?
by Mark Collins 01 Aug '08

01 Aug '08

Hi All I was just going through the .help section and website documentation for ordered_solvent. And wonder if somebody could enlighten me as too the meanings of; ordered_solvent { primary_map_type = mFobs-DFmodel secondary_map_type = 2mFobs-DFmodel h_bond_min_mac = 1.8 h_bond_min_sol = 1.8 h_bond_max = 3.2 } peak_search { map_next_to_model { use_hydrogens = False } max_number_of_peaks = None peak_search { peak_search_level = 1 max_peaks = 0 interpolate = True min_distance_sym_equiv = None general_positions_only = False min_cross_distance = 1.8 } What is the difference between the primary and secondary map? Is there away to pick sites in one and remove in another? Eg. pick sites at 3 sigma in FoFc and remove if 1.2 sigma in 2FoFc. I thought h-bonding was generously about 2.4-3.6A so why the 1.8 and 3.2 defaults? Also if use_hydrogens = True, does the refinement use h_bond parameters instead of model_peak_dist and peak_peak_dist parameters, or both? Also what do all of the peak_search parameters do? And finally does anyone have any recommendations for progessively changing the ordered_solvent parameters? In CNS we used to gradually lower the 2FoFc peak picking (and deleting) and increase the bfactor_max for deleting? Thanks Mark

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