Web-t STR,--extend STR write NMD file for the model extended to"backbone" ("bb") or "all"atoms of the residue, model must have one node per residue-b,--beta-factors write beta-factors calculated fromGNM modes-l,--hessian write Hessian matrix-k,--kirchhoff write Kirchhoff matrix output options:-p STR,--file-prefix STR output file prefix (default ... Web(set-hardware-stereo-angle-factor angle-factor) where angle-factor would typically be between 1.0 and 2.0 3.4.2 Pick Cursor. When asked to pick a residue or atom, the cursor changes from the normal arrow shape to a "pick" cursor. Sometimes it is difficult to see the default pick cursor, so you can change it using the function (set-pick-cursor ...
PHENIX Wizards and Tools - CCP4
WebExample 1C: Atomic B factor fitting and reporting model-map agreement. ... The second mover will calculate a model-map FSC (Fourier Shell Correlation), and integrate over the input resolution ranges. ... Phenix contains a wrapper command, phenix.rosetta.run_phenix_interface, that point Rosetta and Phenix to each other. So all … WebThe phenix.form_factor_query command is available for obtaining estimates of f' and f" given an element type and a wavelength, e.g.: % phenix.form_factor_query element=Br wavelength=0.8 Information from Sasaki table about Br (Z = 35) at 0.8 A fp: -1.0333 fdp: … Other links Bibliography Dictionary Index Find a program or regression test Citing … Individual B-factors is restrained atomic B-factor refinement, and is usually … Many of the programs in Phenix, and phenix.refine in particular, allow (or … ted balistreri milwaukee
BDB: Databank of PDB files with consistent B-factors
WebFeb 4, 2024 · The goals were to (1) assess the quality of models that can be produced from cryogenic electron microscopy (cryo-EM) maps using current modeling software, (2) evaluate reproducibility of modeling... WebThe format is the number of electrons followed by the charge sign, for example "1-" or "2+". You can edit the PDB file manually to add this, but we recommend using phenix.pdbtools: … http://phenix.lbl.gov/pipermail/phenixbb/2014-October/021276.html teddi jones music