Phenix refine b factor
http://phenix.lbl.gov/pipermail/phenixbb/2008-February/012013.html WebNov 8, 2024 · 2.1. Code preparation. The integration of the Amber code into phenix.refine uses a thin client. Amber provides a Python API to its sander module, so that a simple `import sander' Python command allows Phenix to obtain Amber energies and forces through a method call. At each step of coordinate refinement, Phenix expands the …
Phenix refine b factor
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WebI'm currently refining an enzyme structure (data from X-ray crystallography). Resolution is 2.8 Å; model was generated using MR on a template with 62% sequence identity and Autobuild (Phenix). I ... Web>>dw = isotropic or anisotropic Debye-Waller factor >occ = occupancy factor (between 0 and 1) >sym_weight = usually 1 except for special positions >x = fractional coordinate of atom >h = Miller index >>f0 = Sum[a_i * exp(-b_i * stol**2)] >>If you scale all the a_i by a constant factor, it is the same as
WebYou can group all the atoms of a residue, or alternatively its side-chain and main-chain atoms as two groups, and refine a single B-factor for them. You can implement this in … Webphenix.refine and phenix.model_vs_data use the same code to perform the bulk solvent correction and scaling, so they should report approximately the same R-factors given …
Webrefinement program (CNS can't do TLS, REFMAC doesn't do grouped B-factors). While REFMAC might still perhaps rule the roost at high resolution I have the impression that phenix.refine And I work mostly at lower resolutions. Like other programs it takes a while to get used to the quirks and syntax.
WebYou can launch phenix.refine directly from Phaser by clicking the button labeled "Run phenix.refine". This will load the output model and the MTZ file; you should also input the sequence (this is not actually used in refinement, but the post-refinement validation will check for sequence errors in the model).
http://phenix.lbl.gov/pipermail/phenixbb/2015-July/022248.html head of steam leeds christmasWebb-factors after molrep were 118.585, R=0.32, and Rfree=0.40. Initial refinement was done with refmac and: mean b-value=117.344 R=0.31 Rfree=0.40 Refinement with Phenix (phenix-installer-dev-2054-intel-linux-2.6-x86_64-centos5) was performed and the Ramachandran plot was bad: OUTLIERS : 6.52 % ALLOWED : 13.67 % FAVORED : 79.82 % gold rush the game panningWebFeb 16, 2015 · Phenix refinement has automatically added water molecules to the models. difraction data was collected to 720 frames 360 degree. mosflm indexing gives solutions in p222 p2, the final model was... head of state watch for free full movieWebNext message: [phenixbb] on B-factor refine Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] Dear All， If in the Phenix refine GUI, I only want to refine based on individual B-factors, can I only click "individual B-factors" without cliking any other items in the "Strategy" and without clicking any items in the "Targets and ... head of steam birmingham pubWebphenix.refine *.pdb *.mtz The program can read in pretty much any reflection file format (so no need to convert your mtz files!) and will run using defaults. Output files Once the … gold rush the game ps4 newsWebphenix.probe: Run PROBE, for analysis of all-atom contacts. phenix.r_factor_statistics: Distribution of Rfree, Rwork and Rfree-Rwork for PDB models at similar resolution. phenix.ramalyze: Validate protein backbone Ramachandran dihedral angles. phenix.reduce: Run REDUCE, software for addition or trimming of hydrogens. head of steam headingley leedsWebDec 8, 2024 · Though the difference in values are small, your refinement shells should not extend beyond your overall refinement range. You may wish to check your refinement details and determine which is... head of steam hull menu