August 2024 - phenixbb - phenix-online.org

Presence of negative density in Sim Omit map
by Renuka Kadirvelraj 12 Aug '24

12 Aug '24

Presence of negative density in Sim Omit map Hi Phenixbb, We would appreciate your advice regarding an odd problem that has cropped up with one of our crystal structures. We have a protein structure in space group P6(3)22 at 2.1 A resolution and in the final refinement stages with Rwork of 0.20 and Rfree of 0.22. When we ran simulated annealing to rebuild an outlier Lysine residue in a loop, the Sim Omit map showed the positive density expected from the omission of the loop (contour level 3 sigma, colored green in attached pics). However, flanking the positive density, there is a complimentary negative density (in red). We are puzzled as to the cause of the appearance of the negative density. Can you help us? Many thanks, Renu --------------------------------------------- Renu Kadirvelraj, Ph.D. Research Scientist A428, Biochemistry and Molecular Biology 120, East Green Street University of Georgia Athens, GA 30602 Tel: (706) 583 0303

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Maatel HC1c humidity controller available
by Jonathan Ruprecht 07 Aug '24

07 Aug '24

Dear bulletin board members, The MRC Mitochondrial Biology Unit in Cambridge, UK, has a Maatel HC1c humidity controller, together with the ancilliary components necessary to make a crystal dehydration rig, including a Nikon SMZ800 microscope, that is now surplus to our requirements and available free of charge (the new owner would be asked to pay for shipping). This was purchased in 2010, last used in approximately 2017 and is thought to be a working system. Please direct any enquiries to David Pate, MBU Laboratory Manager, ddp10(a)cam.ac.uk. Best wishes, Jonathan Ruprecht -- Dr Jonathan Ruprecht MRC Mitochondrial Biology Unit University of Cambridge Keith Peters Building Cambridge Biomedical Campus Hills Road Cambridge CB2 0XY

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phenix.refine command line: what to change on the subsequent def file to point to the desired input pdb
by Alejandro Buschiazzo 02 Aug '24

02 Aug '24

Dear phenix users/developers Some time ago there were several modifications on the names/specifications of important parameters/options (such as miller_array for structure factor files, etc) Running phenix.refine by command lines (no gui) is my favorite, and I am now running into several difficulties: 1- what’s the difference between miller_array and default_miller_array; or model and default_model? 2- what’s the precise definition of phil_files and default_phil? What to change if I manually edit my .eff? 3- how should I use the new automatically created .def file for subsequent refinement cycles after I’ve manually rebuilt (I need to point to the new pdb input file: I usually screw this up, can’t seem to use the newly created .def as my starting instructions file anymore, it complains that I have problems in the right definition of the input pdb, or too many models...) 4- I often fall into a loop where by default newly created .eff files include a dry_run=true option (e.g. when I deliberately tell phenix.refine to overwrite previous .eff files) Thanks a lot for clarifying on these issues: and sorry, for I couldn’t find obvious answers to them in the documentation (probably my fault!!) Also, I am using phenix v 1.21.1-5286 (on a Sonoma MacOS laptop) With best wishes Alejandro

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