February 2018 - phenixbb - phenix-online.org

Residual B values after refinement
by ANAN YUENYAO 07 Feb '18

07 Feb '18

Dear All, I have encountered some error during the PDB validation process after refinement with PHENIX (1.13). After uploading the coordinates and structure factor file, in the header 'Basic coordinate validity', it says that the data contains residual B values. Could anyone please explain the reason behind this error message. Is it going to be problematic for the future PDB deposition? P.S. I have already performed TLS and group B-factor refinement. Thank you in advance! Anan

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FASTA format for sequence file
by egoers＠uoregon.edu 06 Feb '18

06 Feb '18

Hello, I'm trying to run Phase-MR on Phenix (older version) and having trouble formatting my sequence properly. I keep getting error "Protein Sequence not recognized in Composition". I have a good idea of what FASTA should look like (carrot with a name, no spaces or weird characters, followed by the sequence in all capital letter on the next line). I have tried many things, mainly using gedit and plain text files (.txt). I've made sure the file name doesn't have any strange characters as well. If I cut and paste a FASTA file from the PDB into gedit, save that at a .txt, Phaser accepts it. If I cut and paste my protein sequence into the same file, it rejects it. Suggestions?

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how to bypass/deactivate dictionnary check for restraints in phenix.refine
by Maxime Cuypers 03 Feb '18

03 Feb '18

Hello All, I am refining an unusual complex moiety in a protein xl with neutron data. Does anyone know if it is possible to bypass/deactivate dictionnary .cif check i got the blocking error message "it looks like angle and bond restraints are conflicting." and Phenix.refine stops. but really it s not conflicting: my .cif file works great in coot to model the complex. it is hydrogen based, so i really need restraints to get it optimal. any clues welcome, many thanks in advance. Dr. Maxime Cuypers Post-Doctoral Research Associate, Structural Biology St Jude Children s Research Hospital, 262 Danny Thomas Place Memphis, TN 38105-3678, USA

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side-chain on special position.
by Aaron Oakley 02 Feb '18

02 Feb '18

Hello fellow Phenix-ers, I have a structure I am trying to finish in Phenix.refine The is one problem: a glutamate residue sitting on a crystallography 2-fold axis with partial occupancy (picture attached). This residue and its symmetry mate appear to take turns sitting at this position: filling the density leads to severe collision with its symmetry mate. Building the side-chain with occupancy 0.5 doesn’t seem to help, as the residue is pushed out of density during refinement. Any work-arounds? Thanks all, Aaron [cid:[email protected]]

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phenix auto sharpen local sharpening masking artifacts?
by Oliver Clarke 02 Feb '18

02 Feb '18

Hi, I’m trying to run phenix.auto_sharpen with local sharpening, because I have an EM map that has a reasonably substantial variation in local resolution. This is the command I used: phenix.auto_sharpen cryosparc_exp001049_008.mrc resolution=3.26 local_sharpening=true local_aniso_in_local_sharpening=true model.pdb nproc=4 seq_file=seq.fasta >& log & The resulting map looks beautiful (maybe a little too beautiful??) around the model, but shows some funky looking masking artifacts in the density further away from the model (in the micelle region) - see screenshot. Am I doing something wrong? And can I trust that the density is completely free of model bias? Cheers Oli

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