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phenix.pdbtools
by Jianghai Zhu 20 Aug '08

20 Aug '08

Hi, I am trying to use phenix.pdbtools to calculate the geometry statistics for a model from Rosetta. "phenix.pdbtools --show-geometry- statistics foo.pdb" stopped with a message "Sorry: Number of bonds with excessive lengths: 707". Anybody know what happened there? Thanks. -- Jianghai

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placing ligands in coot with phenix.elbow output
by Feldman III, George Franklin 20 Aug '08

20 Aug '08

Hi all, I am having difficulties with my ligand. My ligand is an FMN (flavin mononucleotide) and its pdb file was originally created using PRODRG. I used the DRGFIN.PDB output file to run elbow (phenix.elbow DRGFIN.PDB --opt). The output contains hydrogens, which as we all know do not work well with coot. So when I try to place my ligand in its correct position and save the coordinates in coot, I get an error of duplicated atom labels when trying to merge the molecule to the ligand using phenix.refine. I tried using the command "phenix.elbow DRGFIN.PDB --opt --write-hydrogens=False" but phenix told me that last command doesnt exist (although its posted on the web page). Manually changing the atom names will affect both the connectivity and the cif file (I think), so it is an option I would rather avoid. Is there a way around all of this? Best Regards, George (Trey) Feldman

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Re: [phenixbb] [phenix] generate r free flags in phenix.refine not obeying high resolution limit?
by Pascal EGEA 20 Aug '08

20 Aug '08

Hi All, Following Pavel's answer to Francis Reyes, I have a very basic question about this too. What is a good distribution of reflections and what are thin bins of resolution to ensure correct ML estimations? Are there any basic statistical rules that should be considered. Thanks Pascal Pascal F. Egea, PhD Post Doctoral Researcher University of California San Francisco Department of Biophysics and Biochemistry Robert Stroud Laboratory pascal(a)msg.ucsf.edu

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generate r free flags in phenix.refine not obeying high resolution limit?
by Francis E Reyes 20 Aug '08

20 Aug '08

Hi all When generating R-Free flags from phenix refine, flags are generated all the way to the limit of the data. However, shouldn't flags be generated up to the limit of the data if specified via refinement.input.xray_data.high_resolutio n ? If not, are the statistics for R/Rfree matching to high resolution data that may be suspicious ? 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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(no subject)
by Sudharsan Sridharan 20 Aug '08

20 Aug '08

Hi all, A quick question about extracting info/preparing pdb file for deposition.......... I've got a pdb file after refinement using phenix 1.3b. I was wondering if there is a way to prepare this file / format this the same way as in 1.3 final where we get "REMARK IF THIS FILE IS FOR PDB DEPOSITION: REMOVE ALL FROM THIS LINE UP" and REMARK 3. i'm already running refinement 1.3 final with the same parameters just to quickly compare the resulting refined files/numbers. I guess I could do it manually but curious if there is an easier way using 1.3 final. thanks, Sid.

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Resolution cutoffs. Always debated?
by Francis E Reyes 19 Aug '08

19 Aug '08

I need to put this in front of (this) crystallographic community. What are the criteria for cutting a resolution for data reduction ? Rmerge, I/sig, mean I/sig, completeness... more? I once believed that I/Sig (not averaged) greater than 2 was the cutoff, but I've read online (particularly http://www.mail-archive.com/[email protected]/msg02576.html) that this is no longer the case because of maximum likelihood. I would love to know why this is the case as well as poll the community on how they cut off their data. 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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Autobuild builds more residues after MR?
by Francis E Reyes 19 Aug '08

19 Aug '08

Perhaps a silly question, but suppose after MR, there is additional density to be built (say, another molecule). Will the autobuild after mr build into this new density? 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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ALS user meeting
by Peter Zwart 18 Aug '08

18 Aug '08

Dear All, I would like to draw your attention to this years ALS user meeting, held from October 13-15. In particular, the workshop titled "Recent advances in the automation of protein crystallography" might be of interest to the protein crystallographic community. The workshop consists of a series of short talks and a hands-on session in which various developers and beamline staff will demo latest developments on their beamlines. Scheduled speakers include: Gyorgy Snell (Takeda SD) Aina Cohen (SSRL) Jay Nix (ALS beamline 4.2.2) Babu Pothineni ( GMCA cat, APS) Scheduled Demonstrations are (tentative titles only) : * Efficient screening and data collection using Mini & WebIce (Bl. 5.0.n) Peter Zwart, John Taylor & Nick Sauter * Data collection @ 4.2.2 Jay Nix * SSRL & Webice Aina Cohen * Automated structure solution with PHENIX P. Afonine * Elves & 8.3.1 J. Holton Detailed workshop information can be found at http://bcsb.als.lbl.gov/wiki/index.php/ALS2008_Workshop Other workshops of interest held during the ALS user meeting can be found here: http://www-als.lbl.gov/als/usermtg/workshops.html Registration is now open for all participants: http://www-als.lbl.gov/als/usermtg/index.html Greetings Peter Zwart -- ----------------------------------------------------------------- P.H. Zwart Beamline Scientist Berkeley Center for Structural Biology Lawrence Berkeley National Laboratories 1 Cyclotron Road, Berkeley, CA-94703, USA BCSB: http://bcsb.als.lbl.gov PHENIX: http://www.phenix-online.org CCTBX: http://cctbx.sf.net -----------------------------------------------------------------

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sharing the ext_ref_files between multiple installations
by Ben Eisenbraun 18 Aug '08

18 Aug '08

Howdy, I'm wondering if it's possible for me to put the ext_ref_files directory into a shared location and then symlink that directory into multiple PHENIX installations to save some disk space. Are the files specific to a particular PHENIX version? Or to a specific CPU architecture? Thanks. -ben -- Ben Eisenbraun Structural Biology Grid Harvard Medical School http://sbgrid.org http://hms.harvard.edu

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anomalous difference map calculation option in phenix.refine
by Pavel Afonine 18 Aug '08

18 Aug '08

For many of you who asked for anomalous difference map calculation option in phenix.refine: this is fixed and available in just announced PHENIX release. Pavel.

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