February 2015 - phenixbb - phenix-online.org

labelit distl_minimum_number_spots_for_indexing
by Christian Roth 22 Sep '15

22 Sep '15

Dear Phenix-Team I installed the latest nightly build 1.8-1069. I tried to index some diffraction images and to overwrite the minimum usable spots for indesing I tried the suggested command. However If I try this command, it seems that it does not exist. At least in the list of the possible distl commands it does not show up. Do I have to install some additional stuff or change some preferences to get this command? Best Regards Christian

6 8

Refinement with new mtz.file
by Aleksandar Bijelic 14 Jul '15

14 Jul '15

Dear CCP4 user and experts, I refined (with PHENIX) a 3.0 A dataset obtaining Rfree of about 0.24 (with good geometry according to Ramachandran, Beta Outliers, etc.) .... Everything seems to be ok (especially in relation to the resolution) .... because the mtz.file I used was quite old and I cannot find my xscale.hkl file, I processed the data set again (this time with optimizng and polishing) and received a "better" file according to almost everything (resolution limit, I/sigma, CC(1/2), Rmeas), thus I used this new mtz.file and put it in my last refinement step (the refinement which led to the above mentioned Rfree = 0.24). Suprisingly, the refinement starts at Rwork = 0.18 and Rfree = 0.19 but ending up with 0.20 and 0.22, respectively. So I wanted to know if this is usual? I was expecting my data to become slightlly better but what is irritating me is the starting R-values of the refinement and that it get worse during refinement. Maybe I did something wrong? Is it reasonable to replace the mtz.file with a new one in the last refinement step or should I start the refinement from the scratch? In the sake of completeness, I deleted the header of the used pdb.file because of the R-flag error which occurs, since Phenix reconizes that the pdb.file was already used with other Rflags. Sorry, but I am still a beginner in this field, so I would be very grateful if somebody could explain me this situation and my mistake and if I need to start refinement from the beginning. Thank you in advance! Best Regards. Aleksandar -- ------------------------------------------- Aleksandar Bijelic, MSc. Institut für Biophysikalische Chemie Universität Wien Althanstrasse 14 A-1090 Wien Tel: +43 1 4277 52536 e-Mail: aleksandar.bijelic(a)univie.ac.at --------------------------------------------

7 10

idealizing structure
by PC 27 Apr '15

27 Apr '15

Is there a way to "idealize" a structure in Phenix? I mean, ideal omega, all residues within allowed regions of Ramachandran maps, no clashes..etc. I know it won't fit the map well but I would like to see what it looks like. Thank you. ____________________________________________________________ FREE 3D MARINE AQUARIUM SCREENSAVER - Watch dolphins, sharks & orcas on your desktop! Check it out at http://www.inbox.com/marineaquarium

4 5

get_cc_mtz_pdb for neutron data table
by Maxime Cuypers 27 Feb '15

27 Feb '15

hi, i need the correlation coefficients map/residues for a publication, which command should i use to get phenix.get_cc_mtz_pdb to take into account the neutron scattering tables? seems it uses the x ray tables by default. i can not find it on this page: http://www.phenix-online.org/version_docs/1.8.3-1472/get_cc_mtz_pdb.htm#anc… many thanks for your reply. -- Dr. Maxime Cuypers

2 1

hiding clash dots
by Sebastiano Pasqualato 26 Feb '15

26 Feb '15

Hi all, a quick question: how do I get rid of the clash dots that appear in Coot, when opened from a phenix job? thanks a lot in advance, best, Sebastiano -- Sebastiano Pasqualato, PhD Crystallography Unit Department of Experimental Oncology European Institute of Oncology IFOM-IEO Campus via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5167 fax +39 02 9437 5990 web http://is.gd/IEO_XtalUnit <http://is.gd/IEO_XtalUnit>

3 3

on phenix.cut_out_density
by Smith Lee 26 Feb '15

26 Feb '15

Dear All, Can the mtz file produced by phenix.cut_out_density be used by Phenix refine for refinement? Smith

2 1

a sharp rise of R-free in resolution bin
by Singh, Bishal 25 Feb '15

25 Feb '15

Hello everyone, I am refining a structure at 2.3 A resolution. R-work/R-free is 26/31 and is not reducing further. When I looked into the resolution bin, I notices a sharp rise of R-free between resolution range 2.5-2.6 A (marked in figure below). However R-work is fine. I am doubtful of reducing the resolution to 2.5 A or lower. Please suggest me your opinion. Your words will be highly appreciated. With regards, Bishal Singh PhD Student University of Heidelberg, Germany

2 1

How to define a disulfide bond between symmetry related molecules in phenix.refine
by Michael Hothorn 25 Feb '15

25 Feb '15

Dear all, I am trying to refine an intermolecular disulfide bond in phenix.refine. The disulfide involves Cys 188 in chain A and Cys 188 of chain B of a symmetry related molecule, with symop -X, Y+1/2, Z+1/2. There are two molecules in the AU, SG is P212121. I generated the following SSBOND entry in the pdb header: SSBOND 2 CYS A 188 CYS B 188 1555 3555 2.04 Based on this: http://www.wwpdb.org/documentation/file-format/format33/sect6.html the format seems fine, but the disulfide is not being recognized during refinement. Could someone point out to me how to correctly define this for phenix.refine. Thanks! Michael

3 2

sharp rise of R-free in resolution bins
by Singh, Bishal 25 Feb '15

25 Feb '15

Hello everyone, I am refining a structure at 2.3 A resolution. R-work/R-free is 26/31 and is not reducing further. When I looked into the resolution bin, I notices a sharp rise of R-free between resolution range 2.5-2.6 A (marked in figure below). However R-work is fine. I am doubtful of reducing the resolution to 2.5 A or lower. Please suggest me your opinion. Your words will be highly appreciated. With regards, Bishal Singh PhD Student University of Heidelberg, Germany

1 0

On Ramachandran restraints of Phenix refine
by Smith Lee 25 Feb '15

25 Feb '15

Dear All, If my resolution was between 2.5-3.0 A, and if I did not use Ramachandran restraints in the Phenix refine the Ramachandran outliers would be increased significantly during the refinement process, in this situation may I use Ramachandran restraints in the Phenix refine? I am looking forward to getting your reply. Smith

2 1