July 2008 - phenixbb - phenix-online.org

ordered solvent - parameters?
by Mark Collins 31 Jul '08

31 Jul '08

Hi All I was just going through the .help section and website documentation for ordered_solvent. And wonder if somebody could enlighten me as too the meanings of; ordered_solvent { primary_map_type = mFobs-DFmodel secondary_map_type = 2mFobs-DFmodel h_bond_min_mac = 1.8 h_bond_min_sol = 1.8 h_bond_max = 3.2 } peak_search { map_next_to_model { use_hydrogens = False } max_number_of_peaks = None peak_search { peak_search_level = 1 max_peaks = 0 interpolate = True min_distance_sym_equiv = None general_positions_only = False min_cross_distance = 1.8 } What is the difference between the primary and secondary map? Is there away to pick sites in one and remove in another? Eg. pick sites at 3 sigma in FoFc and remove if 1.2 sigma in 2FoFc. I thought h-bonding was generously about 2.4-3.6A so why the 1.8 and 3.2 defaults? Also if use_hydrogens = True, does the refinement use h_bond parameters instead of model_peak_dist and peak_peak_dist parameters, or both? Also what do all of the peak_search parameters do? And finally does anyone have any recommendations for progessively changing the ordered_solvent parameters? In CNS we used to gradually lower the 2FoFc peak picking (and deleting) and increase the bfactor_max for deleting? Thanks Mark

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Maintaining the sugar puckerings
by YS. Chung 31 Jul '08

31 Jul '08

Hi all, I have a protein-DNA structure at 3 angstroms that I have been refining with refmac5. I have recently started to look into using phenix.refine instead. However, I am still having some problems with the sugar puckering of my DNA which is an ideal B-DNA and should be kept C2'-endo, but keeps changing to C1'-exo or C3'-endo after refinement with phenix. I have looked at the .cif files for the DNA and may update the restraints. Is this the easiest way to go about restraining the sugar puckering? Thank you, Yu Seon Chung

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calculating a phased anomalous difference map for twinned data in phenix.refine
by Michael Hothorn 31 Jul '08

31 Jul '08

Hi, to confirm the nature of a metal ion in my active site, I want to calculate a phased anomalous difference map in phenix.refine. However my crystals in SG P3(2) are twinned with twin law h,-h-k,-l and a fraction of about 40%. Is there a way to calculate an informative map in phenix.refine in this case? best Michael

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SA-omit maps for carbohydrates
by Enrico Girardi 30 Jul '08

30 Jul '08

Dear All, I would like to create a SA-omit map for two carbohydrate chains present in my structure. My attempts using the command phenix.autobuild data=data.mtz model=final.pdb omit_box_pdb=cho2.pdb composite_omit_type=sa_omit lead to a message in the log file saying: Failed to carry out AutoBuild_set_up_build: Sorry, unable to define an omit region with cho2.pdb res_start = None res end = None chain = '' ? Possibly no atoms? The procedure works fine with protein residues so I am assuming that phenix.autobuild is ignoring the sugars in the original pdb file (as it says in the log file..). Is this correct? How can I fix the problem? I am running Phenix 1.3b. Many thanks in advance for your help. Regards Enrico -- Enrico Girardi Randall Division of Cell and Molecular Biophysics King's College London New Hunt's House Guy's Campus London SE1 1UL Tel +44 (0)20 7848 6419 Fax +44 (0)20 7848 6435

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New PHENIX prerelease 1.3-rc4
by Paul Adams 28 Jul '08

28 Jul '08

Dear PHENIX Users, there is a new prerelease of PHENIX available (1.3, release candidate 4). It can be downloaded from the PHENIX web page as usual: http://www.phenix-online.org/ Cheers, Paul -- Paul Adams Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Head, Berkeley Center for Structural Biology Building 64, Room 248 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. Administrator: Delia Clark [ DNClark(a)lbl.gov ][ 1-510-486-6331 ] --

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phenix.automr
by Ivan Campeotto 28 Jul '08

28 Jul '08

Dear All, I am trying to use Phenix AutoMR followed by Autobuild. The problem is that in the output file "overall_best_refine_map_coeffs.mtz" from Autobuild the Fc values have been set to zero. The Fc values are not zero in the output file MR.1.mtz coming from AutoMR if it may be of help. Any suggestion to fix this problem will be appreciated. Thank you in advance Ivan

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phenix.automr problem
by allbette＠gmail.com 25 Jul '08

25 Jul '08

Dear all I tried to solve a structure by using phenix.automr. I am not sure how many molecules in the asymmetric unit(2-8molecules). How I can tell phenix.automr (phaser) that search at least 2 molecules in asymmetric unit use command line. Any suggestions are welcome.Thank you in advance. carl soja

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Re: [phenixbb] autobuild failed
by Thomas C. Terwilliger 24 Jul '08

24 Jul '08

Dear Kaituo, I'm sorry for the problem! I'm not certain what went wrong in this case. It could be that the size of the structure is too big, or it could be a problem with autobuild, or it could be a problem with slow read/write to your file system. The error message "Unable to read ok_file...trying bigger version" will occur if resolve does not finish writing out the file "resolve.ok" immediately after finishing. If you are running on a system that is NFS-mounted, you might try instead running on the local disk. This might fix it. Otherwise, can you help me figure this out by eliminating other possibilities: 1. Can you tell me the version of phenix you are using and what machine this is on: echo $PHENIX_VERSION uname -a 2. Can you send me the entire log file AutoBuild_run_1_1.log 3. Can you send me the file AutoBuild_run_1_/TEMP0/temporary.com 4. If you are willing to send your data, that would be helpful: just tar up your data files and command file and then attach it to an email (but rename the file ".txt" so that it will get sent properly through my email system). Then I can try to reproduce the problem here. All the best, Tom T > My autobuild failed and the log file said: > Columns used: labin FP=F SIGFP=SIGF FreeR_flag=FreeR_flag > Unable to read ok_file...trying bigger version > Failed to run resolve > ---------------------------------- > TRIED resolve ...but not OK > > ********************************************************************************Failed > to carry out AutoBuild_set_up_build: > failure > > how t solve this? > thanks > > kaituo > > peking University, Beijing > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb >

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autobuild failed
by wang kaituo 24 Jul '08

24 Jul '08

My autobuild failed and the log file said: Columns used: labin FP=F SIGFP=SIGF FreeR_flag=FreeR_flag Unable to read ok_file...trying bigger version Failed to run resolve ---------------------------------- TRIED resolve ...but not OK ********************************************************************************Failed to carry out AutoBuild_set_up_build: failure how t solve this? thanks kaituo peking University, Beijing

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Re: [phenixbb] reflection files, anomalous data, and test set
by Ralf W. Grosse-Kunstleve 23 Jul '08

23 Jul '08

Hi Mark, > input { > xray_data { > file_name = ../testmtz.mtz > labels = "I(+),SIGI(+),I(-),SIGI(-)" > r_free_flags { > file_name = ../SePeak.hkl > label = TEST > test_flag_value = 1 }} Could you try this instead? xray_data { file_name = SePeak.sca labels = None r_free_flags { file_name = ../SePeak.hkl label = TEST test_flag_value = 1 }} Let me know if this gives the same error as before (could be). Ralf

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