- phenixbb - phenix-online.org

phenix.maps: a command line tool to compute various maps
by Pavel Afonine 05 Feb '10

05 Feb '10

Starting PHENIX nightly build version 1.6-295 (or whatever next version), the new command line tool phenix.maps is available. As the name suggests, this is the tool for map calculation: regular (p*Fobs-q*Fcalc) or maximum-likelihood (p*mFobs-q*DFcalc), with any user-defined coefficients p and q, as many as requested. For example, 2mFo-DFc, 3Fo-2Fc, mFo-DFc, Fc, Fo, Anomalous difference maps can be all computed at once. Also, a user has a full control over various map calculation parameters, such as filling missing Fobs with DFc, computing kick maps, etc. Maps can be output in X-plor formatted files or as Fourier map coefficients in MTZ formatted file. X-plor formatted maps can be computed for the whole molecule/unit cell or any selected part of the structure. This new tool is meant to be a replacement for current practice of computing the maps using phenix.refine (although, phenix.refine still output maps as before). For more information and usage examples simply run phenix.maps . This is available from PHENIX GUI too (thanks Nathaniel Echols). For usage instructions and quick manual type phenix.maps and hit Enter. Please let me know should any questions or problems related to using this tool arise. Pavel. P.S. Below is the result of running phenix.maps: phenix.maps: a command line tool to compute various maps. How to run: 1. Run phenix.maps without any arguments: just type phenix.maps in the command line and hit Enter. This will create a parameter file called maps.params, which can be renamed if desired. 2. Edit maps.params file to specify input/output files and the desired maps. It is possible to request as many maps as desired. 3. Run this command to compute requested maps: phenix.maps maps.params Remarks: - The scope of parameters 'map_coefficients' defines the map that will be output as Fourier map coefficients. The scope of parameters 'map' defines the map that will be output as X-plor formatted map. - To create several maps: duplicate either 'map_coefficients' or 'map' or both scopes of parameters as many times as many maps is desired. Then edit each of them to define the maps. - A map is defined by specifying a map type using 'map_type' keyword available within each scope of parameters: 'map_coefficients' or 'map'. The general supported format for 'map_type' is: [p][m]Fo+[q][D]Fc[kick][filled]. For example: 2Fo-Fc, 2mFobs-DFcalc, 3Fobs-2Fmodel, Fo-Fc, mfobs-Dfcalc, anom. The 'map_type' parser will automatically recognize which map is requested. - The program creates as many files with X-plor formatted maps as many X-plor formatted maps is requested, and it creates only one MTZ formatted file with all Fourier map coefficients in it. - The X-plor formatted map can be computed in the entire unit cell or around selected atoms only. - Kick maps and missing Fobs filling is done (if requested) as described in Adams et al. (2010). Acta Cryst. D66, 213-221. - Twinning (if detected) will be accounted for automatically. - All arrays used in map calculation, for example: Fobs, Fmodel, Fcalc, Fmask, m, D, etc., can be output into a CNS or MTZ formatted reflection file.

1 0

Completeness issue by phenix - revisited
by J. Fleming 04 Feb '10

04 Feb '10

Hi, I'm having a problem using phenix.refine with my x-ray data. My completeness is always 89% when it should be 99%. My data was originally processed with CCP4i. I found an old post (see below) with a potential fix that doesn't work for me. I've tried changing the 'Anomalous flag: True' to 'Anomalous flag: False' but my completeness is still 89%. I've clicked through a variety of other setting in the GUI that I thought would help but no luck. Does anyone have any ideas? Thanks in advance, Jon ----- Original Message ----- From: "Ralf W. Grosse-Kunstleve" <rwgk at cci.lbl.gov <http://www.phenix-online.org/mailman/listinfo/phenixbb>> To: phenixbb at phenix-online.org <http://www.phenix-online.org/mailman/listinfo/phenixbb> Sent: Monday, December 15, 2008 12:59:12 PM GMT -05:00 US/Canada Eastern Subject: Re: [phenixbb] Completeness issue by phenix Hi YoungJin, I suspect phenix.refine decided your mtz file contains anomalous data when you actually have non-anomalous data. Could you look in the phenix.refine output for something like this: ================================== X-ray data ================================= F-obs: 1yjp.mtz:FOBS_X,SIGFOBS_X R-free flags: 1yjp.mtz:R-free-flags Miller array info: 1yjp.mtz:FOBS_X,SIGFOBS_X Observation type: xray.amplitude Type of data: double, size=495 Type of sigmas: double, size=495 Number of Miller indices: 495 Anomalous flag: False ^^^^^ in particular here If you see "Anomalous flag: True" try adding this to the phenix.refine command line: xray_data.force_anomalous_flag_to_be_equal_to=False Let me know if this doesn't help. If it does help, I'd be interested to know how the .mtz file was generated. Ralf

3 2

BEAM TIME AVAILABLE FOR MACROMOLECULAR CRYSTALLOGRAPHY
by Cyndi Salbego 02 Feb '10

02 Feb '10

BEAM TIME AVAILABLE FOR MACROMOLECULAR CRYSTALLOGRAPHY AT THE TWO ID BEAMLINES OF NE-CAT AT APS. Beamline 24ID-C: Equipped with MD2 microdiffractometer, tunable between 6-21KeV, ADSC Q315 Detector, MAD Capable. Outfitted with ALS-style robot that can use ALS pucks or Unipucks. Beamline 24ID-E: Equipped with MD2 microdiffractometer, delivering beam as small as 5 microns. Single energy (12662eV) optimized for Se-SAD experiments, ADSC Q315 Detector. Outfitted with ALS-style robot that can use ALS pucks or Unipucks. For more information on our beamlines (beamline and robot manuals) along with updated schedule availability please see: http://necat.chem.cornell.edu or contact Cyndi Salbego (csalbego(a)anl.gov) for further information. To apply for General User Time (Rapid Access for current run cycle) please follow this link: https://beam.aps.anl.gov/pls/apsweb/gup0005.start_page Cyndi Salbego Administrator, NECAT 630.252.0689

1 0

AUTOSOL for MAD data with error message-'Need a symfile for solve'
by m.b.rajasekaran＠reading.ac.uk 02 Feb '10

02 Feb '10

Dear all, I have a query regarding the Autosol option in the PHENIX-1.6-289 version. We are trying to process a MAD data for a zinc bound protein crystal with AuTOSOL. We uploaded the scaled files, sequence and all other details and started running AUTOSOL. But the program stopped with the following error message pasted below mentioning some missing of symfile. We were not able to locate any parameters file on the installation directory. It would be helpful if we get some useful suggestions on this. Thanks in advance, Mohan *********************************************************** PHENIX AutoSol Tue Feb 2 12:37:41 2010 ************************************************************ Working directory: /home/sar06mbr/30JanDiamondI02/107/107_php22121 PHENIX VERSION: 1.6 of 29-01-2010 PHENIX RELEASE_TAG : 289 PHENIX MTYPE : intel-linux-2.6 PHENIX MVERSION : suse AutoSol_start AutoSol Run 2 Tue Feb 2 12:37:41 2010 INPUT FILE LIST: ['/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_2_P22121_scala2.mtz', '/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_3_P22121_scala2.mtz', '/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_4_P22121_scala2.mtz'] Copied /home/sar06mbr/30JanDiamondI02/107/107_php22121/result.seq to /home/sar06mbr/30JanDiamondI02/107/107_php22121/AutoSol_run_2_/sequence_autosol.dat Setting chain_type to PROTEIN Setting defaults for data_quality moderate Setting thorough_denmod to Yes Settin fix_xyz_after_denmod to False Setting max_ha_iterations to 2 Setting fixscattfactors to No Settin defaults for thoroughness quick Setting best_of_n_hyss_always to 1 Setting max_extra_unique_solutions to 0 Settin ha_iteration to No Setting max_choices to 1 Setting number_of_models to 1 Setting number_of_builds to 1 Setting test_mask_type to No Setting n_cycle_build to 0 Setting thorough_loop_fit to Setting create_scoring_table to No Not truncating ha sites at start of resolve as this is not PHASER SAD phasing Trying to guess refinement file for later use from ['/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_2_P22121_scala2.mtz', '/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_3_P22121_scala2.mtz', '/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_4_P22121_scala2.mtz'] Choosing guess of refinement file for later use from all files: ['/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_2_P22121_scala2.mtz', '/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_3_P22121_scala2.mtz', '/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_4_P22121_scala2.mtz'] FILE TYPE ccp4_mtz COLUMN LABELS: ['H', 'K', 'L', 'FreeR_flag', 'F_107_2re', 'SIGF_107_2re', 'F_107_2re(+)', 'SIGF_107_2re(+)', 'F_107_2re(-)', 'SIGF_107_2re(-)', 'DANO_107_2re', 'SIGDANO_107_2re', 'IMEAN_107_2re', 'SIGIMEAN_107_2re', 'I_107_2re(+)', 'SIGI_107_2re(+)', 'I_107_2re(-)', 'SIGI_107_2re(-)'] GUESS FILE TYPE MERGE TYPE mtz premerged TARGET LABELS ['F1', 'SIGF1', 'DANO1', 'SIGDANO1'] Unit cell: (34.79, 108.92, 134.88, 90, 90, 90) Space group: P 2 21 21 (No. 18) CONTENTS: ['/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_2_P22121_scala2.mtz', 'mtz', 'premerged', 'P 2 21 21', [34.790000915527344, 108.92009735107422, 134.8800048828125, 90.0, 90.0, 90.0], 2.4890566908055836, ['F1', 'SIGF1', 'DANO1', 'SIGDANO1']] File /home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_2_P22121_scala2.mtz RES: 2.5 FILE TYPE ccp4_mtz COLUMN LABELS: ['H', 'K', 'L', 'FreeR_flag', 'F_107_3re', 'SIGF_107_3re', 'F_107_3re(+)', 'SIGF_107_3re(+)', 'F_107_3re(-)', 'SIGF_107_3re(-)', 'DANO_107_3re', 'SIGDANO_107_3re', 'IMEAN_107_3re', 'SIGIMEAN_107_3re', 'I_107_3re(+)', 'SIGI_107_3re(+)', 'I_107_3re(-)', 'SIGI_107_3re(-)'] GUESS FILE TYPE MERGE TYPE mtz premerged TARGET LABELS ['F1', 'SIGF1', 'DANO1', 'SIGDANO1'] Unit cell: (34.85, 109.18, 135.27, 90, 90, 90) Space group: P 2 21 21 (No. 18) CONTENTS: ['/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_3_P22121_scala2.mtz', 'mtz', 'premerged', 'P 2 21 21', [34.849998474121094, 109.18000030517578, 135.26980590820312, 90.0, 90.0, 90.0], 2.4889952912293629, ['F1', 'SIGF1', 'DANO1', 'SIGDANO1']] File /home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_3_P22121_scala2.mtz RES: 2.5 FILE TYPE ccp4_mtz COLUMN LABELS: ['H', 'K', 'L', 'FreeR_flag', 'F_107_4re', 'SIGF_107_4re', 'F_107_4re(+)', 'SIGF_107_4re(+)', 'F_107_4re(-)', 'SIGF_107_4re(-)', 'DANO_107_4re', 'SIGDANO_107_4re', 'IMEAN_107_4re', 'SIGIMEAN_107_4re', 'I_107_4re(+)', 'SIGI_107_4re(+)', 'I_107_4re(-)', 'SIGI_107_4re(-)'] GUESS FIL TARGET LABELS ['F1', 'SIGF1', 'DANO1', 'SIGDANO1'] Unit cell: (34.87, 109.2, 135.33, 90, 90, 90) Space group: P 2 21 21 (No. 18) CONTENTS: ['/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_4_P22121_scala2.mtz', 'mtz', 'premerged', 'P 2 21 21', [34.869998931884766, 109.19999694824219, 135.32989501953125, 90.0, 90.0, 90.0], 2.4890134311310943, ['F1', 'SIGF1', 'DANO1', 'SIGDANO1']] File /home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_4_P22121_scala2.mtz RES: 2.5 Guess of datafile for refinement: /home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_3_P22121_scala2.mtz Using /home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_3_P22121_scala2.mtz for refinement Specify input_refinement_file=/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_3_P22121_scala2.mtz to change this HKLIN ENTRY: /home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_2_P22121_scala2.mtz FILE TYPE ccp4_mtz COLUMN LABELS: ['H', 'K', 'L', 'FreeR_flag', 'F_107_2re', 'SIGF_107_2re', 'F_107_2re(+)', 'SIGF_107_2re(+)', 'F_107_2re(-)', 'SIGF_107_2re(-)', 'DANO_107_2re', 'SIGDANO_107_2re', 'IMEAN_107_2re', 'SIGIMEAN_107_2re', 'I_107_2re(+)', 'SIGI_107_2re(+)', 'I_107_2re(-)', 'SIGI_107_2re(-)'] GUESS FILE TYPE MERGE TYPE mtz premerged TARGET LABELS ['F1', 'SIGF1', 'DANO1', 'SIGDANO1'] Unit cell: (34.79, 108.92, 134.88, 90, 90, 90) Space group: P 2 21 21 (No. 18) CONTENTS: ['/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_2_P22121_scala2.mtz', 'mtz', 'premerged', 'P 2 21 21', [34.790000915527344, 108.92009735107422, 134.8800048828125, 90.0, 90.0, 90.0], 2.4890566908055836, ['F1', 'SIGF1', 'DANO1', 'SIGDANO1']] Inverse hand of space group: P 2 21 21 Creating sg entry from /home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_2_P22121_scala2.mtz Unit cell: (34.79, 108.92, 134.88, 90, 90, 90) Space group: P 2 21 21 (No. 18) Space group name is: P 2 21 21 symbol is: p22121 **************************************** AutoSol Input failed Need a symfile for solve ****************************************

4 4

automatically changed refinement parameters
by Sara Züger 02 Feb '10

02 Feb '10

Dear phenixbb, I have some questions regarding refinement parameters: When I run phenix v1.6 via the GUI, starting a fresh refinement session from the main window (I do TLS+isotropic ADP refinement and 5 macrocycles, otherwise everything default), I saw these non-default refinement settings in the run, which I did not specify myself, but the program: adp_restraints { iso { use_u_local_only = True sphere_radius = 1.55 distance_power = 0 average_power = 0 }} In the documentation I found that when doing TLS+isotropic ADP refinement, only Ulocal is restrained, so the first command makes sense. But how is it with the sphere_radius, distance_power and average_power? The default parameters are sphere_radius= 5.0 distance_power= 1.69 average_power= 1.03 What do these parameters mean? What does it mean when these parameters have changed (and why did they change)? And is it ok at all that they changed? And would they have an influence if I modify the start model by setting b_iso to a certain value and then refine "normally" with TLS+isotropic? Another parameter that changed and I did not specify is: Target_weights { wxu_scale = 2.72 } Why did this happen, is it because few cycles before I included optimize_weights? And why would this change the weights permanently? Does it make sense? Thank you for explaining me these things! Sara

2 3

Re: [phenixbb] AUTOSOL for MAD data with error message-'Need a symfile for solve'
by Thomas C. Terwilliger 02 Feb '10

02 Feb '10

Dear Mohan, I'm sorry for the trouble! I have not seen this one, but it must be a bug that I need to fix. Can you possibly send me the data file and exact command used (you can just send data to low-res such as 6 A if you like) and I will fix it? In the meantime...if you split your dataset up into individual files I would expect that to work, particularly if you convert to .sca. All the best, Tom T > >> >> Dear all, >> I have a query regarding the Autosol option in the >> PHENIX-1.6-289 version. We are trying to process a MAD data for a zinc >> bound protein crystal with AuTOSOL. We uploaded the scaled files, sequence >> and all other details and started running AUTOSOL. But the program stopped >> with the following error message pasted below mentioning some missing of >> symfile. We were not able to locate any parameters file on the >> installation >> directory. It would be helpful if we get some useful suggestions on this. >> >> Thanks in advance, >> Mohan >> *********************************************************** >> >> PHENIX AutoSol Tue Feb 2 12:37:41 2010 >> >> ************************************************************ >> >> Working directory: /home/sar06mbr/30JanDiamondI02/107/107_php22121 >> >> PHENIX VERSION: 1.6 of 29-01-2010 PHENIX RELEASE_TAG : 289 PHENIX MTYPE : >> intel-linux-2.6 PHENIX MVERSION : suse AutoSol_start AutoSol Run 2 Tue Feb >> 2 12:37:41 2010 INPUT FILE LIST: >> ['/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_2_P22121_scala2.mtz', >> '/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_3_P22121_scala2.mtz', >> '/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_4_P22121_scala2.mtz'] >> >> Copied /home/sar06mbr/30JanDiamondI02/107/107_php22121/result.seq to >> /home/sar06mbr/30JanDiamondI02/107/107_php22121/AutoSol_run_2_/sequence_autosol.dat >> >> Setting chain_type to PROTEIN Setting defaults for data_quality moderate >> Setting thorough_denmod to Yes Settin fix_xyz_after_denmod to False >> Setting >> max_ha_iterations to 2 Setting fixscattfactors to No Settin defaults for >> thoroughness quick Setting best_of_n_hyss_always to 1 Setting >> max_extra_unique_solutions to 0 Settin ha_iteration to No Setting >> max_choices to 1 Setting number_of_models to 1 Setting number_of_builds to >> 1 Setting test_mask_type to No Setting n_cycle_build to 0 Setting >> thorough_loop_fit to Setting create_scoring_table to No Not truncating ha >> sites at start of resolve as this is not PHASER SAD phasing >> >> Trying to guess refinement file for later use from >> ['/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_2_P22121_scala2.mtz', >> '/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_3_P22121_scala2.mtz', >> '/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_4_P22121_scala2.mtz'] >> >> Choosing guess of refinement file for later use from all files: >> ['/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_2_P22121_scala2.mtz', >> '/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_3_P22121_scala2.mtz', >> '/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_4_P22121_scala2.mtz'] >> >> FILE TYPE ccp4_mtz >> >> COLUMN LABELS: ['H', 'K', 'L', 'FreeR_flag', 'F_107_2re', 'SIGF_107_2re', >> 'F_107_2re(+)', 'SIGF_107_2re(+)', 'F_107_2re(-)', 'SIGF_107_2re(-)', >> 'DANO_107_2re', 'SIGDANO_107_2re', 'IMEAN_107_2re', 'SIGIMEAN_107_2re', >> 'I_107_2re(+)', 'SIGI_107_2re(+)', 'I_107_2re(-)', 'SIGI_107_2re(-)'] >> >> GUESS FILE TYPE MERGE TYPE mtz premerged TARGET LABELS ['F1', 'SIGF1', >> 'DANO1', 'SIGDANO1'] Unit cell: (34.79, 108.92, 134.88, 90, 90, 90) Space >> group: P 2 21 21 (No. 18) CONTENTS: >> ['/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_2_P22121_scala2.mtz', >> 'mtz', 'premerged', 'P 2 21 21', [34.790000915527344, 108.92009735107422, >> 134.8800048828125, 90.0, 90.0, 90.0], 2.4890566908055836, ['F1', 'SIGF1', >> 'DANO1', 'SIGDANO1']] >> >> File >> /home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_2_P22121_scala2.mtz >> RES: 2.5 >> >> FILE TYPE ccp4_mtz COLUMN LABELS: ['H', 'K', 'L', 'FreeR_flag', >> 'F_107_3re', 'SIGF_107_3re', 'F_107_3re(+)', 'SIGF_107_3re(+)', >> 'F_107_3re(-)', 'SIGF_107_3re(-)', 'DANO_107_3re', 'SIGDANO_107_3re', >> 'IMEAN_107_3re', 'SIGIMEAN_107_3re', 'I_107_3re(+)', 'SIGI_107_3re(+)', >> 'I_107_3re(-)', 'SIGI_107_3re(-)'] >> >> GUESS FILE TYPE MERGE TYPE mtz premerged TARGET LABELS ['F1', 'SIGF1', >> 'DANO1', 'SIGDANO1'] Unit cell: (34.85, 109.18, 135.27, 90, 90, 90) Space >> group: P 2 21 21 (No. 18) CONTENTS: >> ['/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_3_P22121_scala2.mtz', >> 'mtz', 'premerged', 'P 2 21 21', [34.849998474121094, 109.18000030517578, >> 135.26980590820312, 90.0, 90.0, 90.0], 2.4889952912293629, ['F1', 'SIGF1', >> 'DANO1', 'SIGDANO1']] >> >> File >> /home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_3_P22121_scala2.mtz >> RES: 2.5 >> >> FILE TYPE ccp4_mtz COLUMN LABELS: ['H', 'K', 'L', 'FreeR_flag', >> 'F_107_4re', 'SIGF_107_4re', 'F_107_4re(+)', 'SIGF_107_4re(+)', >> 'F_107_4re(-)', 'SIGF_107_4re(-)', 'DANO_107_4re', 'SIGDANO_107_4re', >> 'IMEAN_107_4re', 'SIGIMEAN_107_4re', 'I_107_4re(+)', 'SIGI_107_4re(+)', >> 'I_107_4re(-)', 'SIGI_107_4re(-)'] >> >> GUESS FIL TARGET LABELS ['F1', 'SIGF1', 'DANO1', 'SIGDANO1'] Unit cell: >> (34.87, 109.2, 135.33, 90, 90, 90) Space group: P 2 21 21 (No. 18) >> CONTENTS: >> ['/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_4_P22121_scala2.mtz', >> 'mtz', 'premerged', 'P 2 21 21', [34.869998931884766, 109.19999694824219, >> 135.32989501953125, 90.0, 90.0, 90.0], 2.4890134311310943, ['F1', 'SIGF1', >> 'DANO1', 'SIGDANO1']] >> >> File >> /home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_4_P22121_scala2.mtz >> RES: 2.5 >> >> Guess of datafile for refinement: >> /home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_3_P22121_scala2.mtz >> >> Using >> /home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_3_P22121_scala2.mtz >> for refinement >> >> Specify >> input_refinement_file=/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_3_P22121_scala2.mtz >> to change this >> >> HKLIN ENTRY: >> /home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_2_P22121_scala2.mtz >> >> FILE TYPE ccp4_mtz >> >> COLUMN LABELS: ['H', 'K', 'L', 'FreeR_flag', 'F_107_2re', 'SIGF_107_2re', >> 'F_107_2re(+)', 'SIGF_107_2re(+)', 'F_107_2re(-)', 'SIGF_107_2re(-)', >> 'DANO_107_2re', 'SIGDANO_107_2re', 'IMEAN_107_2re', 'SIGIMEAN_107_2re', >> 'I_107_2re(+)', 'SIGI_107_2re(+)', 'I_107_2re(-)', 'SIGI_107_2re(-)'] >> >> GUESS FILE TYPE MERGE TYPE mtz premerged TARGET LABELS ['F1', 'SIGF1', >> 'DANO1', 'SIGDANO1'] Unit cell: (34.79, 108.92, 134.88, 90, 90, 90) Space >> group: P 2 21 21 (No. 18) CONTENTS: >> ['/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_2_P22121_scala2.mtz', >> 'mtz', 'premerged', 'P 2 21 21', [34.790000915527344, 108.92009735107422, >> 134.8800048828125, 90.0, 90.0, 90.0], 2.4890566908055836, ['F1', 'SIGF1', >> 'DANO1', 'SIGDANO1']] >> >> Inverse hand of space group: P 2 21 21 Creating sg entry from >> /home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_2_P22121_scala2.mtz >> Unit cell: (34.79, 108.92, 134.88, 90, 90, 90) Space group: P 2 21 21 (No. >> 18) Space group name is: P 2 21 21 symbol is: p22121 >> >> **************************************** >> >> AutoSol Input failed >> >> Need a symfile for solve >> >> **************************************** >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >>

1 0

Phenix version 1.6 released
by Paul Adams 01 Feb '10

01 Feb '10

The Phenix developers are pleased to announce that version 1.6 of Phenix is now available. Binary installers for Linux, and Mac OSX platforms are available at the download site: http://phenix-online.org/download/ Just some of the new features in this version (1.6) are: - New Graphical User Interfaces for AutoMR, and Phaser (in MR and SAD modes) - Improved reflection file editor GUI and command line tool - Updated map calculation GUI - C++ version of Resolve - Refinement of residues spanning symmetry axes in phenix.refine - New RNA sugar pucker geometry restraints in phenix.refine - Torsion angle dynamics refinement updates - Optional real space refinement of ligands in LigandFit wizard For a full list of changes see: http://www.phenix-online.org/documentation/CHANGES Please note that there is a new publication that should be used to cite use of Phenix: PHENIX: a comprehensive Python-based system for macromolecular structure solution. P. D. Adams, P. V. Afonine, G. Bunkóczi, V. B. Chen, I. W. Davis, N. Echols, J. J. Headd, L.-W. Hung, G. J. Kapral, R. W. Grosse-Kunstleve, A. J. McCoy, N. W. Moriarty, R. Oeffner, R. J. Read, D. C. Richardson, J. S. Richardson, T. C. Terwilliger and P. H. Zwart. Acta Cryst. D66, 213-221 (2010). Full documentation is available here: http://www.phenix-online.org/documentation/ There is a Phenix bulletin board: http://www.phenix-online.org/mailman/listinfo/phenixbb/ Please consult the installer README file or online documentation for installation instructions. Direct questions and problem reports to the bulletin board or: help(a)phenix-online.org and bugs(a)phenix-online.org Commercial users interested in obtaining access to Phenix should visit the Phenix website for information about the Phenix Industrial Consortium. The development of Phenix is principally funded by the National Institute of General Medical Sciences (NIH) under grant P01-GM063210. We also acknowledge the generous support of the members of the Phenix Industrial Consortium. -- Paul Adams Acting 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. Executive Assistant: Patty Jimenez [ PAJimenez(a)lbl.gov ] [ 1-510-486-7963 ] --

1 0

data used in refinement
by Karolina Michalska 01 Feb '10

01 Feb '10

Hi all, I have a question concerning number of reflections used in refinement. In the phenix.refine log I can find a table saying that there are 34314 reflections in a work set and 1104 in a free set. This is in agreement with what Refmac prints out to pdb file under REMARK 3 (DATA USED IN REFINEMENT). However, the same remark in the pdb file produced by phenix.refine says there are 35404, which is neither a work set nor a sum of work and test sets. It is almost the latter option but still 14 reflections are missing and I cannot find in the log file what happened with them. Can anyone help me here? Karolina

3 3

auto-open MTZ scheme
by Paul Emsley 29 Jan '10

29 Jan '10

Dear Phenixers, Prompted by Randy Read, Kevin and I have agreed that Coot should be able to auto-open MTZ files with columns labelled groupname.F_phi.F and groupname.F_phi.phi and groupname.DF_phi.DF, groupname.DF_phi.phi for difference maps for any value of groupname, of course. (Any weights should be applied to Fs before writing the file). We were wondering what the Phenix community/developers thought about that idea (there's not much point in adding this feature if you don't agree). Thanks, Paul.

5 7

For your consideration: Table 1
by SIPPEL,KATHERINE H 29 Jan '10

29 Jan '10

Dear PHENIX programmers, I would like to preface this comment by saying that I love your suite of programs. I have converted to a 100% PHENIX fan girl and am dragging the rest of my lab down with me. I realize that you have a lot on your plates right now, what with all the bug fixes, updates, and bulletin board troubleshooting that you do. I am also primarily a biologist and have no comprehension of the effort required to keep everything running, but I do have a suggestion/request. I was putting the finishing touched on the first draft of a manuscript today and thought to myself, wouldn't it me wonderful if PHENIX could generate that all important crystallographic Table 1. You know the one that I am talking about with the data and refinement statistics. I am thinking a combination of PDB_EXTRACT and MOLEMAN where you input the log files from scaling and refinement and it outputs a handy-dandy test file with "parameter<tab>number that could easily be imported into your favorite spreadsheet (Open Office or Excel). I envision an interface with check boxes for the parameters you want to include and a place were you could input the resid of ligands for atom and b-factor counts. Like I said it is just a suggestion, in case you find yourselves bored and with time on your hands. Thanks for your time, Katherine -- SIPPEL,KATHERINE H Ph. D. candidate McKenna Lab Department of Biochemistry and Molecular Biology College of Medicine University of Florida

3 2

phenix.pdbtools and anomalous?
by Kay Diederichs 28 Jan '10

28 Jan '10

Hi, I like the way I can obtain Fcalc with phenix.pdbtools --f-model. However I need to have the anomalous signal as well, for certain atoms, and a given wavelength. This does not seem to be possible with phenix.pdbtools. Is there a way to do this with phenix.refine ? thanks, Kay -- Kay Diederichs http://strucbio.biologie.uni-konstanz.de email: Kay.Diederichs(a)uni-konstanz.de Tel +49 7531 88 4049 Fax 3183 Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz This e-mail is digitally signed. If your e-mail client does not have the necessary capabilities, just ignore the attached signature "smime.p7s".

2 2

Re: [phenixbb] refinement with alternative molecules?
by Su-Chang Lin 28 Jan '10

28 Jan '10

Hi Ralf, I've done the refinement with alt. conf.. The occupancy is 0.58 for Mol A, 0.42 for Mol B. The maps look OK. R-factors drops a little bit. Before when I put Mol A in that region for refinement, I saw additional densities (a helix) for Mol B. When I put Mol B in the region for refinement, I saw additional densities (loops) for Mol A. Now with alt. conf. there are no additional densities. Can I use the occupancies for publication? Or do I need to do/check something else? Thanks! Su-Chang > Hi Su-Chang, > > I will try to refine the structure without NCS restraints. > I'd be interested to know how it goes, although I'm too busy to get > into the NCS code right now. > If the resolution is low I'd think it is better to use NCS, without > alt. conf. The mismatches you saw between related molcules may > be pure artifacts. But trying is better than guessing! > Ralf > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb

3 2

new release of IL MILIONE
by Dritan Siliqi 28 Jan '10

28 Jan '10

1 0

Using LigandFit to identify unknown density
by Katya Heldwein 28 Jan '10

28 Jan '10

Hi, I'd like to run LigandFit to identify a small molecule accounting for an unknown density. How do I do that, preferably, in a command-line mode? Katya -- Ekaterina Heldwein, Ph.D. Assistant Professor Department of Molecular Biology and Microbiology Tufts University School of Medicine 136 Harrison Ave Boston, MA 02111 phone: 617-636-0858 fax: 617-636-0337 e-mail: katya.heldwein(a)tufts.edu

5 8

refinement with alternative molecules?
by Su-Chang Lin 27 Jan '10

27 Jan '10

Hi, Recently I got a crystal structure of a multiple-molecules protein complex. There are many protein subunits with the same fold. From the likelihood-weighted maps by Phenix, I can see two different subunits occupy the same position. (So I can put the model of either subunit in the same densities, but some loop regions and the C-terminal tail look different. ). I know Phenix can do occupancy refinement with a residue that has N alternative conformations. My question is can Phenix do occupancy refinement with alternative molecules? The RMSD for two subunits is about 1.3 angstrom. The sequence identity is about 30%. Thank you very much! Su-Chang Lin, Ph.D., Postdoc Associate Department of Biochemistry Weill Medical College, Cornell University Whitney Building, room W-212 1300 York Avenue, New York, NY 10021 212-746-6458

3 6

phenix.fmodel: a command line tool to compute structure factors from a model (Fcalc or Fmodel).
by Pavel Afonine 27 Jan '10

27 Jan '10

Starting PHENIX nightly build version 1.6-295 (2010-01-27), a new command line tool phenix.fmodel is available. This is a replacement for "phenix.pdbtools --f-model" command, which is not available anymore. phenix.fmodel is a comprehensive tool to compute structure factors from a model. For more information and usage examples simply run phenix.fmodel . Pavel. P.S. Below is the result of running phenix.fmodel: phenix.fmodel: a tool to compute structure factors, Fmodel: Fmodel = scale * exp(AnisoScale) * (Fcalc + k_sol * exp(-b_sol*s^2/4) * Fmask) where: - Fmodel - total model structure factor (complex value) - AnisoScale = -ht*A(-1)*b_cart*A(-1)th/4 - h - column vector with Miller indices - A - orthogonalization matrix - b_cart - anisotropic scale matrix - t and (-1) denotes transposition and inversion operations - scale - overall scale factor - Fcalc - structure factors calculated from atomic model - k_sol and b_sol - Flat Bulk solvent model parameters - Fmask - structure factors calculated from bulk solvent mask Usage examples: 1) phenix.fmodel model.pdb high_resolution=1.5 will result in a file containing complete set of Fmodel = Fcalc computed from atomic model up to 1.5A resolution. 2) phenix.fmodel model.pdb scale=2 k_sol=0.35 b_sol=50 b_cart="1 2 3 0 4 7" high_res=1.5 low_res=10 will result in a file containing complete set of Fmodel computed using the above formula in resolution range 1.5-20.0A. 3) phenix.fmodel model.pdb high_resolution=1.5 algorithm=direct is similar to "1)" but the Fcalc are computed using direct summation algorithm. 4) phenix.fmodel model.pdb high_res=1.5 format=cns label=FOBS type=real r_free=0.1 will result in CNS formatted file containing complete set of amplitudes of Fmodel = Fcalc computed up to 1.5A resolution, labelled as FOBS, and free-R flags with 10% of test reflections. This is a typical command to simulate Fobs. 5) phenix.fmodel model.pdb high_res=1.5 scattering_table=neutron will result in a file containing complete set of Fmodel = Fcalc computed from atomic model up to 1.5A resolution using neutron scattering table. 6) phenix.fmodel model.pdb parameters.txt will result in a structure factor file, where Fmodel were computed using parameters defined in parameters.txt file. The parameters.txt file can contain all or any subset of parameters listed below. Note, that each { must have a matching one }. 7) phenix.fmodel model.pdb reflection_data.mtz will result in a file containing a set of Fmodel = Fcalc that will match the set of Miller indices of the data in reflection_data.mtz file. 8) phenix.fmodel model.pdb reflection_data.mtz data_column_label="FOBS,SIGMA" similar to "7)", where the specific data array is selected. See below for complete list of available parameters. ------------------------------------------------------------------------------- Parameters to compute Fmodel:: high_resolution = None low_resolution = None r_free_flags_fraction = None add_sigmas = False scattering_table = wk1995 it1992 *n_gaussian neutron data_column_label = None fmodel { k_sol = 0.0 b_sol = 0.0 b_cart = 0 0 0 0 0 0 scale = 1.0 } structure_factors_accuracy { algorithm = *fft direct cos_sin_table = False grid_resolution_factor = 1/3. quality_factor = None u_base = None b_base = None wing_cutoff = None exp_table_one_over_step_size = None } mask { use_asu_masks = True solvent_radius = 1.11 shrink_truncation_radius = 0.9 grid_step_factor = 4.0 verbose = 1 mean_shift_for_mask_update = 0.1 ignore_zero_occupancy_atoms = True ignore_hydrogens = True } output { format = *mtz cns label = FMODEL type = real *complex file_name = None } anomalous_scatterers { group { selection = None f_prime = 0 f_double_prime = 0 } }

1 0

occupancy refinement
by Christian Roth 27 Jan '10

27 Jan '10

Dear all, I refine a structure of a protein to 1.4 A and found a few SO4-Ions. I tried to refine this sulfurs and some of these seems to be not fully occupied, as the negative difference density suggest. I tried to refine the occupancy of the sulfate ions to get an idea how strong the different binding sites might be occupied. All sulfate ions are in Chain C of my pdb. I tried to refine the occupancy individually using refine.occupancy.individual SO4 but this lead to different occupnacies for every atom for every atom and theix cant be the case for sure. Then I tried and group occupancy with resname=SO4 but now every sulfate ion has the same occupancy, which is indicated from my previous refinements also not the case, because two ions have no negative difference density. At the momentI can not figure out how I should combine the keywords for the individual occupancy refinement of the different sulfate ions. In my structure. Should I define for every ion a different chain or how I could overcome this problem? I would be very happy if anyone has a idea to sove this problem or tell me what keyword I misunderstood in the documentation. Best regards Christian

5 6

GUI for Auto-MR
by Laurie Betts 27 Jan '10

27 Jan '10

I installed version PHENIX 1-5-2 under Linux, and the main GUI has an option for AutoMR Phaser that says (old PHENIX GUI) - if that crashes is it because we don't have the old GUI installed? THe other main items seem to work fine. The last error message in the terminal window seems to suggest that is the case.... Thx, Laurie BEtts

2 1

twin data set
by r n 26 Jan '10

26 Jan '10

Hi I did processed a data set, which seems P3. I did molecular replacement and end up with solution with higher R factor. Then, I did used xtriage to check the data, it gave me possible space group P321 and few twin laws, this space group did not given me any solution , data seems have translation symmetry along z axis? Also I did processed in P1 and did molecular replacement end up in high R-factor. I really appreciate if any one has any suggestion what is going on with data? I given log file from xtriage, --------------------------------------------------------------------------------------------- | Point group | mean R_used | max R_used | mean R_unused | min R_unused | BIC | choice | ---------------------------------------------------------------------------------------------- | P 3 | None | None | 0.314 | 0.027 | 8.149e+03 | | | P 6 2 2 | 0.314 | 0.460 | None | None | 1.856e+05 | | | P 3 2 1 | 0.027 | 0.027 | 0.446 | 0.432 | 5.667e+03 | <--- | | P 6 | 0.432 | 0.432 | 0.249 | 0.027 | 1.856e+05 | | | P 3 1 2 | 0.460 | 0.460 | 0.242 | 0.027 | 1.859e+05 | | ---------------------------------------------------------------------------------------------- Statistics depending on twin laws ------------------------------------------------------------------ | Operator | type | R obs. | Britton alpha | H alpha | ML alpha | ------------------------------------------------------------------ | -h,-k,l | M | 0.432 | -0.009 | 0.046 | 0.022 | | h,-h-k,-l | M | 0.027 | 0.450 | 0.478 | 0.478 | | -k,-h,-l | M | 0.460 | -0.012 | 0.049 | 0.022 | ------------------------------------------------------------------ Patterson analyses - Largest peak height : 34.261 (corresponding p value : 7.017e-04)

1 0

map averaging
by Gabriela Guédez 25 Jan '10

25 Jan '10

Hi dear Phenixbb, Is there a command tool to make ncs density averaging in a high oligomerization model that has some maps clearer than others? not multi-crystal but the same crystal. Thank you, Gabriela -- ---------------------------------------------------------------------- Gabriela Guédez R. gabriela.guedez(a)bzh.uni-heidelberg.de

2 1

how to convert .cif with multiple datasets
by Zheng Zhou 24 Jan '10

24 Jan '10

Dear phenix experts: I am using phenix.cif_as_mtz to convert a .cif file downloaded from pdb, but when I run ################################################ phenix.cif_as_mtz XXXX-sf.cif Sorry: Crystal symmetry is not defined. Please use the --symmetry option. ################################################ Then I run ############################################### phenix.cif_as_mtz XXXX-sf.cif --symmetry=XXXX.pdb Multiple data sets found => ignored: XXXX-sf.cif What should I do? Thanks for your help. Joe

2 1

explicit pdb output file name (refine)
by Ed Pozharski 21 Jan '10

21 Jan '10

Do I understand correctly that there is no way to force refine to skip the serial in the output pdb file name, i.e. foo.pdb, not foo_001.pdb? -- Ed Pozharski <epozh001(a)umaryland.edu> University of Maryland - Baltimore

4 6

polygon resolution control
by Young-Jin Cho 21 Jan '10

21 Jan '10

Hi I was using polygon from GUI. One question I have now is how I can control the resolution limit. As I cut the resolution during refinements but polygon gave me from the uncut-high resolution. Is there any way, I can ask polygon to get statistics upto certain resolution as shown on pdb file? As always, thanks in advance. YoungJin

3 3

Re: [phenixbb] polygon resolution control
by Alexandre Urzhumtsev 21 Jan '10

21 Jan '10

Dear YoungJin >I was using polygon from GUI. One question I have now is how I can control >the resolution limit. As I cut the resolution during refinements but >polygon gave me from the uncut-high resolution. Is there any way, I can >ask polygon to get statistics upto certain resolution as shown on pdb file? Honestly, I do not know for the phenix version; let's wait what Pavel & Nat answer you. Very probably they already implemented it and your problem will be solved easy. Another simple solution will be to cut explicitly your MTZ file by the resolution you wish before run the polygon. If not, such an option (to define explicitely the resolution; that will select for comparison the PDB structures refined previously at such a resoluton) exists in the original Tcl/tk based version of the polygon. Please, let me know if your are interested in it. Best regards, Sacha

1 0

occupancy refinement default selections - bug or feature?
by Ed Pozharski 21 Jan '10

21 Jan '10

There is a ligand residue in the structure that have its occupancy set to 0.75. refine with default parameters apparently refines every atom individually, so in the end I have a strange situation where ligand atoms have different occupancies. Of course, regular alternate conformers in the protein part of the structure have single occupancy refined per residue. Interestingly, when I place altLoc identifier "A" in front of the residue name of the ligand, single occupancy value is refined (although there is no second conformation). It settles down near 0.7 (close to what I selected previously based on a traditional approach of eliminating difference density and roughly matching B-factors of hydrogen-bonded protein atoms with ligand), so apparently constraints (e.g. total occupancy for all the conformers) are not applied. Is this intentional behavior (I understand that groups can be defined in the input file but adding altLoc letter seems like a simple trick)? I think most people would initially expect that occupancy will not vary within a residue, so the default behavior may seem like a bug to some (the only situation I can think of where such variation is justified is to model radiation damage). -- Ed Pozharski <epozh001(a)umaryland.edu> University of Maryland - Baltimore

2 1

Dear everybody
by YuYong Tao 21 Jan '10

21 Jan '10

Dear everybody: I installed phenix-1.6, when i run 'phenix.solve', it showed as follows: ustc-lifescience:~> phenix.solve binary=/usr/local/phenix-1.6-288/build/intel-linux-2.6/solve_resolve/exe/solve SOLVEDIR=/usr/local/phenix-1.6-288/solve_resolve/ext_ref_files SYMOP=/usr/local/phenix-1.6-288/solve_resolve/ext_ref_files/symop.lib SYMINFO=/usr/local/phenix-1.6-288/solve_resolve/ext_ref_files/syminfo.lib CCP4_OPEN=UNKNOWN SOLVE_RESOLVE_MALLOC_MAX=399459600 /usr/local/phenix-1.6-288/build/intel-linux-2.6/solve_resolve/exe/solve: error while loading shared libraries: libsvml.so: cannot open shared object file: No such file or directory and when i run 'phenix.resolve' ,it seems to be ok. So i donn't know what to do. Can you tell me? Best Wishes!

2 1

How do different sections of TLS groups affect refinment
by Bart, Aaron G 21 Jan '10

21 Jan '10

Greetings everyone, I am still fairly new to crystallography, so forgive me for my naivety. My question involves how the TLSMD server segments my protein and the effects it has on refinement. For instance when i use "Multi-Chain Alignment Analysis", which lines the sequence for all of my chains (a total of 12) and shows how TLS groups are divided among them, it shows varying selections of TLS groups among the different chains. It should be noted that the sequence is the same for all the chains in my protein. Also if a TLS group splits a alpha helix into multiple parts, would this be valid? I have come to understand that helices move more like rigid bodies than segmented groups... Thanks! -Aaron

5 6

K(sol) and B(sol)
by J. Fleming 20 Jan '10

20 Jan '10

Hi, I'm working on a structure but am having problems with K(sol) and B(sol). What are they and how do I get them into range? I thought they might have something to do with my waters but I have no water B-factors <25. Thanks for any help! -Jon

4 3

twin refinement in phenix-1.5-2
by Kelly Daughtry 19 Jan '10

19 Jan '10

Hello all, I am wondering if anyone has run across this problem and knows how to fix it. I have a twinned dateset and I am using phenix.refine to refine the dataset. I have the full 1.5-2 installation. When I include the twin law (-k, -h, -l) in the refinement, I get this error: File "/usr/swr/phenix-1.5-2/cctbx_project/mmtbx/twinning/twin_f_model.py", line 1651, in map_coefficients "m_gradient" AssertionError If I do not include the twin law, I do not get the error and the refinment continues as normal. When I downgraded to Phenix.1.4-3 (full install), And use the same twin law, I am able to run phenix.refine without an error. I have attached my definition file for phenix.1.5-2 amd the log file. Thanks in advance for any help you can provide, Kelly Daughtry ******************************************************* Kelly Daughtry PhD Candidate Department of Physiology and Biophysics Boston University School of Medicine 590 Commonwealth Ave R 390 Boston MA, 02215 (P) 617-358-5548 *******************************************************

5 5

Reflection file conversion
by Nate Nicely 19 Jan '10

19 Jan '10

I use d*TREK to reduce my data and phenix.reflection_file_converter to import the data. I seem to have had a bit of trouble generating the free R flags. It seems that the cap for the max number of free R reflections takes precedence over the percentage, even when the percentage is given expressly on the command line. I find myself setting the cap artificially high on the command line so that a full 10% is set aside. I was taught to set aside 10% for the free R set, only going lower if setting aside the full 10% compromised completeness. I'm just wondering what is the rationale for the numeric cap? Am I making any error(s) with my methodology? Nate N

4 4

Re: [phenixbb] clash guarde failure phenix coot
by Pavel Afonine 19 Jan '10

19 Jan '10

Hi Georg, I think the refinement .log file should contain the lines like these below: Warning: very small nonbonded interaction distances. Nonbonded interactions: 12604 Sorted by model distance: nonbonded pdb=" CG ARG A 3 " pdb=" CG ARG A 4 " model vdw 0.000 3.840 nonbonded pdb=" NE ARG A 3 " pdb=" NE ARG A 4 " model vdw 0.000 3.200 which pinpoints you the offending atoms. Does this answer your question? Pavel. On 1/19/10 9:57 AM, Georg Mlynek wrote: > > Dear All, > > I´m refining a 2.1A with phenix 1.5-2 and get when I click on > automatically add hydrogens to model following error message: > refinement.pdb_interpretation.clash_guard.failure: Number of nonbonded > interaction distances < 0.5:391 > > I suppose that this comes, because coot mixes up the hydrogens. >

1 0

rigid body refinement problem
by Jianghai Zhu 19 Jan '10

19 Jan '10

Hi, I am using phenix.refine_dev_282 for a rigid body refinement. The output pdb file is exactly the same as the input model even though there are obviously some large movements. Here are some information from the log file. Information about total rigid body shift of selected groups: rotation (deg) translation (A) xyz total xyz total group 1: 0.051 -5.493 -1.073 5.60 0.55 -3.15 -1.35 3.47 group 2: 0.254 0.562 0.252 0.67 0.36 -3.99 0.87 4.10 group 3: 3.807 4.001 -2.262 5.92 -0.81 -3.17 1.06 3.44 group 4: 2.275 -4.215 1.909 5.12 -0.18 -2.95 -1.43 3.28 group 5: -1.902 -5.750 -3.206 6.81 -1.99 -4.44 0.27 4.88 group 6: -4.932 -3.939 -5.340 8.16 -0.18 -2.08 -0.25 2.11 group 7: -1.140 -0.769 -7.715 7.83 0.73 -2.91 0.04 3.00 group 8: 2.008 -1.858 -1.236 3.02 -1.10 -5.44 -0.82 5.61 But then the model didn't change at all. stage Deviation of refined model from start model max min mean 0 : 0.000 0.000 0.000 1_bss: 0.000 0.000 0.000 1_rbr: 0.000 0.000 0.000 1_bss: 0.000 0.000 0.000 1_adp: 0.000 0.000 0.000 1_bss: 0.000 0.000 0.000 Is this a bug? -- Jianghai

2 2

difference density map
by 丁玮 19 Jan '10

19 Jan '10

4 3

Where is phenix.refine finding starting r values?
by Bart, Aaron G 19 Jan '10

19 Jan '10

Greetings, I am fairly new to crystallography, and have just started to use Phenix for structural refinement. I am currently working on a 2.8A structure that was run through multiple rounds of rigid body refinement via Refmac and manual revision using Coot. I eventually got stuck where large portions of my molecule had very poor density and the rwork and rfree stayed around 0.3. I then performed a TLS refinement which resulted in better density, and tried running it through phenix.refine with default ADP settings, as well as simulated annealing. It worked beautifully, however when I looked at the log file for the refinement, phenix was reporting a starting rwork and rfree that represented my first stage of refinement in refmac, 0.38/0.44. My question is, is phenix somehow neglecting the refinement that was done in refmac? Regards -Aaron

2 1

Re: [phenixbb] merohedral twinned refinement
by JXQI 19 Jan '10

19 Jan '10

Zwart, Cherney and all, Thanks for the suggestions.The problem is fixed when I tried P31. Best regards J.X. Qi > > 3. If I try P3,the Matthews coeffs tell 2 or 3 molecules in the ASU,the > molecules will crash.Besides,the overall FOM ( lower than 0.4) and the > R/Rfree values (about 0.45/0.56) suggest that the P3 is the wrong sg. try P31 or otherwise P1. You should get a solution in those groups. It could of course mean that there are OD type issues, but I would not jump there yet. Can you send the intensity statistics from xtriage?

1 0

right symmetry?
by Gabriela Guédez 18 Jan '10

18 Jan '10

Hi Phenixbb, I have a data that indexes in P6122, also P61 and P31. Data analysis in phenix.xtriage says no twinning is suspected according to the L-test. However, after MR and twin RB refinement, the model improves from P6122 or P61 to P31 5% Rfacs and 0.5 the FOM. I thought the data might have RPS and twinning not detected with the L-test. So, i ran xtriage to compute the RvsR statistics using the obs_and_calc.mtz file and the results were: in P61 R_abs_twin observed data : 0.112 R_abs_twin calculated data : 0.047 in P31 R_abs_twin observed data : 0.117 R_abs_twin calculated data : 0.139 "misespecified crystal symmetry", according to Lebedev, Vagin, Murshudov et al 2006, Acta Cryst. D62,83-95. I would like to know a test that tells me the right symmetry. I appreciate your help. Thanks, Gabriela

2 4

Re: [phenixbb] merohedral twinned refinement
by JXQI 18 Jan '10

18 Jan '10

Dr.Zwart, Thanks for the reply. 2. The systematic absences and the Rsym support the P3121.I already mentioned the model fit very with the map if I use the P3121. 3. If I try P3,the Matthews coeffs tell 2 or 3 molecules in the ASU,the molecules will crash.Besides,the overall FOM ( lower than 0.4) and the R/Rfree values (about 0.45/0.56) suggest that the P3 is the wrong sg. 4. TLS refinement also did not imrove the results. 5. There are totally 88 aa in my protein, I could build 86 aa clearly. The intensity ststistics is attached in the message. J.X. QI ************************************************************************ Shell I/Sigma in resolution shells: Lower Upper % of of reflections with I / Sigma less than limit limit 0 1 2 3 5 10 20 >20 total 50.00 4.95 0.9 1.5 1.9 2.4 2.8 4.0 9.5 90.5 100.0 4.95 3.93 0.0 0.2 0.3 0.5 0.8 2.0 6.6 93.4 100.0 3.93 3.44 0.2 0.3 0.6 1.0 2.5 5.4 15.4 84.6 100.0 3.44 3.12 0.0 0.2 0.5 0.7 2.5 7.6 22.7 77.3 100.0 3.12 2.90 0.3 1.0 2.1 3.2 7.2 17.6 41.4 58.6 100.0 2.90 2.73 0.0 0.7 2.0 3.2 9.9 20.8 52.9 47.1 100.0 2.73 2.59 0.0 1.4 2.9 5.7 12.4 30.0 60.8 39.2 100.0 2.59 2.48 0.7 1.6 4.7 7.7 16.3 36.0 71.5 28.5 100.0 2.48 2.38 0.6 2.1 5.0 10.2 21.9 42.0 76.2 23.8 100.0 2.38 2.30 0.8 2.3 7.4 12.7 25.3 49.4 83.4 16.6 100.0 All hkl 0.4 1.1 2.7 4.7 10.0 21.1 43.4 56.6 100.0 Summary of reflections intensities and R-factors by shells R linear = SUM ( ABS(I - <I>)) / SUM (I) R square = SUM ( (I - <I>) ** 2) / SUM (I ** 2) Chi**2 = SUM ( (I - <I>) ** 2) / (Error ** 2 * N / (N-1) ) ) In all sums single measurements are excluded Shell Lower Upper Average Average Norm. Linear Square limit Angstrom I error stat. Chi**2 R-fac R-fac 50.00 4.95 619.8 13.8 3.5 1.039 0.046 0.050 4.95 3.93 834.6 17.5 5.0 1.156 0.048 0.052 3.93 3.44 521.9 14.6 4.5 1.026 0.059 0.062 3.44 3.12 333.7 11.1 4.1 1.073 0.071 0.068 3.12 2.90 172.5 7.1 3.6 1.153 0.098 0.096 2.90 2.73 131.4 6.0 3.4 1.256 0.116 0.108 2.73 2.59 102.8 5.2 3.4 1.306 0.140 0.130 2.59 2.48 77.7 4.6 3.4 1.381 0.173 0.158 2.48 2.38 64.1 4.3 3.3 1.355 0.195 0.177 2.38 2.30 54.7 4.1 3.3 1.345 0.221 0.197 All reflections 297.8 8.9 3.7 1.209 0.071 0.059 Intensities of systematic absences h k l Intensity Sigma I/Sigma 0 0 2 -0.2 0.4 -0.5 0 0 4 0.1 1.0 0.1 0 0 5 0.4 1.4 0.3 0 0 7 1.1 2.5 0.4 0 0 8 0.4 2.1 0.2 0 0 10 7.3 3.4 2.2 0 0 11 6.0 3.5 1.7 0 0 13 -2.3 4.9 -0.5 0 0 14 6.1 4.3 1.4 0 0 16 8.1 5.1 1.6 0 0 17 3.9 4.9 0.8 0 0 19 0.8 4.5 0.2 0 0 20 4.0 4.6 0.9 ********************************************************************* 1. How do the intensity statistic look like? 2. How did you choose P3121? 3. Did you try solving and refining in P3? 4. TLS? 5. How complete is your model 2010/1/17 JXQI <jxqi at mail.im.ac.cn>: > Dear all, > > I have a 2.3A data set processed with HKL2000. The space group is P3121 with > 63% of solvent content and 1 molecule in the ASU. I used a 40% homology > model to do molecular replacement. Both the Phaser and Molrep gave similar > solution with good packing. After further refinement with phenix, the built > model fit well with the 2mFo-DFc map. However the R/Rfree were stuck to > 0.34/0.38. > > I rechedked the data set with xtriage and found the data set is merohedral > twinned (with twin law"-h,-k,l", the estimated twin fraction is about 0.05). > When I used the twin law in further refinement, the R/Rfree were only > decreased to 0.32/0.36. Any suggestions are appreciated, thanks! > > > J.X. QI > _______________________________________________ > phenixbb mailing list > phenixbb at phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb

3 2

merohedral twinned refinement
by JXQI 18 Jan '10

18 Jan '10

Dear all, I have a 2.3A data set processed with HKL2000. The space group is P3121 with 63% of solvent content and 1 molecule in the ASU. I used a 40% homology model to do molecular replacement. Both the Phaser and Molrep gave similar solution with good packing. After further refinement with phenix, the built model fit well with the 2mFo-DFc map. However the R/Rfree were stuck to 0.34/0.38. I rechedked the data set with xtriage and found the data set is merohedral twinned (with twin law"-h,-k,l", the estimated twin fraction is about 0.05). When I used the twin law in further refinement, the R/Rfree were only decreased to 0.32/0.36. Any suggestions are appreciated, thanks! J.X. QI

3 2

Twin fraction in phenix refine
by Pietro Roversi 18 Jan '10

18 Jan '10

Dear all, phenix.xtriage estimates a twin fraction of between 24 and 30% but then when I start the refinement I get 47-49%. In CNS if I fix the twin fraction in a series of refinements the Rfactors jump from 44% (twin fraction 0) to 37% (from 25% to 49%, only marginal improvement upon going from alpha=25% to 49%). Questions: 1. Is the refinement of alpha dependent on the model? 2. I am tempted to work with the 30% that xtriage estimates but do not know how: is there a way to fix alpha? Thanks Pietro -- Sent from my Desktop Pietro Roversi EP Abraham Fellow in Biochemistry - Lincoln College - Oxford Sir William Dunn School of Pathology, Oxford University South Parks Road, Oxford OX1 3RE, England UK Tel. 0044-1865-275385

8 13

Re: [phenixbb] [ccp4bb] Adding H in refinement
by Schubert, Carsten [PRDUS] 13 Jan '10

13 Jan '10

Hi Pavel, sorry I hijacked the thread a bit... A question about the riding Hydrogens and their B-factors. I noticed that at least with earlier versions of PHENIX the B-factor of the Hydrogens was not fixed to the B-factor of the bonded atoms. If I would generate the Hydrogens in reduce they would inherit the appropriate B-factors, but during the course of the refinement and rebuilding they would start to diverge, sometimes drastically. Are you saying the current implementation restrains the B-factors to the bonded atoms and forces them to be equal or are they just inherited and are allowed to float afterwards? Cheers, Carsten > -----Original Message----- > From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of > Pavel Afonine > Sent: Tuesday, January 12, 2010 12:24 PM > To: CCP4BB(a)JISCMAIL.AC.UK > Subject: Re: [ccp4bb] Adding H in refinement > > Hi Sara, > > - what you observe should not happen since phenix.refine uses riding > model for H atoms. The hydrogen's B-factors are automatically inherited > from the atoms these hydrogens are bonded to. For example, in X-H bond > the B-factor of X should be equal to B-factor of H. > > - make sure you are using the latest version of PHENIX: > http://www.phenix-online.org/download/ > > - if this does not help, please contact me directly, and send the data > and model so I can tell you what exactly is not right (all the files > will be handled confidentially). > > - there is PHENIX bulletin board: > http://www.phenix-online.org/mailman/listinfo/phenixbb > > Pavel. > > > I did refinement with phenix of my 1.9-2.0 Angstroem structures and > included the hydrogens (riding). However, when I checked on the > statistics (refinement close to the end), the average B-factor was > extremely high (in phenix.polygon it was higher than with any other > structure in similar resolution range). It makes sense though that this > happens, if you have a residue which has a high B-factor and carries a > lot of hydrogens the average B-factor will raise quite a lot (since the > B-factor of hydrogens is calculated 1-1.5x of B-factor from the atom > it sits on), right? > > (When I removed the hydrogens again, the average B-factor was > fine...) > > > > My question is now did I do something wrong in my refinement (-> do I > have to change something that this does not happen), or is this > something everybody sees? > > > > If this is common, what would happen (during evaluation) if you want > to publish a structure and the statistics show such a high average B- > factor? Is it better to have hydrogens on, but a bad average B, or no > hydrogens on and a good average B... Obviously, I never published a > structure ;) > >

2 1

Beamtime at the ALS
by Peter Zwart 12 Jan '10

12 Jan '10

Dear All, January 15, 2010 is the deadline for the March/April 2010 Rapid Access Proposal cycle. All Berkeley Center for Structural Biology(BCSB) beamlines are equipped with ADSC Q315/Q315R detectors, automated sample changers and data collection software enabling high-throughput crystal screening and data collection. Remote data collection is available on all BCSB beamlines, providing the user with the full complement of sample visualization, sample manipulation, beamline control, data acquisition and data analysis tools exactly as they would see them if they were stationed at the beamline. This enhanced remote operation capability is coupled with 22hr onsite support by BCSB staff who are able to assist immediately with loading additional samples for remote users or troubleshoot any issues that might arise. Remote users can furthermore be kept up-to-date on changes in ring status via an SMS service (http://bcsb.als.lbl.gov/wiki/index.php/Ring_Status_Notifications_to_Cell_Ph…) Specific features are summarized below. Beamlines 8.2.1 and 8.2.2: To facilitate studies on small crystals, a microdiffractometer was installed in the beamline 8.2.1 endstation. The new equipment allows precise sample positioning to within 2 microns, excellent sample viewing of very small crystals, and an off-axis crystal positioning stage. Both beamlines 8.2.1 and 8.2.2 feature a Rigaku sample changer (Actor), allowing remote operations to now be a routine mode of access for these beamlines. Beamlines 5.0.1, 5.0.2, 5.0.3: The Berkeley Automounter sample handling system has a routine capacity of 96 samples (6 pucks). In a typical high-throughput screening mode, the mount-to-mount time is around 2.5 minutes per sample, allowing users to screen a full puck within 45 minutes. The sector 5 beamline user stations are equipped with fully high-adjustable, ergonomically friendly work stations. Data analyses in the BCSB is facilitated by software maintained by sbgrid (http://www.sbgrid.org). A 16 core linux machine is available for our users to process their data and solve/refine their structure. An additional mode of access to the BCSB beamlines is through the Collaborative Crystallography (CC) Program. Users apply for beamtime via the general user program, and collaborate with an expert crystallographer who will conduct the experiments and data reduction on behalf of the researchers. Depending on the users, structure solution, model building and refinement can be carried out as well. Please contact BCSBBeamtime(a)lbl.gov for more information. Please visit http://bcsb.lbl.gov/ for more details about the Center and its beamlines. To find out more, click on: http://www.als.lbl.gov/als/quickguide/independinvest.html We invite you to submit a proposal at: http://alsusweb.lbl.gov/ Scroll down to "Structural Biology beamines (includes protein SAXS)." Click on "New Proposal." If you'd like to apply for May/June 2010 beamtime at the Advanced Light Source, please submit a General User proposal by March 15, 2010. If you have any questions or would like to request open beamtime, please e-mail BCSBBeamtime(a)lbl.gov. Please note that executed user agreements must be received by LBNL prior to beamtime. Proprietary fees, if applicable, must be received by LBNL at least five working days prior to scheduled beamtime. -- ----------------------------------------------------------------- P.H. Zwart Beamline Scientist Berkeley Center for Structural Biology Lawrence Berkeley National Laboratories 1 Cyclotron Road, Berkeley, CA-94703, USA Cell: 510 289 9246 BCSB: http://bcsb.als.lbl.gov PHENIX: http://www.phenix-online.org CCTBX: http://cctbx.sf.net -----------------------------------------------------------------

1 0

January 15, 2009 deadline- User proposal submission for Collaborative Crystallography at BCSB
by Banumathi Sankaran 12 Jan '10

12 Jan '10

Dear Users, The deadline for Mar/April 2010 Collaborative Crystallography proposals will be *January 15, 2009. * ------------------------------------------------------------------------ Through the Collaborative Crystallography Program (CC) at the Advanced Light Source (ALS), scientists can send protein crystals to Berkeley Center for Structural Biology (BCSB) staff researchers for data collection and analysis. The CC Program can provide a number of benefits to researchers: * Obtain high quality data and analysis through collaborating with expert beamline researchers; * Rapid turn around on projects; and * Reduced travel costs. To apply, please submit a proposal through the ALS General User proposal review process for beamtime allocation. Proposals are reviewed and ranked by the Proposal Study Panel, and beamtime is allocated accordingly. BCSB staff schedule the CC projects on Beamlines 5.0.1 and 5.0.2 to fit into the available resources. Only non-proprietary projects will be accepted. As a condition of participation, BCSB staff researchers who participate in data collection and/or analysis must be appropriately acknowledged - typically being included as authors on publications and in PDB depositions. Please consult the website for additional information at: http://bcsb.als.lbl.gov/wiki/index.php/Collaborative_Crystallography ----------------------------------------------------------------------------------------- How To Apply: To learn more, go to: http://www-als.lbl.gov/als/quickguide/independinvest.html To submit a proposal, go to: http://alsusweb.lbl.gov/. Scroll down to "*Structural Biology beamlines (includes protein SAXS)*" and click on "New Proposal." Enter your proposal information, with attention to the following details: * For question 3/First choice, select "5.0.1 (Monochromatic);" for question 3/Second choice, select "5.0.2 (MAD)." * Check box (yes) in response to question (7) "Do you want collaborative crystallography (beamline 5.0.1 or 5.0.2 only) * In question 4, please describe a specific research project with a clear end point. In order to request CC time for Mar/April 2010 allocation period, proposals must be submitted by *January 15, 2009.* The deadline for CC proposals for the time period May/June 2010 will be March 15, 2010. Regards, Banumathi Sankaran

1 0

reduce and ready_set problem
by Jianghai Zhu 11 Jan '10

11 Jan '10

Hi, I believe I have reported this bug before, but it is not fixed in the phenix.reduce and phenix.ready_set yet. The problem is the hydrogens added by reduce when there is a glycan. Here is the error message. Number of atoms with unknown nonbonded energy type symbols: 12 "ATOM 8332 HD22 ASN B 99 .*. H " "ATOM 11820 HD22 ASN B 320 .*. H " "ATOM 12615 HD22 ASN B 371 .*. H " "ATOM 14058 HO4 NAG B3320 .*. H " "ATOM 14086 HO4 NAG B3321 .*. H " "ATOM 14136 HO4 NAG B3371 .*. H " "ATOM 22458 HD22 ASN D 99 .*. H " "ATOM 25955 HD22 ASN D 320 .*. H " "ATOM 26750 HD22 ASN D 371 .*. H " "ATOM 28256 HO4 NAG D3320 .*. H " ... (remaining 2 not shown) ... Sorry: Fatal problems interpreting PDB file: Number of atoms with unknown nonbonded energy type symbols: 12 Please edit the PDB file to resolve the problems and/or supply a CIF file with matching restraint definitions, along with apply_cif_modification and apply_cif_link parameter definitions if necessary. Also note that phenix.ready_set and phenix.elbow are available for creating restraint definitions (CIF files). The hydrogen left on the N atom of the ASN is correct, but should be named as HD21 as defined in the ccp4 cif library. And the HO4 for the NAG glycan is just wrong. I have to delete all these hydrogens to get phenix.refine going. -- Jianghai

2 1

Resolve after Phaser SAD module - question
by Peter Grey 11 Jan '10

11 Jan '10

Dear Phenix experts, It is recommended to use FWT/PHWT after Phaser SAD module for initial map calculation. Could you please explain how to tell Resolve to pick these fields for the initial map ? With MR it is clear since you need FWT and PHIC but with SAD you really need FWT and PHWT . I thank you in advance, Peter

2 1

Phenix.refine RuntimeError
by JXQI 10 Jan '10

10 Jan '10

Dear PHENIXBBs, I tried to refine a N-linked glycan using phenix.refine and used the data_link=NAG-ASN for ASN-NAG connection. But I got a RuntimeError of unknown atom_id: HD22. From the mon_lib_list.cif file of Phenix-1.5-2, the atom_id HD22 is already defined. Any suggestions are appreciated. Thanks J.X. QI ********************************************************* Monomer Library directory: "/home/jxqi/152Phenix/phenix-1.5-2/chem_data/mon_lib" Total number of atoms: 11844 apply_cif_link: data_link: NAG-ASN mod_id_1: DEL-O1 mod_id_2: DEL-HD22 residue_selection_1: chain A and resname ASN and resid 170 residue_selection_2: chain A and resname NAG and resid 1 apply_cif_link: data_link: NAG-ASN mod_id_1: DEL-O1 mod_id_2: DEL-HD22 residue_selection_1: chain C and resname ASN and resid 170 residue_selection_2: chain C and resname NAG and resid 1 apply_cif_link: data_link: NAG-ASN mod_id_1: DEL-O1 mod_id_2: DEL-HD22 residue_selection_1: chain E and resname ASN and resid 170 residue_selection_2: chain E and resname NAG and resid 1 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2559 Number of conformers: 1 Conformer: "" Traceback (most recent call last): File "/home/jxqi/152Phenix/phenix-1.5-2/phenix/phenix/command_line/refine.py", line 11, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/home/jxqi/152Phenix/phenix-1.5-2/phenix/phenix/refinement/command_line.py", line 68, in run log=log) File "/home/jxqi/152Phenix/phenix-1.5-2/phenix/phenix/refinement/command_line.py", line 227, in __init__ self.pdb_file_names) File "/home/jxqi/152Phenix/phenix-1.5-2/cctbx_project/mmtbx/utils.py", line 907, in process_pdb_files stop_if_duplicate_labels = stop_if_duplicate_labels) File "/home/jxqi/152Phenix/phenix-1.5-2/cctbx_project/mmtbx/utils.py", line 940, in _process_pdb_file log = self.log) File "/home/jxqi/152Phenix/phenix-1.5-2/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 2995, in __init__ log=log) File "/home/jxqi/152Phenix/phenix-1.5-2/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 2105, in __init__ log=log) File "/home/jxqi/152Phenix/phenix-1.5-2/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 1575, in __init__ prev_mm=prev_mm) File "/home/jxqi/152Phenix/phenix-1.5-2/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 543, in __init__ mod_mod_id=self.mon_lib_srv.mod_mod_id_dict[apply_data_mod]) File "/home/jxqi/152Phenix/phenix-1.5-2/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 819, in apply_mod mod_mon = self.monomer.apply_mod(mod_mod_id) File "/home/jxqi/152Phenix/phenix-1.5-2/cctbx_project/mmtbx/monomer_library/cif_types.py", line 359, in apply_mod result.delete_atom_in_place(mod_atom.atom_id) File "/home/jxqi/152Phenix/phenix-1.5-2/cctbx_project/mmtbx/monomer_library/cif_types.py", line 264, in delete_atom_in_place raise RuntimeError("delete_atom_in_place: unknown atom_id: %s" % atom_id) RuntimeError: delete_atom_in_place: unknown atom_id: HD22 **********************************************************

2 1

Hello
by Pankaj Chauhan 06 Jan '10

06 Jan '10

Hello, While during NCS based restrained refinement, how can we take two chains as single translation unit as the pdb model is a dimer-dimer. Thanks -- Pankaj Chauhan Senior Research Fellow, PhD Scholar Crystallography Laboratory Division of Protein Science & Engg. IMTECH , Chandigarh, INDIA

1 0

coot - display map
by r n 06 Jan '10

06 Jan '10

Hi I am using Phenix GUI, after refinement , tried to load the coot interface in Phenix, it opens up the coot, but did not load the map or model file. I am using coot0.6 version, Is there any place in phenix enviroment that I could mention the path for coot? Thanks

2 4

refinement
by r n 05 Jan '10

05 Jan '10

Hi I am doing refinement using phenix. I did simulated annealing, Rfree goes up to 10% more than before. (40%) and R stays at 35%. If use previous phenix refinment file for same pdb and data , R and Rfree is 25/27%. I thought even different r-free set after simulated annealing and 7 cycles of refinement in phenix should bring Rfree down, but not ? But same data set and model , in CNS, R/Rfree 26/28%. Any suggestions will be appreciated. I am using phenix-dev249 - linux. thanks ram

2 1

text output for model quality and validation report at phenix
by Ravindra D. Makde 04 Jan '10

04 Jan '10

Hi all, I will greatly appreciate the answers to following query: How can I get the text or excel output of the model quality and validation report of a model after phenix refinement? I am specially interested in real space CC of the various residues. I am using phenix.refine_gui at phenix-1.4-162. I have searched all output files, but couldn't find. Thanks in advance. Ravi Ravindra D. Makde, PhD Postdoctoral fellow, Tan lab, The Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802 USA

3 2

optimize phenix
by r n 04 Jan '10

04 Jan '10

hi all I am trying to optimize the model, in which secondary structures are distorted and I did pdbtools , geometry regulatization , after optimization still the helices are distorted. Is it any tools in the phenix that could optimize the secondary structures alone in the pdb? Thanks ram

3 4