- phenixbb - phenix-online.org

poor phasing
by vennila Natesan 27 Apr '09

27 Apr '09

Dear Tom Thankyou for your kind reply.I checked my data witn phenix.xtriage and there are good anomalous signal (>0.05)in all the resolution shells. Also the systematic absences show it is P43212.Still i couldnt solve using phenix.Where is the thing going wrong? Xtriage results also showed no twinning. My previous message: I am using phenix1.4-4 version. In autosol, got the score of 10.24 for one iodine soaked data. FOM:0.27 and only 54 residues ( that too wrongly) were built out of 129.(CC=0.4), R=0.49 and Rfree=0.574. Regrading the data quality, Rsym:0.0448, Ranom:0.055, Resln:25.0-2.6A Spacegroup is P43212, completeness:99.4%, Multiplicity:11.7, anomalos signal is 1.52 at lowest resoln and higher in high resolution shells. What might be reason for not able to solve this structure?

4 8

observed reflection numbers of refinement greater than the experiment
by carlbluesky＠yahoo.co.jp 24 Apr '09

24 Apr '09

Hi all, I have a problem with reflection numbers of phenix.refine. I did the phenix.refine then i found that the number of observed reflections given for the refinement 75747 (48-2.85A) is greater than the number of observed reflections for the experiment 40434 (50-2.85A). It shoud be around 40000. . This is a peak of MAD data about 2.85A. I used the TLS parameters to refine the structure. I really don't know why because this is my first time use phenix to do refinement. Any advice and suggestion are welcome! Thanks. Carl --------------------------------- Power up the Internet with Yahoo! Toolbar.

3 3

rfree checksums version 1.3 and 1.4
by hari jayaram 24 Apr '09

24 Apr '09

Hi am using the same exact mtz data file from CCP4 uniquefy for two refinements in phenix. I did one round of refinement in phenix 1.3 and then used the output pdb of that refinement and input into the next round of refinement . Only I switched versions to phenix version 1.4. Most other things weere the same including the resolution cutoff used and the input mtz. But phenix tells me that the md5checksums dont match. i am very sure its the same input mtz and identical data resolution ( both cases specifying refinement.input.xray_data.high_resolution=3.0) Could this message of mismatched checksums be an error due to chaging versions midtsream . I certainly dont want to be trampling on my Rfree reflections but apart from copying files to a new directory for the next round and changing phenix versions I have changed little else Thanks for your help in advance hari

2 4

Re: [phenixbb] poor phasing
by vennila Natesan 24 Apr '09

24 Apr '09

Dear members, > > I am using phenix1.4-4 version. In autosol, got the score of 10.24 for one > iodine soaked data. > FOM:0.27 and only 54 residues ( that too wrongly) were built out of > 129.(CC=0.4), R=0.49 and Rfree=0.574. > Regrading the data quality, Rsym:0.0448, Ranom:0.055, Resln:25.0-2.6A > Spacegroup is P43212, completeness:99.4%, Multiplicity:11.7, anomalos > signal is 1.52 at lowest resoln and higher in high resolution shells. > > What might be reason for not able to solve this structure? > >

3 2

viewing previous refinement run validation report
by CK 22 Apr '09

22 Apr '09

Hello all, I am using the phenix 1.4-43 gui to run phenix.refine on my structure and so far I'm very impressed. However, after running a refinement job I had to close the gui before I was finished examining the validation report and now would like to look at it again. Upon relaunching the gui I can't seem to find a way to reload log files/ validation reports from previous runs. Am I missing something obvious here or is the feature not yet implemented? Thanks, Chris

2 1

nightly builds nit (and a question)
by Ben Eisenbraun 21 Apr '09

21 Apr '09

Howdy, I'm not sure you are soliciting bugs on the nightly builds, but I thought I'd mention these. Please let me know if you don't need/want them. I downloaded and installed the 1.4-37 nightly builds. The installations went fine for linux and OS X PPC/x86. There are some absolute symlinks in the installation that don't work: phenix-1.4-37/build/intel-linux-2.6/base/bin/wx-config -> /net/longnose/scratch1/phenix/phenix-1.4-37/build/intel-linux-2.6/base/lib/wx/config/gtk2-ansi-release-2.8 On the OS X there are some that don't appear to matter, e.g.: phenix-1.4-37/build/mac-intel-osx/base/bin/MacPyMOL.app/pymol/test/pdb -> /Volumes/Macintosh HD/Users/delwarl/pdb/entries And some that maybe do: phenix-1.4-37/build/mac-intel-osx/base/bin/python2.6 -> /net/patchnose/scratch1/phenix/phenix-1.4-37/build/mac-intel-osx/base/Python.framework/Versions/2.6/bin/python2.6 Since the nightly builds don't build the ext_ref_files, should I just symlink them to the ones in the 1.4-3 release? Thanks. -ben -- | Ben Eisenbraun | Software Gunky | | Structural Biology Grid | http://sbgrid.org | | Harvard Medical School | http://hms.harvard.edu |

2 1

SA_OMIT map at low resolution
by 邬金 21 Apr '09

21 Apr '09

Hi, I would like to calculate sa_omit map for a low resolution structure (4.0 Ang) to validate the conformation in some regions. What's the proper way to do it? Followed the instruction, I tried: phenix.autobuild data=mydata.mtz model=mybestmodel.pdb omit_box_pdb=mybestmodel.pdb \ omit_res_start_list=100 omit_res_end_list=200 omit_chain_list=L \ composite_omit_type=sa_omit I have several questions: 1. "omit_box_pdb=mybestmodel.pdb": If I define the region that I want to omit, do I need to define the omit_box pdb as well? Should it be complete model or the omit region? 2. I have 4 fold NCS axis, if I want to omit a loop in four copies, how can I define 4 corresponding regions in different chains? e.g omit region: 100-200 in chain L, M, N, O: omit_chain_list = L omit_chain_list = M omit_chain_list = N omit_chain_list = O omit_res_end_list = "200" omit_res_start_list = "100" 3. If I want to omit several loops in one copy, should I turn off NCS? Like: find_ncs=False input_ncs_file= None optimize_ncs=False 4. How to define several omit regions in one chain? Many thanks, Jin _________________________________________________________________ 上Windows Live 中国首页，下载最新版 MSN！ http://im.live.cn/

2 1

Re: [phenixbb] phenixbb Digest, Vol 41, Issue 12
by Ho-Leung Ng 21 Apr '09

21 Apr '09

Hi Zach, You probably have the wrong space group. P3 is rarely represented in the PDB, with only 67 deposited structures out of 57000. You can use Phaser to automatically try all the other P3 related space groups. phenix.xtriage will also try to predict the space group for you. Good luck! Ho UC Berkeley

4 5

phenix.automr high zscore but too many clashes
by zach powers 17 Apr '09

17 Apr '09

Hi, I have a problem and i wonder if someone has had a similar experience. I have been using phenix.automr program to find an MR solution for a protein. When I ask Phaser to use copies=2 I find a number of solutions with poor z-scores (3-4). When I ask it to use copies=3, I get great Z-scores (see below) but no solution due to the high number of clashes (>100!). As an x-ray newbie I am a bit perplexed of what to make of this: the solution is not good because there is not enough space in the unit cell to comfortably accommodate all three molecules yet the Z-score indicates the structure is good. My structure does have several loops and these may be contributing to the clashing residues. As a newbie I have a newbie question - what does this mean (great z-score but no solutions)? Is this non-solution a possible solution if I play with it, or is the packing simply too tight and the Z-scores are not valid? In the meantime I am chopping my protein into sub-domains as recommended in the Phaser documentation, but if anyone has seen something like this before, any suggestions are welcome. thanks zach charlop-powers Packing Table: Space Group P 3 ------------------------------ Solutions accepted if number of clashes = 135 (lowest number of clashes in list) provided this number of clashes <= 10 (maximum number of allowed clashes) # #Clashes # Accepted Annotation 1 188 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 TFZ=10.4 2 156 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 TFZ=10.2 3 151 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 TFZ=9.8 4 146 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 TFZ=9.7 5 187 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=16.3 TFZ=10.5 6 202 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 TFZ=9.2 7 170 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 TFZ=9.1 8 144 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=16.3 TFZ=10.2 9 177 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 TFZ=9.1 10 153 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 TFZ=8.9 11 150 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 TFZ=8.8 12 217 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 TFZ=8.6 13 182 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 TFZ=8.6 14 135 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 TFZ=8.5 15 175 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 TFZ=8.3 16 159 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 TFZ=8.3 17 192 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 TFZ=8.3 18 165 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=16.3 TFZ=9.2 19 169 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=16.3 TFZ=9.1 20 158 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 TFZ=8.0 21 173 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 TFZ=8.0 22 154 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=16.3 TFZ=8.9 23 206 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 TFZ=7.8 0 accepted of 23 solutions

4 4

phenix.autobuild error
by Andreas Förster 15 Apr '09

15 Apr '09

Hey all, I'm calling phenix.autobuild with the following command: phenix.autobuild data=second_try_33.1.mtz model=second_try_33.1.pdb \ > seq_file=name_139_414.seq ps_in_rebuild=True On my MacBook Pro (OSX 5.6, phenix Version: 1.4, Release tag: 3, cctbx tag: 2008_12_07_1353, Platform: mac-intel-osx osx-10.5.6), I get the following error: Exception RuntimeError: 'maximum recursion depth exceeded while calling a Python object' in <type 'exceptions.KeyError'> ignored 108409888 On a linux box (RHEL 5.2, phenix Version: 1.4, Release tag: 3, cctbx tag: 2008_12_07_1353, Platform: intel-linux-2.6 redhat-e5.2) I get this error: ******************************************************************************** Failed to carry out AutoBuild_build_cycle: child process stderr output: command: 'csh /csb/home/andreas/name/P6big/second_try/autobuild/AutoBuild_run_2_/TEMP0/RUN_FILE_1' tset: standard error: Invalid argument ******************************************************************************** Each time, the script was run on the same set of files residing on the linux box. I either ssh into the machine and run phenix.autobuild in an ssh shell or mount my linux home directory via MacFusion and run phenix.autobuild on the Mac. I haven't tried copying the files to the Mac, but other phenix commands work with the remote data (e.g. phenix.autobuild data=data.mtz solvent_fraction=.6 ps_in_rebuild=True model=coords.pdb maps_only=True) What's the problem? Andreas -- Andreas Förster, Research Associate Paul Freemont & Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk

2 1

Twin refinement issues?
by Phil Jeffrey 10 Apr '09

10 Apr '09

While experimenting with twin refinement for a crystal in P321 that approximates P622 to varying extents, I noticed: | twin fraction: 0.59 twin operator: -h,-k,l | A bug, perhaps ? This twin fraction would seem to be unlikely, since twin fractions > 0.5 have no meaning. Since this data does not scale well in p622 compared to some more heavily-twinned datasets on this xtal form I think the twin fraction is certainly less than 0.5. Xtriage estimates: Statistics depending on twin laws ----------------------------------------------------------------- | Operator | type | R obs. | Britton alpha | H alpha | ML alpha | ----------------------------------------------------------------- | -h,-k,l | M | 0.150 | 0.343 | 0.347 | 0.283 | ----------------------------------------------------------------- Unless of course phenix.refine is reporting 2*alpha. Phenix v1.4-3 Intel Mac OSX 10.5.6 This particular run with: phenix.refine model-08.pdb pz7e_truncate-unique.mtz refinement.main.ncs=true strategy=individual_sites+group_adp --overwrite xray_data.r_free_flags.generate=True twin_law="-h,-k,l" This is a very early non-finessed model. Phil Jeffrey Princeton

4 6

optimize weighs
by Yusuf Akhter 09 Apr '09

09 Apr '09

Dear all, I am refining a protein structure using phenix.refine, when i tried to use optimize_wxc, optimize_wxu It always crashes and gives following error. May anybody can explain what is the problem?? Traceback (most recent call last): File "/public/xtal/phenix/phenix-1.3b/phenix-1.3b/phenix/phenix/command_line/refine.py", line 5, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/public/xtal/phenix/phenix-1.3b/phenix-1.3b/phenix/phenix/refinement/command_line.py", line 78, in run call_back_after_monitor_collect=call_back_after_monitor_collect) File "/public/xtal/phenix/phenix-1.3b/phenix-1.3b/phenix/phenix/refinement/driver.py", line 1308, in run log = log) File "/public/xtal/phenix/phenix-1.3b/phenix-1.3b/phenix/phenix/refinement/strategies.py", line 642, in refinement_machine log = log) File "/public/xtal/phenix/phenix-1.3b/phenix-1.3b/phenix/phenix/refinement/weight_xray_chem.py", line 327, in __init__ self.wxc_optimization() File "/public/xtal/phenix/phenix-1.3b/phenix-1.3b/phenix/phenix/refinement/weight_xray_chem.py", line 450, in wxc_optimization rw, rf, b, a, a_xc = self.wx_opt_helper(w = wxc_scale_0 * wxc, sites=True) File "/public/xtal/phenix/phenix-1.3b/phenix-1.3b/phenix/phenix/refinement/weight_xray_chem.py", line 387, in wx_opt_helper verbose = 0) TypeError: __init__() takes at least 5 non-keyword arguments (3 given) Thanks in advance. Yusuf

2 1

twin refinement error
by jonathan elegheert 08 Apr '09

08 Apr '09

Dear Phenix developers, I am rigid-body refining a PM-twinned structure (C2221 => P6x22) with the operators suggested from xtriage or SFcheck but I keep running into this same error (version 1.4.3 or latest cci aps bundles); 1/2*h-1/2*k,-3/2*h-1/2*k,-l 1/2*h+1/2*k,3/2*h-1/2*k,-l Any suggestions as to how I can resolve this? Many thanks in advance, Jonathan Elegheert PhD student Ghent University Belgium ------------------------------------------------------------------------- Traceback (most recent call last): File "/usr/local/cciapps/cci_apps_sources/phenix/phenix/command_line/refine.py", line 16, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/cciapps/cci_apps_sources/phenix/phenix/refinement/command_line.py", line 89, in run call_back_after_monitor_collect=call_back_after_monitor_collect) File "/usr/local/cciapps/cci_apps_sources/phenix/phenix/refinement/driver.py", line 1121, in run call_back_after_monitor_collect = call_back_after_monitor_collect) File "/usr/local/cciapps/cci_apps_sources/phenix/phenix/refinement/strategies.py", line 190, in refinement_machine twin_law = sgtbx.rt_mx( params.twinning.twin_law ) RuntimeError: cctbx InternalError: /net/garter/scratch1/rwgk/auto_build/sources/cctbx/sgtbx/rt_mx.cpp(230): Unsuitable value for rational rotation matrix.

4 6

Phenix.refine Rigid Body multi_body_factor
by Mary Fitzgerald 08 Apr '09

08 Apr '09

I was wondering when you would want to change multi_body_factor= 1? Is this something you would change when you have multiple rigid body domains? From the name, that's what I'm guessing it's for. I'm refining a large over 400 kD multimer complex with two complexes in the ASU. So, if I have 5 chains in each multimer would I want to try to change the multi_body_factor to 10? Or does multi_body_factor affect something else. Thanks, Mary X. Fitzgerald Postdoctoral Associate Arnold Lab

2 1

optimize_wxc and wxu
by Scott Classen 08 Apr '09

08 Apr '09

Hello phenixbb, In general should one optimize wxc and wxu ONLY as a final polishing step or can this be done earlier in the refinement and then the optimized values used for subsequent rounds of refinement? If so which values in the log file should be written into the .def file and where? Here is a snippit from my def file after I optimized weights and changed the optimize flags back to False: target_weights { mode = *automatic every_macro_cycle wxc_scale = 0.5 wxu_scale = 1 wc = 1 wu = 1 fix_wxc = None fix_wxu = None optimize_wxc = False bonds_rmsd_max = 0.05 angles_rmsd_max = 3.5 optimize_wxu = False shake_sites = True shake_adp = 10 regularize_ncycles = 50 verbose = 1 wnc_scale = 0.5 wnu_scale = 1 rmsd_cutoff_for_gradient_filtering = 3 } Thanks, Scott ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Scott Classen, Ph.D. SIBYLS Beamline 12.3.1 http://bl1231.als.lbl.gov Advanced Light Source Lawrence Berkeley National Laboratory 1 Cyclotron Rd MS6R2100 Berkeley, CA 94720 C) 510.206.4418 O) 510.495.2697 Beamline) 510.495.2134 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

4 3

restrains for nucleaic acid base pairs
by Imre Toeroe 08 Apr '09

08 Apr '09

Hi, Does anybody know an easy way to restrain nucleic acid base pairs (base stacking+Watson-Crick base pairing) in phenix.refine? I am refining against a 3.3 A dataset. Thanks, Imre

3 4

phenix autobuild and omit map
by rpai＠berkeley.edu 07 Apr '09

07 Apr '09

Hi, I have a loop that was improperly built when I ran autobuild. the density according to the Fobs-Fcalc maps is not that great. Someone told me that autobuild can use omit maps to build / rebuild the loops so you dont have to do it by hand. Looking at the manual, I found the command, but am a little confused. The model used is the entire model correct? the target.pdb is the chain or region that was not correctly built. For iterative building...how many cycles should I go for? phenix.autobuild data=w1.sca model=coords.pdb omit_box_pdb=target.pdb \ composite_omit_type=iterative_build_omit thanks Raj

3 2

imaginary map (anomlous difference Fourier) from phenix
by Ulrich Baumann 06 Apr '09

06 Apr '09

Hi everybody, I used phenix for calculating anomalous Fourier coefficients (script below) and I get the desired file containing columns FANOM PHANOM. When I read this into Coot for displaying the imaginary map, I only get noise, regardless of resolution cutoff etc. When I export the Fcalcs as CNS format and use CNS for the map calculation, I get very high peaks (i.e. excellent signal-to-noise ratio) on the anomalous scatterers. Inspection of the phenix fcalc file reveals that FOFCWT_no_fill equals FANOM and PHFOFCWT_no_fill is identical to PHANOM . Obviously I am doing something stupidly wrong. Setting xray_data.force_anomalous_flag_to_be_equal_to=true doesn't change anything, by the way, and i am using the latest Phenix version. I vaguely remember that there were an issue with anomlous data but can't find the thread. Thank you very much in advance for enlightening me, Ulrich # source /usr/local/phenix-1.4-3/phenix_env phenix.refine m226h1_rfree-unique.mtz m226h1_hkl2000_6_waters_001.pdb main.number_of_macro_cycles=1 \ refinement.input.xray_data.labels="F(+),SIGF(+),F(-),SIGF(-)" \ xray_data.high_resolution =3.5 strategy=none export_final_f_model=cns output.prefix=sfcalc --overwrite * Space group = 'P3121' (number 152) The mapcoeff.mtz looks like OVERALL FILE STATISTICS for resolution range 0.000 - 0.319 ======================= Col Sort Min Max Num % Mean Mean Resolution Type Column num order Missing complete abs. Low High label 1 ASC 0 49 0 100.00 23.7 23.7 88.43 1.77 H H 2 NONE 0 28 0 100.00 8.4 8.4 88.43 1.77 H K 3 NONE -69 69 0 100.00 0.6 26.2 88.43 1.77 H L 4 NONE 0.0 2220.8 0 100.00 235.55 235.55 88.43 1.77 F 2FOFCWT 5 NONE -180.0 180.0 0 100.00 2.65 89.99 88.43 1.77 P PH2FOFCWT 6 NONE 0.0 956.4 0 100.00 72.48 72.48 88.43 1.77 F FOFCWT 7 NONE -180.0 180.0 0 100.00 2.16 89.97 88.43 1.77 P PHFOFCWT 8 NONE 0.0 2202.8 117 99.84 234.51 234.51 37.16 1.77 F 2FOFCWT_no_fill 9 NONE -180.0 180.0 117 99.84 2.78 89.99 37.16 1.77 P PH2FOFCWT_no_fill 10 NONE 0.0 961.2 117 99.84 72.39 72.39 37.16 1.77 F FOFCWT_no_fill 11 NONE -180.0 180.0 117 99.84 2.19 89.95 37.16 1.77 P PHFOFCWT_no_fill 12 NONE 0.0 961.2 117 99.84 72.39 72.39 37.16 1.77 F ANOM 13 NONE -180.0 180.0 117 99.84 2.19 89.95 37.16 1.77 P PHANOM No. of reflections used in FILE STATISTICS 72570 1 1 3 88.81 -133.90 400.50 -133.90 139.90 -134.31 502.82 -134.31 502.82 -134.31 1 1 4 719.55 109.38 336.98 109.38 703.51 104.61 304.13 104.61 304.13 104.61 1 1 5 987.30 124.20 664.11 124.20 985.68 119.49 659.96 119.49 659.96 119.49 1 1 6 871.35 35.76 152.79 35.76 894.80 36.84 198.58 36.84 198.58 36.84 1 1 7 425.64 38.73 189.77 38.73 419.88 34.24 177.78 34.24 177.78 34.24 1 1 8 406.00 -154.97 53.51 25.03 416.82 -153.85 32.47 26.15 32.47 26.15 1 1 9 73.73 139.84 441.04 139.84 92.83 139.16 479.45 139.16 479.45 139.16

2 2

maps and autobuild
by chandra bose 06 Apr '09

06 Apr '09

hello, I am a first time user to phenix , and I have just completed the autobuild function,. My question may have been asked many times before, but.. The output after the cycles of autobuild/refinement gave me a refined file for a 2.2 Angstrom data set with an R/Rfree of .28/.32. I want to take a look at the density modified maps and see what I can adjust further, but am having trouble loading it in coot. Am I correct in understanding that Coot can load and construct 2f0-fc maps? if so How? : exptl_fobs_phases_freeR_flags.mtz overall_best_denmod_map_coeffs.mtz; overall_best_refine_map_coeffs.mtz; Also from reading the manual, as I understand it, the phenix.refine command will automatically generate Coot compatible maps. But if I take my autobuild.pdb file and the original mtz data file, how can I quickly obtain the same R/Rfree, what commands would I have to imput other than phenix.refine mtz pbd? Also, is it possible to make 3Fo-2Fc maps? Thanks Charlie

3 2

phenix.autobuild sa_omit map
by Jianghai Zhu 03 Apr '09

03 Apr '09

Hi, I am using phenix.autobuild to calculate a sa_omit map. The find_ncs is Auto by default. What does Auto mean here? Should I turn it off or does it matter? Thanks. -- Jianghai

2 1

refinment of ligand
by peter hudson 02 Apr '09

02 Apr '09

Hello all I have refined and built model a dataset of 3.0A resolution dataset. This model is assocaied with a ligand. After final refinement and model building i found a big blob of Fo-Fc density of around 4sigma level at the N-terminal of the fianl model. My protein doesnot carry any tag at the N-terminal. But, the template i have used for the molecular replacement carrying a tag at the N-termianl, which can occupy only 1/4th of this positive density after superpostion. My crystallisation conditions component cannot occupy such higher level of positive density. Since my protein binds to a ligand, i looked carefully to the positive density and it seems very similar to the ligand density but its obscure. Refinement after fitting the ligand leads to very high B-factor of the ligan, which vary for various atoms from 50-90 and simultaneously positive density goes off. I also tried to change the occupancy of the ligand but as i reduce the occupancy the B factor comes down at the noraml expected average B factor value but again Fo-Fc density appears in the map over ligand. If i leave to refine the occupancy to the programme automatically, this lead to the zero occupancy of the few atoms in the ligand and avearge B factor remains normal. suggestions would be appreciated. Thanks in advance Peter

1 0

phenix.autobuild disappeared
by Andreas Förster 01 Apr '09

01 Apr '09

Hey there, sorry for the brainfreeze but I can't find phenix.autobuild. It's not part of cci_apps Versions 2008_09_13_0905 or 2009_02_15_2320. What happened? How do I build? Andreas -- Andreas Förster, Research Associate Paul Freemont & Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk

2 1

Re: [phenixbb] phenixbb Digest, Vol 40, Issue 31
by Marjolein Thunnissen 31 Mar '09

31 Mar '09

> > Hi Marjolein, > >> I have been trying to find in the documentation if there is a way to do this >> but I have the following problem: In a recent structure we are currently >> refining we identified a spermine molecule sitting right on a >> crystallographic two-fold axis. Spermine has internal two-fold symmetry and >> it is part of extensive crystal contacts. I just wonder how to refine this >> with Phenix. In Refmac it is easy, I put the occupancies to 0.5 and the >> program ignores the clashes of the symmetry related molecule, but that >> doesn't seem to be the way that Phenix works. Can anyone give me advise on >> this? > > Supporting the occupancy trick is on my to-do list (fairly high up). > > In the meantime, could you try giving only the asymmetric unit of the > spermine? I.e. delete all duplicate atoms from your pdb file. > The restraints across the symmetry bond will not work automatically. > You have to define a "custom bond" instead, and if you also want to > restrain the angles, custom pseudo-bonds. See the > "Definition of custom bonds and angles" section. > In your case you'll have to define symmetry_operations (not shown > in the docs), e.g.: > > bond { > action = *add > atom_selection_1 = resname SPM and name C7 > atom_selection_2 = resname SPM and name C7 > symmetry_operation = -x,-y,z > distance_ideal = 1.5 > sigma = 0.01 > } > > The main difficulty will be to find the correct symmetry_operation > for each custom bond. If you send my the CRYST1 card from your > PDB file and the part with the SPM residue I could help out. > > Ralf > > > ------------------------------ Hi, The commands worked indeed the trick. Luckily it is actually not that difficult to find the symmetry operators when using coot. One just has to switch drawing symmetry atoms on and clicking on a symmetry atom, coot will tell you in the bottom line which atom it is and which symmetry operator was used to draw it... Thanks again Marjolein __________________________________________________________________________ | Marjolein Thunnissen Phone +46-(0)46-22 24584| | Associate Professor Fax +46-(0)46-22 24692| | Dept of Molecular Biophysics, Lund University http://www.mbfys.lu.se | | PO-Box 124 S-221 00 Lund, Sweden | | | |Scientific coordinator I911 (Max-lab): MAD and fixed-wavelength stations | | for macromolecular crystallography | |__________________________________________________________________________|

2 1

Re: [phenixbb] PHENIX user mailing list <[email protected]>
by Ralf W. Grosse-Kunstleve 30 Mar '09

30 Mar '09

Hi Maia, > I have a Ca2+ ion in a special position. the ocupancy should be 0.5, as > the other half belongs to a symmetry-related molecule. However, > refinement makes the occupansy 1. What should I do to prevent this? > Should not it find automatically that? phenix.refine uses the correct symmetry factor automatically (internally). Unless you have an actual partial occupancy, the occupancy factor in the pdb file should be 1, irrespective of the multiplicity of the special position. Let me know if this doesn't answer your question. Ralf

4 4

can I turn off TLS for subsequent rounds of refinement?
by Scott Classen 30 Mar '09

30 Mar '09

Hi all, As the TLS refinement can take a significant amount of time, I'm wondering if I can turn it off after a few rounds with it on? or will phenix.refine "see" the ANISOU records and assume I am doing anisotropic ADP? Thanks, Scott

2 1