September 2014 - phenixbb - phenix-online.org

labelit distl_minimum_number_spots_for_indexing
by Christian Roth 22 Sep '15

22 Sep '15

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

6 8

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

14 Jul '15

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

7 10

help on MIR dataset
by Ni, Fengyun 25 Oct '14

25 Oct '14

Hi everyone, I am working on a MIR dataset: one native data, three EMTS soaked data at different concentration, one PbAc2 data. My initial trial with phenix autosol did not give positive solutions. I hope I could get some information from all of you. I index and integrate the data in Mosflm and possible group is P3, though the Pointless said the most possible is P3121. But for now, I only tried P3 at different resolutions for the reason that a potential MR solution (below 20% identities, TFZ=7.1) was found in P31 space group. If P3121 is the real space group, the space is too crowed to fit my molecules unless they have some unexpected symmetry. For the difference among dataset in P3 space group, the output from SCALEIT of CCP4 gives as follows, RMS differences|RMSiso RMSano ---------------------------------------- FP-hg |172.30 22.50 FP-hg2 |159.20 24.07 FP-hg3 |85.08 27.92 FP-pb |31.15 24.55 The native data's resolution cutoff is 3.2 A, and 3.2/3.8/3.5 for different EMTS data, 3.5 for Pb data.I did notice some radiation damage for EMTS (Hg) data (large negative B-factors in SCALA), but not for Pb data. And the anomalous signal only extend to 5.6 and 4.5 A for EMTS and Pb data, respectively, as indicated by phenix.xtriage. These are all the possible heavy atom data we could obtain. So i tried all of them in phenix.autosol. The input is like follows, autosol { seq_file = ../seq.dat crystal_info { solvent_fraction = 0.62 #determined from matthews coefficient to assure "reasonable" content in asymmetric unit. } native { data = nat.mtz } deriv { data = hg1.mtz atom_type = Hg inano = noinano *inano anoonly lambda = 1.00394 } deriv { data = hg2.mtz atom_type = Hg inano = noinano *inano anoonly lambda = 1.00394 } deriv { data = hg3.mtz atom_type = Hg inano = noinano *inano anoonly lambda = 1.00394 } deriv { data = pb.mtz atom_type = Pb inano = noinano *inano anoonly lambda = 0.94640 } model_building { build = False #my structure is DNA/protein complex, so i choose to stop the building process. } } I tried at different resolutions, 3.6/4.0/4.4/4.8/5.2/5.6/6.0 A. One solution was given based on Pb data at 4.8 A with following statistics, Solution # 6 BAYES-CC: 59.7 +/- 17.2 (2SD) Dataset #4 FOM: 0.24 Score type: SKEW CORR_RMS NCS_OVERLAP Raw scores: 0.31 0.69 0.00 100x EST OF CC: 59.74 17.55 31.25 Refined heavy atom sites (fractional): X Y Z xyz 0.033 0.020 0.538 xyz 0.417 0.217 0.113 xyz 0.041 0.010 0.721 The statistics is almost the same for its inverse, and i read from the output that the statistics for phasing other Hg datasets are very low (BAYES-CC is lower than 20) based on the above solution. The resulting map does not make much sense yet. Sorry for the long post. Any suggestion is welcome. Thank you very much! Fengyun

2 8

how to refine everything except n residues in phenix.refine?
by Murpholino Peligro 23 Oct '14

23 Oct '14

Hi everybody! Everytime when I (within coot) do "real space refine" two arginines that have two alternate conformations ..(interacting by hydrogen bonds); and then phenix.refine everything, both conformers move away. Therefore, when I open my mtz and pdb files from phenix.refine in coot, I'll have green blobs where there should be guanidium groups. Can I tell phenix.refine not to move only those two residues? It should be something like the following lines in the eff file? sites { individual = None torsion_angles = None rigid_body = None remove_selection=resid 45 remove_selection=resid 68 } Thank you very much

4 8

anomalous difference map
by CPMAS Chen 10 Oct '14

10 Oct '14

Hi, phenix users, A difference map is used to identify whether there is anything not-modeled, say some ligands, ions. Then when I generate anomalous difference map, I should not put the ligand(which contains Br) in the model, right? Or in phenix, after I put the Br-ligand in the model, I should not see the anomalous difference density at the site, right? Could anyone give me a confirmation of this? Thanks! Charles -- *************************************************** Charles Chen Research Associate University of Pittsburgh School of Medicine Department of Anesthesiology ******************************************************

6 15

PHENIX installation errors with CentOS 6
by Mark A. White 01 Oct '14

01 Oct '14

Hello, I am getting install errors with several phenix installations after upgrading to CentOS 6. I started with the nightly-build ========================================================================== PHENIX Installation version: dev release tag: 1807 machine type: intel-linux-2.6-x86_64 OS version: 2.6.32-431.29.2.el6.x86_64 user shell: /bin/tcsh destination: /usr/local ========================================================================= Warning: /usr/local/phenix-dev-1807 already exists, will be overwritten removing existing temporary directory... ok finding existing installations... Removing out-of-date lib directory... ok Removing out-of-date base software directory... ok Installing new binary package... ok Configuring PHENIX components... ******************************************************************************** configuration step incomplete! See the log file for detailed error messages. ******************************************************************************** The log contains only a list of files ending with (./docutils/._MANIFEST.in) and no error messages. Then I went back to the latest stable version, which was installed on my server when it ran CentOS 5. Both my server and WS now produce the same error (CentOS 6). ========================================================================== PHENIX Installation version: 1.9 release tag: 1692 machine type: intel-linux-2.6-x86_64 source machine type: intel-linux-2.6-x86_64 OS version: redhat-e6.5 user shell: /bin/tcsh destination: /usr/local ========================================================================= ========================================================================== Installing from binary bundle ========================================================================== bundle file: bundle-1.9-1692-intel-linux-2.6-x86_64.tar.gz PHENIX installation source directory set to: /home/white/downloads/phenix-installer-1.9-1692 PHENIX installation target directory <PHENIX_LOC > set to: /usr/local/phenix-1.9-1692 PHENIX installation build directory set to: <PHENIX_LOC > /build/intel-linux-2.6-x86_64 PHENIX temporary build directory set to: build-binary/intel-linux-2.6-x86_64/marvin/tmp PHENIX installation log directory set to: build-binary/intel-linux-2.6-x86_64/marvin/log ==== warning: "/usr/local/phenix-1.9-1692" already exists ==== ==== warning: cannot determine installation time-stamp, proceeding ==== installing binary components removing existing files in build-binary/intel-linux-2.6-x86_64/marvin/tmp/binary finding installed versions finding binary versions binary components up-to-date the binary package will not be installed setting environment configuring PHENIX components /home/white/downloads/phenix-installer-1.9-1692/bin/install-from-binary: line 361: 19688 Segmentation fault $PHENIX_BUILD/base/bin/python $PHENIX_LOC/cctbx_project/libtbx/configure.py --current_working_directory="$PHENIX_BUILD" $PHENIX_COMPONENTS $CONFIG_OPTS >> $PHENIX_LOG/binary.log 2>&1 Error configuring: see /home/white/downloads/phenix-installer-1.9-1692/build-binary/intel-linux-2.6-x86_64/marvin/log/binary.log for details The log contains only a list of files ending with (./docutils/._MANIFEST.in) and no error messages. Then I tried installing phenix-dev-1810 from source: Installing cairo... log file is /home/white/downloads/phenix-installer-dev-1810/install_tmp/intel-linux-2.6-x86_64/marvin/cairo_install_log getting package cairo-1.8.10.tar.gz... using /home/white/downloads/phenix-installer-dev-1810/gui/cairo-1.8.10.tar.gz Traceback (most recent call last): File "./bin/install.py", line 815, in <module> run(sys.argv[1:]) File "./bin/install.py", line 72, in __init__ self.install_from_source() File "./bin/install.py", line 292, in install_from_source log=out) File "/home/white/downloads/phenix-installer-dev-1810/lib/libtbx/auto_build/install_base_packages.py", line 113, in __init__ self.build_cctbx_dependencies() File "/home/white/downloads/phenix-installer-dev-1810/lib/libtbx/auto_build/install_base_packages.py", line 168, in build_cctbx_dependencies self.build_wxpython_dependencies() File "/home/white/downloads/phenix-installer-dev-1810/lib/libtbx/auto_build/install_base_packages.py", line 425, in build_wxpython_dependencies self.build_wxpython_dependencies_linux() File "/home/white/downloads/phenix-installer-dev-1810/lib/libtbx/auto_build/install_base_packages.py", line 504, in build_wxpython_dependencies_linux self.build_compiled_package_simple(pkg_name=pkg, pkg_name_label=name) File "/home/white/downloads/phenix-installer-dev-1810/lib/libtbx/auto_build/install_base_packages.py", line 377, in build_compiled_package_simple log=pkg_log) File "/home/white/downloads/phenix-installer-dev-1810/lib/libtbx/auto_build/install_base_packages.py", line 196, in configure_and_build self.call("make -j %d %s" % (self.nproc, " ".join(list(make_args))), log=log) File "/home/white/downloads/phenix-installer-dev-1810/lib/libtbx/auto_build/install_base_packages.py", line 192, in call return call(args, log=log) File "/home/white/downloads/phenix-installer-dev-1810/lib/libtbx/auto_build/installer_utils.py", line 53, in call raise RuntimeError("Call to '%s' failed with exit code %d" % (args, rc)) RuntimeError: Call to 'make -j 8 ' failed with exit code 2 I would like to install the latest developmental version. Any idea what could be going wrong? I have the latest updates installed. -- Yours sincerely, Mark A. White, Ph.D. Associate Professor of Biochemistry and Molecular Biology, Manager, Sealy Center for Structural Biology and Molecular Biophysics Macromolecular X-ray Laboratory, Basic Science Building, Room 6.630 University of Texas Medical Branch Galveston, TX 77555-0647 Tel. (409) 747-4747 Fax. (409) 747-1404 mailto://[email protected] http://xray.utmb.edu QQ: "Life is no brief candle to me. It is a sort of splendid torch which I have got a hold of for the moment, and I want to make it burn as brightly as possible before handing it on to future generations. " - George Bernard Shaw

3 4

refinement problem
by Sneha Rangarajan 30 Sep '14

30 Sep '14

Hello, I have a 1.9A dataset for a single chain Fv-peptide complex that shows psedomerohedral twin operators in Xtriage (1 in p212121, 3 in p21 and 7 in p1). Although most programs (in CCP4) identify the best SG to be p212121, MR cannot find a solution with p212121 due to packing clashes. I tried reprocessing it in p21 and MR can find only one molecule in the asu. The map looks quite good with good density for the sidechains. However the Rfactors wont come down. After a few rounds of refinement (rigidbody, Xray, TLS and Ind B fac) it is still 38/48. I tried processing it in p1 and have managed to find 3 molecules in the asu (missing one molecule). The map looks good. While the Rfactors are lower, the gap between Rwork and Rfree is still high (27/40). I don't know what space group I should choose to ultimately refine it and get the Rfactors low. If you need any more information, I would be happy to provide it. Does anyone have any suggestions? Thanks a lot, Sneha

2 2

Target function for refinement in case of Pseudo-translational symmetry
by Varun Bhaskar 29 Sep '14

29 Sep '14

Hi, I collected a dataset for a binary complex (72kDa size) to 3.62A resolution which could be processed in P32 2 1 space group. Data quality analysis with phenix.xtriage showed a presence of Pseudotranslational symmetry (Non-origin peak in the patterson with 60% intensity at 0.33, -0.33, -0.013). I determined the structure with MR. I have 6 copies in ASU. I tried Zanuda for SG validation and this looks like the right space group. For refinement when I use Maximum likelihood (ML) as the target function, my Rfactor/Rfree is around 31.3/32 but when I change it to Least square (LS) my Rfactor/Rfree drops to 27.3/29.8. The map quality after ML or LS refinement looks very similar for most of the molecule, except for few places where the map from ML has slightly better features. I read people use LS instead of ML only in the case of twinning but I am not sure if it could also be used in the case of PST. Would the use of LS as the target function for refinement be right in this case? Thanks in advance Best Regards Varun

2 1

Histidine as a hydrogen bond acceptor in Phenix refine
by Phan, Jason 26 Sep '14

26 Sep '14

Hi All, I've been refining a 1.1 Å structure with explicit hydrogen atoms and noticed that the serine HG atom (hydrogen atom attached to oxygen gamma) is rotated more than 90 degrees from the OG - NE2 (histidine) line (5 cases observed). In this position, the HG is staggered with the two carbon beta hydrogens and should be the preferred configuration. However, there is a histidine nearby with atom NE2 at 2.7 Å from the serine OG and in good geometry for Hbond formation. The other nitrogen, ND1, is protonated and interacting with an aspartic acid (similar to the catalytic triad configuration). In this protomer, the NE2 atom has a lone pair and should act as an acceptor. Thus, the OG - H - NE2 angle should be as close to 180 as possible for an ideal hydrogen bond angle. The OG - H - NE2 angle of more than 90 degrees looks a little off to me. I checked the other program, e.g. Schrodinger Prime to see how it treats this situation and found that all the OG - H - NE2 angles are within 10-60 degrees from the ideal value of 180, certainly not 90 as observed in Phenix refine. My question is is NE2 or ND1 atom of the HID or HIE protomer treated as a potential hydrogen bond acceptor in Phenix? For other acceptors like the backbone carbonyl oxygen, carboxylic acid oxygen, and water oxygen, the hydrogen bond angle OG -H -O looks good. Not when it involves histidine atom NE2 or ND1 though. The pH of the crystallization is 7 by the way. Also, there's no water nearby that would draw the HG away from the histidine. Jason

4 5

Fo-Fc omit map for ligand in the protein-ligand structure
by Wei Shi 20 Sep '14

20 Sep '14

Hi all, I am working with a protein dimer-ligand structure (resolution: 2.8Å) and am going to make a figure showing the bound ligand superimposed with the electron density (Fo-Fc) map obtained after omit refinement. What I did is to make the ligand-free structure model and then use Phenix.refine using the following parameters plus simulated annealing (torsion angle) or (Cartesian): Default: XYZ coordinates + Real-space+ Individual B factors + Occupancies. Also click: Optimize X-ray/stereochemistry weight + Optimize X-ray/ADP weight + Secondary structure restraints + NCS. Contoured at 2σ, the Fo-Fc map generated show green density for most part of the ligand, but for several atoms in the middle of the ligand, the green density is missing... It's like this: some atoms have green density and the next few no green density and then a couple few has green density and then a couple more no green denisty.... The missing green density usually means that part is disordered in the structure, right? I am not sure why the density is missing for some atoms in the middle of the ligand. It would makes more sense if the missing green density is at the end of the ligand... Does anyone happen to have any clue about what it means for the green density missing in my case? Also, I am not sure whether I did the omit refinement right: (1). For simulated annealing, it has two options, one is Cartesian and the other is Torsion angle, and it's said that torsion angle is more suitable of low resolution data. Is there any difference about which one to choose in my case? (2). Is it Okay to run the omit refinement in the presence of the following parameters as I did: Optimize X-ray/stereochemistry weight + Optimize X-ray/ADP weight + Secondary structure restraints + NCS. Thank you so much! Best, Wei

5 24