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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 Removing out-of-date lib directory... ok Removing out-of-date base software directory...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

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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

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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

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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

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Increase in R/R(free) after phenix.real_space_refine
by George Devaniranjan 19 Sep '14

19 Sep '14

Hi, I refined (phenix.refine) a 1.0Å structure but it had a few CB outliers and some rotamer outliers. I decided to try real_space_refine, to check if they could be fixed (given that it has a higher radius of convergence). (using run=local_grid_search+minimization_global in real_space_refine) But, the R/R(free) increased from 11.39/13.24( for the refine model) to 16.51/17.55 (real_space_refine model). It seemed a big increase, when I looked at the map against the structure the protein itself seemed fine. The rotamers outliers had decreased, the CB outliers were fixed..etc The solvent fit to the density had worsened in COOT. What am I doing wrong? Any suggestions, advice would be much appreciated. Thank you, George

3 2

RMS angles and comprehensive validation in phenix
by C 19 Sep '14

19 Sep '14

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Problems getting rigid and tls to run
by David Shin 19 Sep '14

19 Sep '14

Hi - Running versions: Version: 1.9.1692 mac-intel-osx-x86_64 osx-10.6.8 Version: 1.9.1692 intel-linux-2.6-x86_64 redhat-e5.10 In both cases, I can run an input model I used previously and get rigid and tls to work. With a newer model, I cannot get either to work (and yes, there was a reason I tested rigid on a model that was refined once). Weirder is I have gone from gui on mac to produce an .eff file to transfer to linux - in the .eff file I get: strategy = *individual_sites *individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous despite having checked the rigid and tls boxes Weirder yet, is I hand edit the file to add *rigid *tls and run on the linux machine, and both still get turned off. I diff the input refine.eff files between using the older model and newer, and nothing appears very different. The only thing I can think of is that there could be some legacy .hidden files in the working directory that change something, but it makes no sense once I port everything to a different computer. Anyone have this trouble? Thanks, Dave

1 0

Refining structure with overlapping conformations of different residues
by Igor Petrik 18 Sep '14

18 Sep '14

Hi, I am trying to refine a structure in which there are two sets of linked conformations of two residues. Around half of the occupancy (altloc A) corresponds to the sidechain of residue 29 pointing into the pocket and residue 65 pointing out and the other conformation (altloc B) has the side chain of residue 65 in the pocket (where residue 29 is in altloc A) and residue 29 pointing out of the pocket. I am refining them by using occupancy refinement groups in, but phenix refine seems to think that altloc A of residue 29 and altloc B of residue 65 may exist at the same time and pushes them apart to avoid clashes. Is there any way around this? - Igor

2 1

calculate TLS contribution to total B-factor
by Michael Thompson 18 Sep '14

18 Sep '14

Hello All, I have a structure that was refined with phenix.refine using TLS, so my PDB file contains B-total in the isotropic B-factor column as well as ANISOU lines. For the sake of analysis, I am interested in determining the TLS contribution to these total B-factors. How can I split B-total into isotropic and TLS contributions? I'm fairly certain this is possible, as it is the inverse of what one would do after refining a structure with TLS in Refmac, which requires that the isotropic and TLS components be added together prior to deposition. I feel like perhaps there has been some discussion of this in the past, but I'm not able to dig anything up from the bb archives. Any help would be much appreciated. Thanks, Mike

2 1