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Twin Refinement in P 1 21 1
by Yuri 27 Sep '11

27 Sep '11

So in other words, if I input the reflection and the space group as P 1 21 1 (lower symmetry vs the initially attempted C 2 2 21), and I specified the operator in the refinement parameters I should be ok, right? Thank you -- Yuri Pompeu

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Twin Refinement in P 1 21 1
by Yuri 27 Sep '11

27 Sep '11

Hello everyone, I have a twinned data set with PM twin operator h,-k,-h-l I was able to input the twin law into the refinement parameters, however I do not see a place that asks me for the law when generating the Rfree flags. Could someone point me in the right direction? Best, -- Yuri Pompeu

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renaming an holo PDB after the alo one
by Francois Berenger 27 Sep '11

27 Sep '11

Hello, I have one bound complexe (a ligand + a protein in holo conformation). I also have the apo structure for a very similar protein. Is there a tool to create a new PDB, whose coordinates are taken from the holo structure but residue names and numbers are taken from the alo structure (by looking at the corresponding residues in the output of a sequence alignment program)? I thought about doing a script using clustalw for the alignment part, but the task seems not trivial. Thanks a lot, Francois.

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real space residuals
by Bradley Hintze 26 Sep '11

26 Sep '11

Hey phenix, I see a util for real space correlation. Real space residuals are slightly different. Is the a tool to calculate RSR in phenix? -- Bradley J. Hintze Duke University Graduate Student Department of Biochemistry

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map CC given a model and map coefficients
by Francis E Reyes 26 Sep '11

26 Sep '11

Hi all I'd like to compute a resid by resid and overall map CC between a set of coefficients I specify and a model. Any utils to get this to me quickly? phenix.model_vs_data doesn't seem to take in custom coefficients. Thanks! F --------------------------------------------- Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

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Pseudo-merohedral twinning refinement in C2, when beta = 94 degrees
by John Pak 22 Sep '11

22 Sep '11

Hi all, I currently have a dataset that scales well in C2. (a = 224,b = 129,c = 392. beta= 94.5 degrees). Previously, I had thought that these crystals were in P6322 (posted this a few months ago), but I've since grown better crystals, where the beta angle is now 94.5, and not close to 90.0. I'm reasonably confident with the scaling - however, it has always been really difficult to index these crystals in HKL2000. Like the previous crystals, this new C2 dataset looks like it might be perfectly twinned, based on Xtriage's L test. I've solved the structure by MR, and refined it to 3.0 angstroms to R=30%, Rfree=33%, but I am running out of things to fix. I'd like to perform twinning refinement, based on this Xtriage L test result. The problem is that Xtriage cannot find any pseudomerohedral twinning laws, likely because the beta angle is too far from 90 degrees?? For kicks and giggles, I started to enter arbitrary beta angles in Xtriage, and at a beta angle below 93.4, Xtriage can find two twinning laws (closer to 90 degrees, Xtriage can find 5 twin laws). Using "-1/2*h+3/2*k, 1/2*h+1/2*k, -l" in Phenix refine (the beta angle is still 94.5 degrees, I haven't changed this) results in the R and Rfree dropping a lot to 25.5 and 28.6, respectively. Used the same random seed as previous runs to generate the test set from the scalepack file, with the "use lattice symmetry to generate test set" flag enabled. The maps look a lot noisier. So my questions are: 1. Is this twinning refinement valid? I'm really thinking no - since the maps didn't improve. Suppose the maps didn't get worse though - would this twinning refinement then be valid? 2. How do I go about reindexing this dataset in I2? i.e. to see if the beta angle with this unit cell selection is closer to 90 degrees. Would this even help, with respect to pseudomerohedral twinning refinement? Thanks!

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Maps Bias
by Yuri 22 Sep '11

22 Sep '11

I was having a discussion with a friend about maps and model bias. Is the Fobs/PHImodel more biased than 2FOFCWT/PHI2FOFCWt? What about an omit region of these two? Thanks for any opinion on this -- Yuri Pompeu

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Ligand / Loop occupancy refinement
by Antony Oliver 19 Sep '11

19 Sep '11

Dear all, Apologies if this has been covered already in a previous post — but I can't find a suitable response in the archive. We have the following situation... We have soaked a ligand into an apo-crystal, collected diffraction data, and solved the structure. What is apparent from the electron density, is that the ligand isn't in the crystal at full occupancy, it's roughly about 70-80%. However, as the ligand binds, it causes a small conformation change in the active site of the protein, altering the position of around 4 amino acids. What I want to do, and can't quite get phenix.refine to do is the following... Refine the occupancy of the ligand (chain C resname LIG) with the "A" conformation of the active site residues (which should be the same, as they are mutually dependent) — and then refine the occupancy of the "B" conformation of the active site residues — which should all theoretically add up to a total of 1. Could anyone help me with how the occupancies / constrained_group parameters should be set up in this case? With thanks, Tony. --- Dr Antony W Oliver Senior Research Fellow CR-UK DNA Repair Enzymes Group Genome Damage and Stability Centre Science Park Road University of Sussex Falmer, Brighton, BN1 9RQ email: antony.oliver(a)sussex.ac.uk<mailto:[email protected]> tel (office): +44 (0)1273 678349 tel (lab): +44 (0)1273 677512

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bulk solvent mask question
by Laurie Betts 16 Sep '11

16 Sep '11

I notice that during refinement of a MR solution for a protein (search model is 100% homologous to target), a very large ligand-binding cavity (as much as 20 A wide in some parts) in my protein gives weak positive difference density for a ligand soaked into the crystals, unless I turn off bulk solvent modeling. Then the fo-fc difference density is quite strong (2.6 Angstrom data). I think this is due to part of the cavity being included in bulk solvent? Can I edit the mask easily, or flag parts of the protein as NOT exposed to solvent? Thanks Laurie Betts

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Refinement with optimize weights
by Ankit Gupta 16 Sep '11

16 Sep '11

Hello Forum, I am using Phenix 1.7.1-743 to refine my structure. My R/Rfree values for a 2.5 A structure were 0.22/0.305. I used optimize weights along with TLS and the R/Rfree values improved to 0.23/0.29. I wanted to know what parameters should I use for subsequent refinement. I read on phenix bb that one needs to fix the wxc_scale and wxu_scale. Is this correct? What values should be used for these parameters after running optimize wxc/wxu weights. Is there any place where I can get starting values for my future refinement? Also, I would like to know what Fix X-ray/stereochemistry weight and Fix X-ray/ADP weights are for? Thanks for the help.

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Phenix.refine distorts geometry during rigid body refinement
by Ian Slaymaker 14 Sep '11

14 Sep '11

I am bringing a PDB refined in Refmac back to phenix.refine. After an initial rigid body refinement to compare numbers (one chain per group), the geometry (specifically the bond length rmsd) had surprisingly increased. Phenix.validate confirmed the Refmac (initial) geometry numbers and then afterwards confirmed the distorted geometry. What is strange is that when opened in COOT, the initial and final models are completely super imposed. REMARK Start: r_work = 0.3375 r_free = 0.3624 bonds = 0.006 angles = 0.768 REMARK Final: r_work = 0.3379 r_free = 0.3626 bonds = 0.145 angles = 1.019 can you help me figure out what is going on here? These are the final few refinements of a 4.1 A structure. Thanks, Ian

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Linux kernel version 3.0 detection
by Ben Eisenbraun 14 Sep '11

14 Sep '11

Hi, Robert Campbell at Queens pointed out to me that the "machine_type" script bundled with PHENIX doesn't understand the new version 3.0 linux kernel strings. He tweaked his local copy for testing purposes on a Debian testing machine, and just forcing the 3.0 version to use the 2.6 binaries worked: case "$KERNEL" in 2.4.*) kernel_version=2.4 ;; 2.6.*) kernel_version=2.6 ;; 3.0.*) kernel_version=2.6 ;; *) kernel_version="$KERNEL" ;; esac I haven't tested it myself. It looks like Fedora 16 and Ubuntu 11.10, both targeted for November releases, will be using the new 3.0 kernel. -ben -- | Ben Eisenbraun | SBGrid Consortium | http://sbgrid.org | | Harvard Medical School | http://hms.harvard.edu |

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Multiple conformations of disulfide
by Matthew Merski 13 Sep '11

13 Sep '11

Hello, I am trying to refine a surface cys that is alkylated by beta-mercaptoethanol (BME). The BME appears to have two poses and I am having trouble with getting phenix to understand the restraints. When I give the BME two conformations I get the error: Sorry: No atom selected: "chain A and resname ABME and resid 165 and name S2" My link_params file looks like this: refinement.geometry_restraints.edits { drgA_selection1 = chain A and resname ABME and resid 165 and name S2 bond { action = *add atom_selection_1 = $drgA_selection1 atom_selection_2 = $cys215_selection distance_ideal = 2.05 sigma = 0.02 slack = None } Not calling it ABME of course results in a non-unique atom error. Thanks for your help. Matthew Merski UCSF Shoichet Group

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phenix.refine restraint
by Simon Kolstoe 12 Sep '11

12 Sep '11

Dear phenixbb, I'm trying to constrain a ligand-metal bond that is continuously getting altered by phenix.refine (my data's only 3.2A). I've added the following restraint but it just doesn't seem to be holding the bond length during refinement. Is there a different way of telling phenix.refine not to alter this distance? (I'm doing it all on the command line & by editing the .def file). refinement.geometry_restraints.edits { bond { action = *add atom_selection_1 = name CA and chain X and resname CA and resseq 1 atom_selection_2 = name O1 and chain L and resname ROC and resseq 1 distance_ideal = 2.380000 sigma = 0.100 } } Thanks, Simon --------------------------------------------------------------- Dr Simon Kolstoe Laboratory for Protein Crystallography Centre for Amyloidosis & Acute Phase Proteins UCL Medical School Rowland Hill Street, London NW3 2PF Tel: 020 7433 2765 http://www.ucl.ac.uk/~rmhasek ---------------------------------------------------------------

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phenix.refine and ice rings.
by Francis E Reyes 08 Sep '11

08 Sep '11

Hi phenixer's / developers. A quick question: Curious, how are spots that lie on ice rings dealt with? At which step? Thanks! F --------------------------------------------- Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

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FOM in output MTZ file from phenix.refine
by Joern Krausze 08 Sep '11

08 Sep '11

Dear all, there is no FOM comlumn in my output MTZ file from phenix.refine. According to the documentation, the MTZ with FOM should be written out by default. I did not find any option that would trigger FOM inclusion. What can I do to include FOM? Thanks, Joern ****************************************** Address: Joern Krausze Molecular Structural Biology Helmholtz Centre for Infection Research Inhoffenstrasse 7 38124 Braunschweig Germany Email: joern.krausze(a)helmholtz-hzi.de Phone: +49 (0)531 6181 7023 (office) +49 (0)531 6181 7020 (lab) ****************************************** Helmholtz-Zentrum für Infektionsforschung GmbH | Inhoffenstraße 7 | 38124 Braunschweig | www.helmholtz-hzi.de Vorsitzende des Aufsichtsrates: MinDir’in Bärbel Brumme-Bothe, Bundesministerium für Bildung und Forschung Stellvertreter: MinDirig Heiko Gevers, Niedersächsisches Ministerium für Wissenschaft und Kultur Geschäftsführung: Prof. Dr. Dirk Heinz; Ulf Richter, MBA Gesellschaft mit beschränkter Haftung (GmbH) Sitz der Gesellschaft: Braunschweig Handelsregister: Amtsgericht Braunschweig, HRB 477

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Postdoc Position at LBNL
by Nicholas Sauter 07 Sep '11

07 Sep '11

Exploring New Horizons in Data Processing. The Computational Crystallography group at Lawrence Berkeley National Lab ( http://cci.lbl.gov) would like to recruit an outstanding postdoctoral scientist with a strong interest in the computational challenges at the forefront of structural biology. With synchrotron beamlines increasingly controlled automatically and remotely, and with CCDs being replaced by pixel-array detectors, software development is critical to future experimental success. Better algorithms are needed to realistically model the diffraction observed on the new detectors, and the blinding data acquisition speed will require a new focus on efficiency. Difficult challenges also remain for deriving structural information from free-electron laser experiments. Two years after first light at the LCLS, new research on data analysis has become increasingly vital. This position offers the opportunity to collaborate with Bay Area beamline developers at both the ALS and SSRL, and access to unprecedented data sets from LCLS nanocrystallography studies. Local resources include numerous groups developing crystallography methods, as well as expertise in computational hardware including graphics processing units. Software will be developed within an open-source paradigm, and is expected to have a worldwide influence on high-throughput structural biology. Candidates should have a recent Ph.D. in computational biology or a related field, as well as strong experience in instrumentation, software, or data analysis. Applications consisting of a statement of research interests, CV, list of publications, and three references should be submitted on the Web at https://lbl.taleo.net/careersection/2/jobdetail.ftl?lang=en&job=73565 -- Nicholas K. Sauter, Ph. D. Computer Staff Scientist/Engineer Physical BioSciences Division Lawrence Berkeley National Laboratory 1 Cyclotron Rd., Bldg. 64R0121 Berkeley, CA 94720-8118 (510) 486-5713

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Restraints for keeping base-pairs co-planar in RNA/DNA
by jens j birktoft 06 Sep '11

06 Sep '11

Hi everybody: What would be proper approach to generate restraints that will keep base pairs coplanar (or nearly coplanar) in RNA/DNA helical structures? Hydrogen bonds by themselves are not sufficient, at least not for low resolution refinement, <4Å Jens *+++++++++++++++++++++++++++++++++++++++++++++++++++++++* * * *Jens J. Birktoft e-mail: jens.knold(a)gmail.com slow-mail: Dept. Chemistry, NYU, 350 CPW , Suite 9F, New York, NY 10025 Phone: 212-749-5057 *

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MemoryError in phenix.refine
by Tanner, John J. 05 Sep '11

05 Sep '11

I get the following error at the end of a phenix.refine run. The pdb file is produced, but the mtz file is empty. The resolution is 1.15 A and the cell is CRYST1 84.808 93.803 132.080 90.00 90.00 90.00 P 21 21 21 The version is PHENIX: Python-based Hierarchical ENvironment for Integrated Xtallography Version: 1.7.1 Release tag: 743 Platform: intel-linux-2.6 redhat-e5.6 I've seen this sort of thread on the bb previously. Is there a fix for this, other than using refmac? Thanks. Traceback (most recent call last): File "/linux/src/phenix-1.7.1-743/phenix/phenix/command_line/refine.py", line 11, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/linux/src/phenix-1.7.1-743/phenix/phenix/refinement/command_line.py", line 107, in run map_manger.write_files() File "/linux/src/phenix-1.7.1-743/phenix/phenix/refinement/driver.py", line 1430, in write_files map_coeff_dataset=self.write_mtz_file(), File "/linux/src/phenix-1.7.1-743/phenix/phenix/refinement/driver.py", line 1419, in write_mtz_file params = self.map_params.map_coefficients) File "/linux/src/phenix-1.7.1-743/cctbx_project/mmtbx/maps/__init__.py", line 512, in __init__ coeffs = map_coefficients_from_fmodel(fmodel = fmodel, params = mcp) File "/linux/src/phenix-1.7.1-743/cctbx_project/mmtbx/maps/__init__.py", line 359, in map_coefficients_from_fmodel fill_mode = "dfmodel") File "/linux/src/phenix-1.7.1-743/cctbx_project/mmtbx/f_model.py", line 1920, in electron_density_map fill_mode = fill_mode) File "/linux/src/phenix-1.7.1-743/cctbx_project/mmtbx/map_tools.py", line 137, in __init__ self.fmodel = self.fmodel.fill_missing_f_obs(fill_mode = fill_mode) File "/linux/src/phenix-1.7.1-743/cctbx_project/mmtbx/f_model.py", line 1681, in fill_missing_f_obs fmodel=self, fill_mode=fill_mode) File "/linux/src/phenix-1.7.1-743/cctbx_project/mmtbx/missing_reflections_handler .py", line 129, in fill_missing_f_obs fmodel = select_by_map_cc(fmodel = fmodel.deep_copy())) File "/linux/src/phenix-1.7.1-743/cctbx_project/mmtbx/missing_reflections_handler .py", line 113, in select_by_map_cc update_f_mask = True) File "/linux/src/phenix-1.7.1-743/cctbx_project/mmtbx/f_model.py", line 723, in update_xray_structure force_update = force_update_f_mask) File "/linux/src/phenix-1.7.1-743/cctbx_project/mmtbx/masks.py", line 268, in shell_f_masks self.compute_f_mask() File "/linux/src/phenix-1.7.1-743/cctbx_project/mmtbx/masks.py", line 321, in compute_f_mask fm_asu = asu_mask_obj.structure_factors(self.miller_array.indices(),i+1) MemoryError -- John J. Tanner Professor of Chemistry and Biochemistry University of Missouri-Columbia 125 Chemistry Building Columbia, MO 65211 Phone: 573-884-1280 Fax: 573-882-2754 Email: tannerjj(a)missouri.edu http://www.chem.missouri.edu/TannerGroup/tanner.html

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Error on Fedora 15
by Yuri 05 Sep '11

05 Sep '11

I tried the installer and the binary both give the same result. I notice every utility that is essentially a graphics utility (i.e. dataViewer3D, REEL, dataviewer2D) crashes. Any ideas? -- Yuri Pompeu

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Sep 15, 2011 deadline- User proposal submission for Collaborative Crystallography at BCSB
by Banumathi Sankaran 05 Sep '11

05 Sep '11

Dear Users, > > The deadline for Nov/Dec 2011 Collaborative > Crystallography proposals will be *Sep 15, 2011. * > > ---------------------------------------------------------------------------------------- > 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/becomealsuser.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 Nov/Dec 2011 allocation period, > proposals must be submitted by *Sep 15, 2011.* > > The deadline for CC proposals for the time period Jan/Feb 2012 will be > Nov 15, 2011. > > Regards, > Banumathi Sankaran >

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Error on Fedora 15
by Yuri 04 Sep '11

04 Sep '11

Hello everyone, I just installed fedora 15 on a machine and tried to get phenix running, Installation seems to have proceeded normally. When I tried opening REEL the program crashes and it gives me the following. error The program 'python' received an X Window System error. This probably reflects a bug in the program. The error was 'BadDrawable (invalid Pixmap or Window parameter)'. (Details: serial 100331 error_code 9 request_code 137 minor_code 8) (Note to programmers: normally, X errors are reported asynchronously; that is, you will receive the error a while after causing it. To debug your program, run it with the --sync command line option to change this behavior. You can then get a meaningful backtrace from your debugger if you break on the gdk_x_error() function.) I know its a problem with my machine because this same version runs great on RHEL5 I also see some funny behavior with COOT...but thats another story Any help is greatly appreciated, I am not sure how to fix this situation. Best, -- Yuri Pompeu

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phenix.refine is renaming experimental phase labels and the purpose of _refine_data.mtz?
by Francis E Reyes 04 Sep '11

04 Sep '11

Hi all When specifying exptl_fobs_phases_freeR_flags_1.mtz (HLAM,HLBM.HLCM,HLDM) as an experimental phase file in phenix.refine via the .def file, these HL coefficients are written to *_refine_data.mtz as HLA,HLB,HLC,HLD. Now forgive me if I'm incorrect but HLA,HLB,HLC,HLD != HLAM,HLBM,HLCM,HLDM ? (where the former should come from phaser_1.mtz and the latter from resolve_1.mtz reflecting the density modification step). Also it's not desirable to create a _refine_data.mtz as it's unclear where the experimental phase labels came from the first place. Suppose I'm doing iterative rounds of MRSAD (with updated models during model building), I may have several AutoSol directories containing MRSAD runs for updated models. How am I going to know where the HL's in *_refine_data.mtz came from? (grepping .def files?) It would be easier if the .def's contained the full paths of the original .mtz files and not a phenix combined data file. I may have my original reflections in one mtz, an R-free set in another, experimental phases in another, etc. F --------------------------------------------- Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

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Problem with R-free assignment
by Jose Arcadio 02 Sep '11

02 Sep '11

Dear phenix.refine community: I am solving a protein structure using experimental phasing. In order to do that I combined two derivative isomorphous datasets into a double SAD experiment (to increase the individual weak anomalous power from each dataset) using SHARP.My resolution is 3.2 A, and the space group is C2221. I managed to build a model using the density-modified phases from SHARP. Then I started refining against one of my derivative datasets because my native dataset is non-isomorphous due to the heavy meal soaking.Then I made two mistakes :( 1. I did not realize at the beginning of my refinement-building rounds that I was refining against the dataset that showed the worst statistics. 2. I was using a dataset with only FP and SIGFP but not DANO and SIGDANO. I used the phases from my SHARP map (also the experimental phase restraints) Now I did a new run of refinement using my best dataset (better statistics) and also including the anomalous data FP, SIGFP, DANO and SIGDANO. Obviously, my R-work and R-free got pretty much better. Nevertheless, the R-free was better than R-work at the beginning of the run, at the end of the refinement R-free and R-work inverted as usually (being R-free worst than R-work) r_work = 0.2582 r_free = 0.2888 . Certainly, there was a mistake with a new assignment of the free set of reflections. Now I am aware that the set of free reflections has to be the same all over the refining procedure. Here are the questions How can I be sure that my R-free is still a safe cross validation of the correctness of my structure? Is it useful to perform a round of simulated annealing in order to erase any wrong information in my model and start the refinement rounds again? Do you have any suggestions? All the best Jose Farias

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model minimzation?
by r n 02 Sep '11

02 Sep '11

Dear all, Is it possible to do force field energy minimization for protein/peptide using Phenix? I am interested in doing energy minimization for different side chain rotamers. Thanks ram

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Zinc-cysteine bond refinement in phenix_refine
by Zhang yu 31 Aug '11

31 Aug '11

Dear all, I have been stuck in the problem for a while. I appreciate any suggestions. I have two zinc binding domain in my 3A structure which are Cys4 type. The geometry is OK for one domain, but it is not refined properly in the other one. The problems during phenix refinement are 1. Zinc is always refined to position ~0.5A off from its correct position 2. The refined bond lengths of four Cys-Zn are all below 2.3 3. Sometimes, distances between SG atoms of nearby cysteines are too close, and coot just connect them as disulfate bond. 4. Sometimes, I get the following message showing that all bond angles are outliers with >8 sigmas, I listed part of the outliers. Top angle outliers (sorted by deviation): atoms ideal model difference deviation (sigma) ---------------------------------------------------------------------------- SG CYS D1204 57.894 104.470 46.576 9.32 ZN ZN D2001 SG CYS D1112 SG CYS D1201 50.842 92.496 41.654 8.33 ZN ZN D2001 SG CYS D1204 SG CYS D1204 126.952 92.496 -34.455 -6.89 ZN ZN D2001 SG CYS D1201 SG CYS D1201 52.183 86.105 33.922 6.78 ZN ZN D2001 SG CYS D1112 SG CYS D1194 152.275 119.729 -32.546 -6.51 ZN ZN D2001 SG CYS D1112 SG CYS D1112 89.273 119.729 30.456 6.09 ZN ZN D2001 SG CYS D1194 I also post my metal.edit file for refinement refinement.geometry_restraints.edits { bond { action = *add atom_selection_1 = name ZN and chain D and resname ZN and resseq 2001 atom_selection_2 = name SG and chain D and resname CYS and resseq 1201 distance_ideal = 2.310000 sigma = 0.100 } } refinement.geometry_restraints.edits { bond { action = *add atom_selection_1 = name ZN and chain D and resname ZN and resseq 2001 atom_selection_2 = name SG and chain D and resname CYS and resseq 1194 distance_ideal = 2.310000 sigma = 0.100 } } refinement.geometry_restraints.edits { bond { action = *add atom_selection_1 = name ZN and chain D and resname ZN and resseq 2001 atom_selection_2 = name SG and chain D and resname CYS and resseq 1112 distance_ideal = 2.310000 sigma = 0.100 } } refinement.geometry_restraints.edits { bond { action = *add atom_selection_1 = name ZN and chain D and resname ZN and resseq 2001 atom_selection_2 = name SG and chain D and resname CYS and resseq 1204 distance_ideal = 2.310000 sigma = 0.100 } } refinement.geometry_restraints.edits { angle { action = *add atom_selection_1 = name SG and chain D and resname CYS and resseq 1194 atom_selection_2 = name ZN and chain D and resname ZN and resseq 2001 atom_selection_3 = name SG and chain D and resname CYS and resseq 1201 angle_ideal = 112.172178 sigma = 5 } } refinement.geometry_restraints.edits { angle { action = *add atom_selection_1 = name SG and chain D and resname CYS and resseq 1112 atom_selection_2 = name ZN and chain D and resname ZN and resseq 2001 atom_selection_3 = name SG and chain D and resname CYS and resseq 1201 angle_ideal = 87.092184 sigma = 5 } } refinement.geometry_restraints.edits { angle { action = *add atom_selection_1 = name SG and chain D and resname CYS and resseq 1112 atom_selection_2 = name ZN and chain D and resname ZN and resseq 2001 atom_selection_3 = name SG and chain D and resname CYS and resseq 1194 angle_ideal = 118.116518 sigma = 5 } } refinement.geometry_restraints.edits { angle { action = *add atom_selection_1 = name SG and chain D and resname CYS and resseq 1204 atom_selection_2 = name ZN and chain D and resname ZN and resseq 2001 atom_selection_3 = name SG and chain D and resname CYS and resseq 1201 angle_ideal = 91.677138 sigma = 5 } } refinement.geometry_restraints.edits { angle { action = *add atom_selection_1 = name SG and chain D and resname CYS and resseq 1204 atom_selection_2 = name ZN and chain D and resname ZN and resseq 2001 atom_selection_3 = name SG and chain D and resname CYS and resseq 1194 angle_ideal = 130.829256 sigma = 5 } } refinement.geometry_restraints.edits { angle { action = *add atom_selection_1 = name SG and chain D and resname CYS and resseq 1204 atom_selection_2 = name ZN and chain D and resname ZN and resseq 2001 atom_selection_3 = name SG and chain D and resname CYS and resseq 1112 angle_ideal = 104.886672 sigma = 5 } } Questions, 1. Why the ideal bond angle are different in the metal.edit file and final model ? How does phenix determine the ideal bond_angle? For example, in the metal.edit file atom_selection_1 = name SG and chain D and resname CYS and resseq 1204 atom_selection_2 = name ZN and chain D and resname ZN and resseq 2001 atom_selection_3 = name SG and chain D and resname CYS and resseq 1112 The angle_ideal = 104.886672 But in the final model atoms ideal model difference deviation (sigma) ---------------------------------------------------------------------------- SG CYS D1204 57.894 104.470 46.576 9.32 ZN ZN D2001 SG CYS D1112 2. Do I need to put the following LINK in the pdb header to run refinement? LINK ZN ZN D2001 SG CYS D1201 1555 1555 2.34 LINK ZN ZN D2001 SG CYS D1112 1555 1555 2.33 LINK ZN ZN D2001 SG CYS D1194 1555 1555 2.38 LINK ZN ZN D2001 SG CYS D1204 1555 1555 2.37 3. After phenix refinement, the output pdb doesn't contain these LINK lines no matter what the inpout pdb is. Does phenix_refine use these restrains of LINK lines? Thanks. Yu Zhang Postdoc fellow Rutgers University

3 2

phenix utility for cif->pdb?
by Francis E Reyes 29 Aug '11

29 Aug '11

I need to check a monomer library definition. Is there a phenix utility that'll make cif -> pdb easily? Thanks! F --------------------------------------------- Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

2 1

Parallelization for optimization of wxu/wxc?
by Schubert, Carsten [JRDUS] 29 Aug '11

29 Aug '11

Hi, I was wondering if the optimization of the xyz and adp target weight could be parallelized and take advantage of multi-cpu systems? On the project I am working on now, the refinement time increased ~5.4 fold when with active optimization of these weights. Are there any plans for that in the works? Cheers, Carsten

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symmetry related bond restraint
by Bryan Lepore 28 Aug '11

28 Aug '11

[ dev-837 ] I am trying to understand a symmetry operation from coot as it bears on phenix bond in the geometry restraints. in essence: in coot, origin-pre-shift is (-1 0 0) and the symmetry-related atom I want is Y,X,-Z + (0 1 1) however, the correct operation in phenix is Y,X,-Z+1 ... I suspect I simply do not understand the transformation. if i could at least confirm this math is correct, i'd appreciate it. -Bryan supplemental: * SG92 * apparently correct because the geometry checks fail otherwise * the scenario is similar to the thread linked below: http://www.phenix-online.org/pipermail/phenixbb/2010-April/015000.html * essentially a crosspost by me on coot the other day : https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=COOT;e45be09a.1108 * coot 0.6.2 rev-3562

3 2

Recovering Autobuild from tty disconnect
by Francis E Reyes 27 Aug '11

27 Aug '11

Our job submission node disconnects 'idle' after 4 hours of inactivity. As most grid / autobuild jobs take about that long I end being disconnected while the grid jobs complete. [1] Screen is not an option since access to the job submission node is via a load balancer and none of the job submission nodes allow access unless you're coming from the load balancer . i.e. there's no way to get to original machine where your screen has been started [2] all processes are sent SIGKILL during this automatic logout preventing the use of nohup.. will background=True work? [3] In the meantime, is it possible to resurrect the current autobuild? I've got FINISHED in all the autobuild's submitted to the grid, but everytime I try to combine_only=True run=my_run_number, I start from the beginning (with submitting the autobuild jobs to the cluster) even when I've moved the best of each build into MULTIPLE_MODELS. Thanks! F --------------------------------------------- Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

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occ are not zerp
by Kenneth A. Satyshur 26 Aug '11

26 Aug '11

I am running omit map on pdb file and I get Failed to carry out AutoBuild_build_cycle: Initial phenix refinement of AutoBuild_run_22_/edited_pdb.pdb with exptl_fobs_phases_freeR_flags.mtz failed...quitting... /usr/keck/u1/PriA/APS_Aug2011/phasing/AutoBuild_run_22_/LAST.LOG may have additional information... All occupancies in input PDB file are zero. yet CRYST1 85.433 85.433 111.682 90.00 90.00 120.00 P 32 SCALE1 0.011705 0.006758 0.000000 0.00000 SCALE2 0.000000 0.013516 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008954 0.00000 ATOM 931 N ALA N 308 4.340 -30.086 -9.129 1.00 39.02 N ATOM 932 CA ALA N 308 4.553 -29.451 -10.458 1.00 38.92 C ATOM 933 CB ALA N 308 3.225 -29.326 -11.198 1.00 38.66 C ATOM 934 C ALA N 308 5.202 -28.079 -10.295 1.00 37.85 C ATOM 935 O ALA N 308 5.278 -27.555 -9.185 1.00 38.80 O ATOM 936 N ALA N 309 5.633 -27.505 -11.414 1.00 36.99 N ATOM 937 CA ALA N 309 6.216 -26.142 -11.498 1.00 37.18 C ATOM 938 CB ALA N 309 5.194 -25.019 -11.222 1.00 36.42 C ATOM 939 C ALA N 309 7.457 -25.985 -10.646 1.00 34.05 C ATOM 940 O ALA N 309 7.404 -26.148 -9.436 1.00 31.65 O ATOM 941 N ALA N 310 8.570 -25.673 -11.311 1.00 34.03 N ATOM 942 CA ALA N 310 9.883 -25.614 -10.696 1.00 34.33 C ATOM 943 CB ALA N 310 10.332 -24.166 -10.573 1.00 31.89 C ATOM 944 C ALA N 310 9.895 -26.350 -9.337 1.00 36.59 C ATOM 945 O ALA N 310 10.250 -25.773 -8.304 1.00 40.46 O ATOM 946 N ALA N 311 9.479 -27.623 -9.364 1.00 36.20 N ATOM 947 CA ALA N 311 9.321 -28.471 -8.174 1.00 33.93 C ATOM 948 CB ALA N 311 8.446 -29.664 -8.503 1.00 34.46 C ATOM 949 C ALA N 311 10.659 -28.948 -7.641 1.00 32.37 C ATOM 950 O ALA N 311 10.943 -30.156 -7.619 1.00 31.59 O ATOM 951 N ALA N 312 11.479 -27.982 -7.229 1.00 30.93 N ATOM 952 CA ALA N 312 12.821 -28.234 -6.694 1.00 30.94 C ATOM 953 CB ALA N 312 12.740 -28.872 -5.308 1.00 30.60 C ATOM 954 C ALA N 312 13.680 -29.080 -7.647 1.00 30.22 C ATOM 955 O ALA N 312 13.405 -29.148 -8.853 1.00 32.14 O ATOM 956 N PRO N 313 14.739 -29.702 -7.116 1.00 28.06 N ATOM 957 CA PRO N 313 15.519 -30.706 -7.852 1.00 27.14 C ATOM 958 CB PRO N 313 16.820 -30.771 -7.044 1.00 27.81 C ATOM 959 CG PRO N 313 16.871 -29.482 -6.264 1.00 28.11 C they don't look zero to me. anyone get this error? -- Kenneth A. Satyshur, M.S.,Ph.D. Associate Scientist University of Wisconsin Madison, Wisconsin 53706 608-215-5207

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Dealing with malformed ligand geometries in phenix.refine
by Francis E Reyes 26 Aug '11

26 Aug '11

Hi all I've got 3.0A data and I'm ending up with distorted ligand geometry in phenix.refine. The model is complete and fitting the ligand is the final step (refined with individual_sites and individual_sites_real_space as suggested by an earlier posting). I've tried with a wxc_scale of 0.001 and it still looks wonky (tetrahedral C's not being so, etc). My cif is coming from phenix's internal db. Any suggestions? F --------------------------------------------- Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

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maybe not a phenix issue, but with mr_rosetta:
by Francis E Reyes 26 Aug '11

26 Aug '11

What exactly is the nature of the fragment files used for MR/rebuilding? I'm an RNA guy and may have to generate them myself for certain projects. F --------------------------------------------- Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

2 1

unstable phenix?
by Kenneth A. Satyshur 25 Aug '11

25 Aug '11

We are running phenix (743) on a RHEL5 dual quad, multithread, making a composite omit map pf a very large structure (750 AA) and the system keeps getting locked up. Have anyone else seen this type of problem? Does multiprocessing work well on RHEL or just FC versions? We needed to install the FC8 version (/phenix-1.7.1-743/build/intel-linux-2.6-x86_64) to get it to work. So maybe we are using the wrong version? Shoiuld I recompile it for our system? Why is the gui always open when we are running long jobs (many days)? We need to put this stuff in the background and log out so someone else can run. Should scripts be used instead of the gui? Great program but too unstable. kas -- Kenneth A. Satyshur, M.S.,Ph.D. Associate Scientist University of Wisconsin Madison, Wisconsin 53706 608-215-5207

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Weird Hydorgen refinement
by Yuri 23 Aug '11

23 Aug '11

Hi guys, I DEFINETELY ran refinement after I removed the hydrogens. My Rfree went up from 0.159 to about 0.167. Thanks for the tips. Ill give pdb.tools a try... -- Yuri Pompeu

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Reference model restraints in autobuild?
by Francis E Reyes 23 Aug '11

23 Aug '11

Hi all While it is possible to generate refinement parameters to pass into autobuild, how does one pass the reference structure into the autobuild jobs if one were to refine using geometry restraints from the reference structure? (command line autobuild) If I can't supply the reference pdb, is there a phenix cmd utility that'll spit out all the restraints given a pdb so I can supply them in the refinement parameters file? F --------------------------------------------- Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

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Re: [phenixbb] Weird Hydorgen refinement
by Yuri 23 Aug '11

23 Aug '11

Hi Pavel, The pdb did have anisou records for H's. I believe that is because in some previous runs I had only selected chain 'A' - I left out "and not elemnt H" - which I believe caused the H's to get refined anisotropically. I am trying to get rid of the ANISOU records and Ill run refinement again. ps. I am getting ready to deposit the coordinates and I dont want to keep hydrogens in the model, how can I get rid of them? I ve been using pyMol to remove them, but pymol gets rid of all the info -including symmetry -that phenix adds... Thanks -- Yuri Pompeu

3 2

Weird Hydorgen refinement
by Yuri 23 Aug '11

23 Aug '11

Hello everyone. I was trying to refine my model anisotropically. I selected element NA or (chain A and not element H). I looked at the output pdb shows that hydrogens were being refined anisou as well as the protein. I believe its because technically they are also in chain A, but shouldnt the default be never refine H's anisotropically, especially at 1.5A ?. -- Yuri Pompeu

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autosol error in GUI
by r n 23 Aug '11

23 Aug '11

Hi all I downloaded the Phenix developing version 842, autosol gui running gave me the following error, "The key gui_output_dir is not in var_type_dict....command line wizzard needs conversion in the autosol.py script uing translating inputs or else in excluded inputs....wizard setVars routine needs this variable set". I have not had this error earlier version. any help? Thanks ram

2 1

pdb conversion to 3.2 format
by Luca Pellegrini 22 Aug '11

22 Aug '11

Hi, I am trying to use iotbx.pdb_remediator to convert PDB atom names to 3.2 format (as suggested by Nat Echols in a recent post to Coot mail-list). Unfortunately I get the following error message: lp212-mp2281 58% iotbx.pdb_remediator file_name=refine.pdb output_file=refine_3.2.pdb_file Traceback (most recent call last): File "/usr/local/cctbx/cctbx_sources/iotbx/command_line/pdb_remediator.py", line 54, in <module> run(sys.argv[1:]) File "/usr/local/cctbx/cctbx_sources/iotbx/command_line/pdb_remediator.py", line 51, in run remediator.remediator(params) File "/usr/local/cctbx/cctbx_sources/iotbx/pdb/remediation/remediator.py", line 257, in remediator user_dict) File "/usr/local/cctbx/cctbx_sources/iotbx/pdb/remediation/remediator.py", line 95, in build_hash test=os.path.isfile), "rb") TypeError: coercing to Unicode: need string or buffer, NoneType found It looks like a python problem, but I am afraid my insight ends here. Can anyone tell me how to fix this, please? I am not sure if it matters, but iotbx_pdb_remediator was not in my phenix installation (PHENIX-1.7.1-743 on MacOSX 10.6.8), so I installed cctbx separately. Thanks! Luca Luca Pellegrini Department of Biochemistry University of Cambridge 80 Tennis Court Road Cambridge CB2 1GA - UK Email: lp212(a)cam.ac.uk Tel: 0044-1223-760469 Fax: 0044-1223-766002 Sanger building, room 3.59

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MR problem
by intekhab alam 22 Aug '11

22 Aug '11

Hi there I have a data of heterotrimer protein complex at 2.9A resolution. One protein consists of two domains. I tried phaser as well as molrep which gives a solution with only one domain. Rotation function and translation function were found to be fine for these solutions. I tried to find missing domain of the protein after fixing one of the domain or the other partner proteins using whole part or various truncations of missing domain. I also tried to find and build missing domain using Rosetta with the solutions of Molrep or Phaser as template. But, there were no solutions, or the solutions are clashed with other domain or proteins. Furthermore, R and Rfree is 30 and 40, respectively, and I could not reduce them further. There was almost no electron density map in the empty space so that I could not model manually. Plz guide me ,how can i look for the missing domain in the protein. regards -- INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL

2 1

matplotlib
by Ed Pozharski 21 Aug '11

21 Aug '11

This is really a rather esoteric issue, but I feel I need to mention this to save someone, depending on the situation, anywhere between five minutes of googling or two hours of hair-pulling. In a nutshell, phenix gui may in some circumstances screw up other programs that use matplotlib. I can't track down which specific phenix gui action causes it, but it's safe to assume that whenever matplotlib libs are used the subsequent calls to logarithmic scale plots (and likely other things) throw this error TypeError: coercing to Unicode: need string or buffer, dict found The solution is to erase the ~/.matplotlib/fontList.cache. The likely cause is that phinix gui calls on bundled matplotlib which is different from one I have installed (not to mention that I am using Lucid (because it's LTS) which has python 2.6 and not the 2.7 that is bundled with phenix). However, it still writes into the same ~/.matplotlib folder, thus I end up with incompatible data. Certainly, the problem will be gone when matplotlib gets bumped up to 1.0.1 in next Ubuntu release. This is yet another example of why the standalone installation approach is ideologically objectionable on modern Linux. But of course, the practical advantage gained by not having to package the software for any possible OS flavor/version users may choose outweighs the lower risks of package incompatibility and the reduced size of the packaged product. -- Oh, suddenly throwing a giraffe into a volcano to make water is crazy? Julian, King of Lemurs

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formyl-methionine
by Yuri 19 Aug '11

19 Aug '11

Hello Everyone, Stupid question. I see density at my N-terminus that really looks like formyl-Met. I want to model it and refine. I notice REEl has FME ligand for the formyl-methionine, but I dont want to treat it as a "ligand" since it is covalently attached to SER 2. What is the best way to modify the MET residue? Cheers -- Yuri Pompeu

3 3

Definition of "Saenger Class"
by jens j birktoft 19 Aug '11

19 Aug '11

Hi All, Could somebody direct me to "saenger class" definitions used in base-pair restraints for DNA/RNA. Cheers Jens *+++++++++++++++++++++++++++++++++++++++++++++++++++++++* * * *Jens J. Birktoft e-mail: birktoft(a)nyu.edu <jens.knold(a)gmail.com> New York University, Dept. Chemistry Phone: 212-749-5057 *

2 1

phenix.phaser multiple pdbs
by G Y 17 Aug '11

17 Aug '11

Dear all, I am writing a bash script for running phenix.phaser automatically on an ensemble of multiple pdbs. These pdbs have been superimposed by other tools before running phaser. The following is what I wrote for the ensemble part in params.eff file: ensemble { model_id = a1 coordinates { pdb = model1.pdb pdb = model2.pdb pdb = model3.pdb pdb = model4.pdb rmsd = None identity = 0.9 } It runs well. When it finished, I want to confirm that it really run MR on all four models or on a ensemble of these models. However in .log file, I found at the refinement part it shown me: ---------- REFINEMENT ---------- There is 1 solution to refine Refining solutions 0% 100% |==| DONE Configuring ensembles --------------------- PDB file # 1: model1.pdb This pdb file contains 1 models The (input) RmsD of this model with respect to the real structure is 0.8 **************************** Does this mean that phenix.phaser only run MR with the first model? Does it due to the way I wrote in my params.eff file? What would be the correct way? Many thanks! best, G

3 5

changing project directory
by Jens Kaiser 16 Aug '11

16 Aug '11

Hi all, I have project data on external hard drives. As I use several different file systems, and mount the drives in random order, I cannot rely on the device being mounted in the same mount point. In order to keep paths consistent, I link the project directories into my home. This used to work fine. I recently created a project, and phenix seemed to have used the real path instead of the link-path (That's not the problem, yet). I tried to manually edit ~/.phenix/project_db.phil, but it still tries to write in a non-existing directory. A naive 'grep -R "disk-1" ~/.phenix' did not reveal any obvious file either. Where can I change the directory associated with a project {per,con}sistently? Thanks for your time, Jens

2 1

nucleic acid secondary restraints breaking in 1.7.1-743
by Francis E Reyes 16 Aug '11

16 Aug '11

Hi all Traceback (most recent call last): File "/usr/local/phenix-1.7.1-743/phenix/phenix/command_line/refine.py", line 11, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/phenix-1.7.1-743/phenix/phenix/refinement/command_line.py", line 67, in run overwrite = command_line_interpreter.command_line.options.overwrite) File "/usr/local/phenix-1.7.1-743/phenix/phenix/refinement/driver.py", line 112, in __init__ hbond_params=self.params.hydrogen_bonding) File "/usr/local/phenix-1.7.1-743/cctbx_project/mmtbx/secondary_structure/__init__.py", line 494, in create_hbond_proxies log=log) File "/usr/local/phenix-1.7.1-743/cctbx_project/mmtbx/secondary_structure/__init__.py", line 286, in hydrogen_bond_proxies_from_selections log=log) File "/usr/local/phenix-1.7.1-743/cctbx_project/mmtbx/secondary_structure/base_pairing.py", line 415, in create_hbond_proxies if distance_values[i][2] != '_': IndexError: tuple index out of range When specifying a single base pair when using secondary_structure nucleic acids restraints Any ideas? Thanks! F --------------------------------------------- Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

2 6

modelling of disordered protein
by intekhab alam 16 Aug '11

16 Aug '11

Hi I solved an RNA polymerase structure in its native as well as in complex with chemical ligands (2.5A and C2 space group). The structure has been solved by MR a protein having 60% identity. The ASU has a monomer and dimer. Recently i complexed this RNA polymerase (protein A) with a highly flexible protein B and got the crystal. These crytsal also have C2 space group (resolution 2.3A) having similar cell parameters but has psudotranslation (17.34%). I tried MR using rosetta. HHpred server selected one of my deposited structure in PDB (3NAI 100% identity) as template. Rosetta MR gave 2 solutions one of which is dimer-monomer arrangement while the other one is a trimer. The values of these solution are below. Solution 1: trimer REMARK Log-Likelihood Gain: 10662.548 REMARK RFZ=16.5 TFZ=14.4 PAK=0 LLG=959 TFZ==23.2 RFZ=0.0 TFZ=48.9 PAK=0 LLG=3195 TFZ==55.6 (& TFZ==52.6) LLG+=(3191 & 7008) LLG=7024 TFZ==72.0 LLG=10663 TFZ==90.1 Solution 2: Monomer and dimer in ASU REMARK Log-Likelihood Gain: 2120.965 REMARK RFZ=39.7 TFZ=21.9 PAK=0 LLG=811 TFZ==37.7 LLG=2121 TFZ==43.6 REMARK ENSEMBLE ensemble_1 EULER 204.07 178.91 204.37 FRAC 0.499 Map and model fits well in both the cases with R and R free 26 and 30% respectively. My queries: 1. which one will be the correct solution? Is it possible that the protein B has resulted in the trimeric arrangement? 2. i cannot find any continuous 2Fo-Fc map for proteinB, but there are some continuous density at 0.7 which is very ambiguous. how can i improve the map so that i can model some fragments of my proteinB (protein B is of 73 amino acids and is predicted to be highly flexible and disordered. ((biochemical as well as bioinformatical analysis done )) I already have tried autobuild but it fails to build even a partial fragment of the proteinB. Kindly suggest how to proceed , or how can i prove the presence of protein B in the structure. Regards INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL

2 1

LigandFit error
by Priit Eek 14 Aug '11

14 Aug '11

Hi, I'm getting this error when trying to run LigandFit from the GUI: The key gui_output_dir is not in var_type_dict…this means the command-line Wizard needs a conversion in the ligandfit.py script under 'Translating inputs' or else in excluded_inputs or else the Wizard SetVars routine needs this variable set Is this a bug? I am using the 64-bit dev-842 version on OS X 10.7 Lion. Best regards, Priit

2 1

Unexpected Occupancy refiniement for ligands...
by Yuri 13 Aug '11

13 Aug '11

Hey, So I am finishing up a model at 1.5 A and I tried to refine my ligands (3) and waters (468) in addition to altloc residues. The residues refine as expected e.g OccA + OccB = 1.0 and all atoms in A have OccA and all the atoms in B have OccB. My ligands on the other are being refined as the following: HETATM 6867 C1 MLA L 3 32.357 -28.612 7.978 0.93 23.77 C C HETATM 6868 O1A MLA L 3 31.209 -28.949 7.502 0.85 24.79 C O HETATM 6869 O1B MLA L 3 32.454 -28.160 9.141 0.70 22.70 C O HETATM 6870 C2 MLA L 3 33.553 -28.727 7.095 1.00 25.46 C C HETATM 6871 C3 MLA L 3 34.774 -28.070 7.627 0.92 28.45 C C HETATM 6872 O3A MLA L 3 34.830 -27.664 8.808 1.00 30.15 C O HETATM 6873 O3B MLA L 3 35.775 -27.948 6.840 1.00 30.23 C O HETATM 6874 HC21 MLA L 3 33.321 -28.281 6.139 1.00 30.56 C H HETATM 6875 HC22 MLA L 3 33.760 -29.776 6.943 1.00 30.56 C H Each atom is getting an individual occupancy assigned, which physically is impossible :) Any light? Could it be my selection syntax? Corrigendum: I think I sent a bug email last night about an error when writing mtz files in refinement. It was an accident. My naming convention was bad, thats why it crashed. Sorry -- Yuri Pompeu

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