- phenixbb - phenix-online.org

following on the anomalous map
by CPMAS Chen 26 Aug '14

26 Aug '14

Hi, All Phenix users, I am following this topic. http://www.phenix-online.org/pipermail/phenixbb/2014-April/020622.html. Here is the point I am not clear. If I am using phenix.refine to generate LLG map, how do I pick the anomalous group since I have not placed them in the model yet? By the way, when I choose ion_placement and specify Br, the result comes with no Br. Let me make my situation clear first. I want to find whether the Br-containing ligand is seen in my protein which I have a high resolution structure available. I have data collected at Br wavelength, peak or higher position. Phenix.xtriage reported that the anomalous signal is present to about 4A. However, both AutoSol or MR-SAD cannot identify the Br position. Simply say, AutoSol or MR-SAD can not generate any solution. Well, of course, the simple answer would be that there is no such ligand cocrystallized. Anyway, I am trying to see if the anomalous difference map or LLG(generated by phenix.maps, this would be the initial one I assume) can tell me anything more useful. So, my question on this topic would be what is a better way you guys would recommend to identify these Br-ligands? By the way, I did have the native datasets for the same protein with ligand. Thanks! Charles -- *************************************************** Charles Chen Research Associate University of Pittsburgh School of Medicine Department of Anesthesiology ******************************************************

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Header accuracy after only refining ligands
by Katherine Sippel 26 Aug '14

26 Aug '14

Hi all, I was trying to prep a structure for PDB deposition. All the protein atoms were good, but I needed to correct some ADP and ligand issues. I ran coordinate refinement only on the ligands and subsequent ADP refinement. Everything was good, except the RSMD values output are clearly only for the ligands. Now I am wondering which values in the header I can trust as far as deposition goes. I tried to do a workaround where I ran refine with 0 macrocycles to see if I could get the proper values, but obviously the bulk solvent is different and I get higher R values. I am wondering if I can run validation to get the correct RMSD values or if there are other header values that might have been affected by not refining all the coordinates? Cheers, Katherine -- "Nil illegitimo carborundum"* - *Didactylos

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DEN refinement
by marinabb phenix 26 Aug '14

26 Aug '14

Dear all, I am trying to use DEN refinement as implemented in the Phenix-1.9 release to refine a structure at 3.6 Angstrom resolution. The asu consists of 8 copies of hetero-dimers (of roughly 40 KDa sunbunits each). The structure of one of the subunits has already been solved at about 2 Angstrom, whereas for the other no homologous model is available. After automatic + manual building, I have now a model with Rfree = 28 / R = 23, with some protomers better built than others. I have used this pdb model as input for DEN refinement, adding the known higher-resolution structure as a (partial) reference model, and ncs restraints previously found (and run a DEN parameters optimisation). The final DEN Rfee got significantly worse. I would appreciate any advise for a better DEN strategy to be adopted in this case, if possible. In particular I was wondering whether it can be worth building a model for the missing subunit (or part of it) based on structural similarity of the current unrefined 3D structure. I thank you in advance for the suggestions. With kind regards, Marina ----- Marina Mapelli, PhD Department of Experimental Oncology European Institute of Oncology Via Adamello 16, 20139 Milan, Italy tel: +39-02-94375018 email: marina.mapelli(a)ieo.eu web: http://www.ifom-ieo-campus.it/research/mapelli.php -----

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overlapping electron density maps
by 李翔 25 Aug '14

25 Aug '14

Hi everyone, I am working on a series of crystals with overall same framework structure plus a different extra part which attaches to the framework. I want to compare the electron density maps of the crystals by overlapping the frameworks and see how the extra parts differ from each other. Is there a way I can do it? Thank you very much for your help! Sincerely, Xiang -- Li Xiang Department of chemistry, Purdue University Email：lixiang1642(a)gmail.com

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table_one
by Andreas Förster 24 Aug '14

24 Aug '14

Dear all, I encounter the following error when running phenix.table_one from the command line (RHEL 6.3 64-bit, phenix-dev-1769): andreas@csbstereo in blah: phenix.table_one Traceback (most recent call last): File "/csb/soft/Linux64/share/phenix-dev-1769/build/intel-linux-2.6-x86_64/../../phenix/phenix/command_line/table_one.py", line 6, in <module> phenix.automation.table_one.run(sys.argv[1:], auto_extract_labels=True, AttributeError: 'module' object has no attribute 'run' Aunt Google insists that this is "a circular import issue". What do the developers say? Thanks. Andreas -- Andreas Förster Crystallization and X-ray Facility Manager Centre for Structural Biology Imperial College London

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Low resolution refinement
by Appu kumar 24 Aug '14

24 Aug '14

Hello All, I have a data from a crystal which we can process to 4.5A, and we are able to get a good molecular replacement model and it is a tetramer in ASU. I tried refining structure with phenix.refine but Rfree stuck at 0.41. I read a paper published by David Baker and phenix developer in 2013 about the low resolution refinement using a combination of rosseta and phenix. I would appreciate if i get a help on the refinement in rosseta along with phenix. This paper convince me that its worth trying the rosseta and phenix together for low resolution structure refinement. Thank you Appu

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Re: [phenixbb] Phenix Webserver Down?
by Chen Zhao 22 Aug '14

22 Aug '14

Thank you all for the info. It is been like this for me for a week, and it might just be some local issues. On Fri, Aug 22, 2014 at 4:20 PM, Paul Adams <pdadams(a)lbl.gov> wrote: > > Appears to be okay from the Bay Area. > > On Aug 22, 2014, at 1:00 PM, Chen Zhao <c.zhao(a)YALE.EDU> wrote: > > > Dear all, > > > > I am sorry to bother you, but I have problems connecting to > www.phenix-online.org. Does anybody have similar problem? > > > > Thank you, > > Chen > > _______________________________________________ > > phenixbb mailing list > > phenixbb(a)phenix-online.org > > http://phenix-online.org/mailman/listinfo/phenixbb > > -- > Paul Adams > Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley > Lab > Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley > Lab > Adjunct Professor, Department of Bioengineering, U.C. Berkeley > Vice President for Technology, the Joint BioEnergy Institute > Laboratory Research Manager, ENIGMA Science Focus Area > > Building 64, Room 248 > Building 80, Room 247 > Building 978, Room 4126 > Tel: 1-510-486-4225, Fax: 1-510-486-5909 > http://cci.lbl.gov/paul > > Lawrence Berkeley Laboratory > 1 Cyclotron Road > BLDG 64R0121 > Berkeley, CA 94720, USA. > > Executive Assistant: Louise Benvenue [ LBenvenue(a)lbl.gov ][ 1-510-495-2506 > ] > -- > > > > > > > > > > > > >

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Phenix Webserver Down?
by Chen Zhao 22 Aug '14

22 Aug '14

Dear all, I am sorry to bother you, but I have problems connecting to www.phenix-online.org. Does anybody have similar problem? Thank you, Chen

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mr_rosetta
by Felipe Trajtenberg 20 Aug '14

20 Aug '14

Dear all I am trying to perform MR of a multidomain protein using phenix.mr_rosetta and building each domain sequentially. The first search works perfect and I have a potential solution. In the second search I am having some troubles in setting up the process. When I fixed the best first model and look for a second domain I found that rosetta only rebuilds the chain A, which was the one that already was fixed and chain B disappears. how can I fix one domain and build the second without loosing any information thanks in advance Felipe

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Stereo Microscope
by jens j birktoft 20 Aug '14

20 Aug '14

Hi: I would be grateful for suggestion regarding stereo microscopes suitable for protein/dna crystal viewing and manipulation. We would need a system that fulfull all of the criteria: 1) Two polarizers one for below the sample holder and one above 2) A fully rotatable stage 3) A camera option, either one that comes included with the unit (the best) or one with a universal camera mount Thanks Jens +++++++++++++++++++++++++++++++++++++++++++++++++++ Jens J. Birktoft Director of Crystallography Structural DNA Nanotechnology New York University e-mail: jens.knold(a)gmail.com; Phone: 212-749-5057 very slow-mail: 350 Central Park West, Suite 9F, New York, NY 10025 +++++++++++++++++++++++++++++++++++++++++++++++++++

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Composite Omit Map with Parallel Processing
by Whitley, Matthew J 19 Aug '14

19 Aug '14

Hello all, I am trying to calculate a simulated annealing composite omit map via parallel processing in Phenix 1.9-1692. Our computer cluster uses a PBS que, and jobs are submitted using the 'qsub' command. In the 'Processes' tab under Phenix Preferences, the queueing system is set to PBS, and the queue submit command is set to qsub + additional flags (walltime, etc). All the usual boxes are checked to indicate to Phenix that jobs should be run in parallel when possible. However, when I actually run the composite omit map calculation, the specified qsub flags do not get carried over into the calculation parameters. If I click on Settings-->View all settings in the Composite Omit map calculation window, the qsub_command parameter under 'parallel' is set to None. Because my desired walltime is not being carried over with the qsub command when the calculation starts, the calculation for each individual box is aborting prematurely when it reaches the default process time limit set by our cluster administrator. In the composite omit map calculation in previous versions of Phenix, when clicking "Run" you used to be able to then click "edit parameters and run" in order to check all settings one last time before starting the job. This option does not seem to be available in Phenix 1.9-1692, and thus I can't verify and/or edit the qsub command directly before firing off the job. Any ideas on how to overcome this? Am I missing something? Thanks, Matthew

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Error: "cannot allocate memory"
by sujata halder 19 Aug '14

19 Aug '14

Hi, I am trying to refine a protein with 60 chains (a T=1 virus; 5-3-2 symmetry) and each chain has 520 amino acids. I am using version 1.9 (Release tag: 1692). The job stopped midway and gave the error below followed by "Cannot allocate memory". I have run a similar job (i.e using a similar sized protein) before on an older version (version 1.7) and that worked. Looking at the error I can't really figure out if the problem is related to installation or a missing module or something different about the code. I can share my input and output files off-list. Here is the error: ====================== XYZ individual (reciprocal space) ====================== R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT TARGETS work free delta bonds angl data restr 28.80 29.29 0.49 0.016 1.6 11.9 0.8 7.4 60 none 0.093 160.8996 Traceback (most recent call last): File "/usr/local/phenix-1.9-1692/build/intel-linux-2.6-x86_64/../../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-1.9-1692/phenix/phenix/refinement/command_line.py", line 163, in run call_back_handler=call_back_handler) File "/usr/local/phenix-1.9-1692/phenix/phenix/refinement/driver.py", line 1577, in run reference_model_manager = self.reference_model_manager).result File "/usr/local/phenix-1.9-1692/phenix/phenix/refinement/strategies.py", line 183, in __init__ ion_placement_manager = ion_placement_manager) File "/usr/local/phenix-1.9-1692/phenix/phenix/refinement/macro_cycle.py", line 114, in __init__ self.call(self.xyzrec, "XYZ individual (reciprocal space)") File "/usr/local/phenix-1.9-1692/phenix/phenix/refinement/macro_cycle.py", line 142, in call func(prefix = prefix) File "/usr/local/phenix-1.9-1692/phenix/phenix/refinement/macro_cycle.py", line 374, in xyzrec prefix = prefix) File "/usr/local/phenix-1.9-1692/phenix/phenix/refinement/xyz_reciprocal_space.py", line 204, in __init__ call_back=(len(trial_weights)==1)) File "/usr/local/phenix-1.9-1692/phenix/phenix/refinement/xyz_reciprocal_space.py", line 314, in try_weight result = self.show(weight=wt, print_stats=print_stats, call_back=call_back) File "/usr/local/phenix-1.9-1692/phenix/phenix/refinement/xyz_reciprocal_space.py", line 365, in show molprobity_scores = self.main.use_molprobity) File "/usr/local/phenix-1.9-1692/cctbx_project/mmtbx/model.py", line 1341, in geometry_statistics molprobity_scores = molprobity_scores) File "/usr/local/phenix-1.9-1692/cctbx_project/mmtbx/model_statistics.py", line 99, in __init__ self.clashscore = clashscore(pdb_hierarchy=pdb_hierarchy).get_clashscore() File "/usr/local/phenix-1.9-1692/cctbx_project/mmtbx/validation/clashscore.py", line 133, in __init__ verbose=verbose) File "/usr/local/phenix-1.9-1692/cctbx_project/mmtbx/validation/clashscore.py", line 257, in __init__ self.run_probe_clashscore(self.h_pdb_string) File "/usr/local/phenix-1.9-1692/cctbx_project/mmtbx/validation/clashscore.py", line 341, in run_probe_clashscore stdin_lines=pdb_string).raise_if_errors().stdout_lines File "/usr/local/phenix-1.9-1692/cctbx_project/libtbx/easy_run.py", line 158, in __init__ close_fds=not subprocess.mswindows) File "/usr/local/phenix-1.9-1692/build/intel-linux-2.6-x86_64/base/lib/python2.7/subprocess.py", line 709, in __init__ errread, errwrite) File "/usr/local/phenix-1.9-1692/build/intel-linux-2.6-x86_64/base/lib/python2.7/subprocess.py", line 1222, in _execute_child self.pid = os.fork() OSError: [Errno 12] Cannot allocate memory ------------------------------------------------------------------------------------------------------------- Thanks, Sujata

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Phenix.refine with Ir
by Chen Zhao 16 Aug '14

16 Aug '14

Dear all, I am sorry for bothering you with this dumb question, but it occurs to me that phenix cannot refine a model with Ir, giving the error message of atoms with unknown nonbonded energy type symbols. Since this is my first time really working on the refinement, I have no clue of how to fix it. Would anybody give me a hint? Thanks a lot in advance! Sincerely, Chen

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maps for PDB without SF's
by PC 15 Aug '14

15 Aug '14

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van der Wall's radii
by Rituparna Sengupta 15 Aug '14

15 Aug '14

Hi! I'm new to the list. This might be a naive question to ask, but I'm looking for information about the set of van der Waal's radii popular with most protein crystallographers. Is there a certain list that phenix uses for building from the x-ray structures. If so, where can I find it. I shall be grateful for any thoughts or inputs on this. Thanks, Ritu Rituparna Sengupta Graduate Student Biophysics Graduate Program Record Lab Department of Biochemistry Biochemical Sciences Building University of Wisconsin-Madison

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Computational Crystallography Newsletter - Volume 5, Number 2
by Nigel Moriarty 13 Aug '14

13 Aug '14

I am pleased to announce the publication of the latest issue of the Computational Crystallography Newsletter: http://www.phenix-online.org/newsletter/ A listing of the articles and short communications is given below. Please note that the newsletter accepts articles of a general nature of interest to all crystallographers. Please send any articles to me at NWMoriarty(a)lbl.gov noting that there is a Word Template on the website to streamline production. Articles Details of the Conformation-Dependent Library <http://phenix-online.org/newsletter/CCN_2014_07.pdf#page=12> Short Communications Connectivity analysis tools in CCTBX <http://phenix-online.org/newsletter/CCN_2014_07.pdf#page=4> phenix.fab_elbow_angle: Fragment Antigen-Binding elbow angle calculation tool <http://phenix-online.org/newsletter/CCN_2014_07.pdf#page=8> Fitting tips #8 – Acetyl Groups are like Peptides: Planar and trans <http://phenix-online.org/newsletter/CCN_2014_07.pdf#page=2> Cheers Nigel -- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov

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PSDI 2014, Registration and Abstract Info
by Anna Gardberg 13 Aug '14

13 Aug '14

*[image: Inline image 1]PROTEIN STRUCTURE DETERMINATION IN INDUSTRY 2014* The 22nd PSDI will take place at the Hotel Miragem in Cascais, Portugal, a coastal town located 30 kilometers west of Lisbon, Portugal. The meeting will start with registration and an opening reception on Sunday, 2nd November. This will be followed by two and a half days of scientific program starting Monday morning and finishing at noon on Wednesday, 5th November. A half day excursion to Lisbon is scheduled as a part of the meeting. The scientific program will include the following sessions: · Drug Discovery Stories · Challenging Targets · Biophysics Supporting Structural Biology · Binding Kinetics in Drug Discovery · Structural Biology of Biopharmaceuticals Registration for participants and exhibitors is open at the website: www.psdi2014.org *Please note the deadline for registration and payment: 31 Aug 2014* If you are interested in speaking in any of the scientific sessions, please contact the organizers at psdi2014(a)merckgroup.com with an abstract. Abstracts for “Binding Kinetics in Drug Discovery” are particularly encouraged. Additional information concerning the conference and further updates can be found at the PSDI2014 website <http://www.psdi2014.org/>. Vendor/Sponsor opportunities are available. If you have any questions, please contact the organizers at psdi2014(a)merckgroup.com. Please feel free to forward this announcement to anyone who may be interested in participating. We look forward to a great conference this fall. With kind regards, The PSDI 2014 organizing committee: · Tiago Bandeiras, IBET, Portugal · Anna Gardberg, EMD Serono, USA · Theresa Johnson, EMD Serono, USA · Beate Matlok, Merck KGaA, Germany · Djordje Musil, Merck KGaA, Germany psdi2014(a)merckgroup.com http://www.psdi2014.org

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random half data sets
by Michael Thompson 12 Aug '14

12 Aug '14

Hello All, I'm interested in doing some comparisons of random half data sets, inspired by statistics like CC1/2, CC*, etc. Does phenix contain some tool to split unmerged data into 2 random sets? Thought I would ask before trying to write my own script. Thanks, Mike -- Michael C. Thompson Postdoctoral Scholar Institute of Genomics and Proteomics University of California, Los Angeles miket(a)chem.ucla.edu

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Alternate sequence
by Mullins, Elwood A. 12 Aug '14

12 Aug '14

Hello all, I'm having trouble refining a protein-DNA complex in which one of the DNA strands has a mixture of two different nucleotides at one position. Both are non-standard and require CIF files. I tried assigning each nucleotide the same chain identifier and the same residue number but unique alternate location identifiers. This didn't work. Phenix refined the model but only linked one of the nucleotides with the rest of the chain, pushing the 3' OH and 5' phosphate out of the density for the other nucleotide. Coot won't even open the model output by Phenix. I assume there's some way to do this. Thanks in advance, Elwood Elwood A. Mullins, Ph.D. <> elwood.mullins(a)vanderbilt.edu<mailto:[email protected]> <> tel 615.936.5234 <> fax 615.343.6707

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Calculate F (model)
by PC 12 Aug '14

12 Aug '14

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Re: [phenixbb] pdb_redo
by Nathaniel Echols 12 Aug '14

12 Aug '14

> > From: "Lenin Domínguez" <acheron24(a)gmail.com> > Subject: Re: [phenixbb] pdb_redo > I was wondering about PDB_REDO too. Your command line is priceless, Nat. > > I have one further question: Using phenix.fetch_pdb --maps shouldn't I be > able tro reproduce a figure from a paper showing the electron density of a > ligand? > Well, yes, usually. But: http://www.ncbi.nlm.nih.gov/pubmed/23385452 The one caveat is that there are a few legitimate manipulations that could make the figure look slightly different from how it appears in e.g. Coot: 1. Use of a finer FFT grid (d_min/5 or smaller, versus d_min/4 or d_min/3 which are the defaults for Phenix and Coot respectively) 2. Maximum entropy treatment (removes Fourier artifacts, extends coefficients to high resolution without actually adding information) 3. Map sharpening (2) and (3) should really be explicitly mentioned, however. And I have yet to see a case where these would make the difference between a ligand being detectable or not by eye. (Maximum entropy can sometimes improve the performance of LigandFit but the density is still pretty obvious to a human.) The maps from PDB_REDO shouldn't be hugely different from the maps that come out of phenix.maps, so looking at those results would be another control. I have tried using phenix.fetch_pdb, PDB_REDO (conservative and aggresive > refinement) as well as the data straight from EDS. > > Any thoughts? > Send me the PDB ID (and ligand name) off-list and I'll take a look. -Nat

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Re: [phenixbb] pdb_redo
by Ed Pozharski 11 Aug '14

11 Aug '14

I believe the intent is to provide electron density maps at the end of pdb_redo re-refinement process. Recent versions of coot allow direct download of pdb_redo maps and there are also pymol plugins. You could ask Robbie Joosten directly whether your specific intended use of pdb_redo output is kosher. Sent on a Sprint Samsung Galaxy S® III <div>-------- Original message --------</div><div>From: Nathaniel Echols <nechols(a)lbl.gov> </div><div>Date:08/11/2014 11:06 AM (GMT-05:00) </div><div>To: PC <patrick.cossins(a)inbox.com> </div><div>Cc: PHENIX user mailing list <phenixbb(a)phenix-online.org> </div><div>Subject: Re: [phenixbb] pdb_redo </div><div> </div>On Mon, Aug 11, 2014 at 10:50 AM, PC <patrick.cossins(a)inbox.com> wrote: I was wondering what the community thought of the use of PDB_REDO for MTZ files? I see that they have easy to download MTZ files but has anyone actively used them? Unless we're looking at something different, these are output from Refmac, and do not include all of the data contained in the original deposition. I am not sure if the data will have undergone other changes as well. For instance, the deposited structure factors for PDB ID 2whz include both the fully processed anomalous differences (DANO) and the anomalous intensities (I+/I- and sigmas). The MTZ file I found on PDB_REDO has neither, just FP with Friedel mates merged. This throws out important information. Personally, I just do this: phenix.fetch_pdb --mtz 2whz or this: phenix.fetch_pdb --maps 2whz (Perhaps someday we'll have a server for this.) I should mention however that this will fail on a significant fraction of PDB entries that do not adhere to the CIF standard, at least as implemented in CCTBX. -Nat

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pdb_redo
by PC 11 Aug '14

11 Aug '14

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Two ions at same position
by Eric Girard 08 Aug '14

08 Aug '14

Dear phenixbb members, I am refining a structure that contains Ca2+ atoms. The structure was determined in presence of lanthanide ions. Thus, the resulting density clearly indicates that a part of each Ca2+ sites is substituted with Eu3+ (let's say 75% Ca2+ and 25% Eu3+ per sites). How can I deal with such situation? Indeed phenix.refine complains when I try to put a Ca2+ ion and a Eu3+ one with the same coordinates (and with the occupancies mentionned above) and stop. Thanks for your help. Eric. -- **************************************************************** Eric Girard Extremophiles and Large Macromolecular Assemblies (ELMA) group Institut de Biologie Structurale UMR 5075 CEA-CNRS-UJF-PSB 71 avenue des Martyrs CS 10090 38044 Grenoble Cedex 9 Phone: +33 (0)4 57 42 86 45 Fax: +33 (0)4 76 50 18 90 Web site: http://www.ibs.fr/ *****************************************************************

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command line
by PC 08 Aug '14

08 Aug '14

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RNA 5' end needs 2 PO4s
by Phoebe A. Rice 08 Aug '14

08 Aug '14

I'm trying to model the first residue of an RNA, which has a di (maybe tri) phosphate on the 5' end I'm sure someone has already worked this out ... should we call the 1st residue GDP or GTP, and somehow tell phenix about the bond to residue #2 (how?) or should we add pyrophosphate to the default 5' phosphate? PS - as a side point, elbow generates GMP with no phosphate thanks, Phoebe

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CIF for Thiol-substituted DNA
by Mark A. White 06 Aug '14

06 Aug '14

Hello, I have a diThiol substituted phosphate on a CYT residue (C2S: S1P & S2P in place of O1P & O2P). So far I have tried using phenix.elbow to produce a CIF, but with limited success. First, the links to the neighbouring nucleotides are not created. I could just add a links.cif to the input, but this would not include the DNA angle restraints. Second, the sugar-base chirality is not preserved, although it is listed in the CIF file. Is there a better way to produce a substituted DNA, similar to the example of adding the O5T to 5pho GUA? Also, why is the sugar-base chirality not preserved if it is in the CIF? C2S chir_03 C1' O4' N1 C2' positiv the comand: phenix.elbow --do-all dt15_C.pdb produced: elbow.C2S.dt15_C_pdb.001.cif Thanks, Mark -- 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 6.660 C University of Texas Medical Branch Galveston, TX 77555-0647 Tel. (409) 747-4747 Cell. (281) 734-3614 Fax. (409) 747-1404 mailto://[email protected] http://xray.utmb.edu QQ: "All opinions are not equal. Some are a very great deal more robust, sophisticated and well supported in logic and argument than others." - Douglas Noel Adams (2002)

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elbow, how to get partial charges in mol2 output file?
by Florian Nachon 06 Aug '14

06 Aug '14

Dear phenixbbers, The partial charges are not written in mol2 output files generated by elbow. Is there any way to change that behavior? Probably by editing tripos_mol2_writer.py? Thanks for helping. Florian -- La chance ne sourit qu'aux esprits bien préparés. Louis Pasteur

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Re: [phenixbb] PEG dependent structural changes in crystal structure
by shivendra singh 05 Aug '14

05 Aug '14

Dear Dr. Van Raaji and Dr. Domínguez, Thank you very much for your reply. The salt and pH of crystallisation recipe were same except PEG avg. mol wt. I agree, it may be due to different crystal packing but i am wondering whether disorderedness observed was intrinsic to the protein under PEG1500 or induced by different crystal packing. Also, is it possible that it may be the molten globule state of this protein? I read somewhere that its almost impossible to crystallise molten globule of any protein due to its transient nature. Is it possible that under the PEG1500 environment this collapsed state is more stable? Also looking at its active site, we are sure that it cant be in active form so i am not sure what may be its significance. Also if its a different conformation of active enzyme so is it possible to find out that whether its prior or later state of native form. The function of this enzyme is not related to polyols but hydrolyze cyclic amide substrate. Kind regards Shiv On 6 August 2014 00:23, shivendra singh <shivendra22(a)gmail.com> wrote: > Dear All, > I have been working on a protein which initially got crystallised in > condition having PEG1500 as precipitant. The space group was P21 and got > solved with reasonable Rfree. Analysis of its structure showed large > deviation and very distinct active site architecture along with > disorderedness in one of its long loop (no density) in comparison with the > expected result, based on related homologous structures. The structure does > not seem to be active with one of its active site residue moved apart from > other catalytic amino acids. Also the substrate entry tunnel looks > distorted. The purified enzyme used for crystallisation showed optimum > activity in vitro. This led us to screen it again for some other > crystallisation condition and got another crystal hit in condition having > PEG3350 as precipitant. Rest of the components of crystallisation cocktail > were same. The data belonged to P212121 space group. The regions which were > disordered or distorted in earlier case were observed to be ordered and in > their expected orientation and position. The enzyme is not reported to be > in different structural or functional states as observed. > I am wondering how the protein from the same batch showed two distinct > structural organizations in conditions with varying PEGs. > What may cause it to follow such transition. > Whether it has some significant functional aspect or just a result of > improper crystal packing. > > Thanks. > > Shiv >

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Phenix/DivCon: IUCr & ACS conferences
by Lance Westerhoff 05 Aug '14

05 Aug '14

Hello all- If you are attending the International Union of Crystallography conference in Montreal this week, be sure to stop by our booth and say hello (we are sharing booth #229 with CCG). We will be there to discuss QuantumBio’s quantum mechanics plugin to Phenix, and we will also be presenting results from some of our recent work with Phenix/DivCon. If you would like more information on our activities at the conference, please take a look at the following link: http://www.quantumbioinc.com/news/show/IUCr-2014 And for those of you planning to attend the American Chemical Society meeting in San Francisco next week, we’ll be there as well (yeah, this will be a busy couple of weeks!). I will be presenting a talk on the subject of quantum mechanics based refinement and its impact on drug discovery efforts. More information is available here: http://www.quantumbioinc.com/news/show/ACS-2014-CA Incidentally, we have a new release of our Phenix plugin coming out. If you are not yet a user and you would like to check it out, certainly feel free contact me for more information. Release Notes: http://www.quantumbioinc.com/news/show/Update-6.0.8 We look forward to seeing you! -Lance ____________________ Lance M. Westerhoff, Ph.D. President and General Manager QuantumBio Inc. WWW: http://www.quantumbioinc.com Email: lance(a)quantumbioinc.com Phone: 814-235-6908 Fax: 814-235-6909

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PEG dependent structural changes in crystal structure
by shivendra singh 05 Aug '14

05 Aug '14

Dear All, I have been working on a protein which initially got crystallised in condition having PEG1500 as precipitant. The space group was P21 and got solved with reasonable Rfree. Analysis of its structure showed large deviation and very distinct active site architecture along with disorderedness in one of its long loop (no density) in comparison with the expected result, based on related homologous structures. The structure does not seem to be active with one of its active site residue moved apart from other catalytic amino acids. Also the substrate entry tunnel looks distorted. The purified enzyme used for crystallisation showed optimum activity in vitro. This led us to screen it again for some other crystallisation condition and got another crystal hit in condition having PEG3350 as precipitant. Rest of the components of crystallisation cocktail were same. The data belonged to P212121 space group. The regions which were disordered or distorted in earlier case were observed to be ordered and in their expected orientation and position. The enzyme is not reported to be in different structural or functional states as observed. I am wondering how the protein from the same batch showed two distinct structural organizations in conditions with varying PEGs. What may cause it to follow such transition. Whether it has some significant functional aspect or just a result of improper crystal packing. Thanks. Shiv

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Two ions at same position
by Eric Girard 04 Aug '14

04 Aug '14

Dear phenixbb members, I am refining a structure that contains Ca2+ atoms. The structure was determined in presence of lanthanide ions. Thus, the resulting density clearly indicates that a part of each Ca2+ sites is substituted with Eu3+ (let's say 75% Ca2+ and 25% Eu3+ per sites). How can I deal with such situation? Indeed phenix.refine complains when I try to put a Ca2+ ion and a Eu3+ one with the same coordinates (and with the occupancies mentionned above) and stop. Thanks for your help. Eric. -- **************************************************************** Eric Girard Extremophiles and Large Macromolecular Assemblies (ELMA) group Institut de Biologie Structurale UMR 5075 CEA-CNRS-UJF-PSB 71 avenue des Martyrs CS 10090 38044 Grenoble Cedex 9 Phone: +33 (0)4 57 42 86 45 Fax: +33 (0)4 76 50 18 90 Web site: http://www.ibs.fr/ *****************************************************************

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lower Rfree in phenix.maps compared to phenix.refine and phenix.reciprocal_space_arrays
by Gregers Rom Andersen 02 Aug '14

02 Aug '14

Dear bb I have encountered a quite significant difference between Rfree reported by phenix.maps, refine and reciprocal_space_arrays. I have used default values in the GUI, and don't find differences in reflections statistics reported in the phenix.maps log that could explain the difference. I have another example also, but with a smaller difference between phenix.maps and phenix.refine. Both are quite large structures with maximum resolution between 3.5 and 4. Any explanation? phenix.maps ------------------------------------------------------------------------------- Bulk solvent correction and anisotropic scaling: |--(resolution: 3.68 - 29.45 A, n_refl.=22769 (all), 10.16 % free)------------| | | | r_work= 0.2550 r_free= 0.2823 coordinate error (max.-lik. estimate): 0.60 A | | | | x-ray target function (ml) for work reflections: 6.433959 | |-----------------------------------------------------------------------------| phenix.reciprocal_space_arrays |--(resolution: 3.68 - 29.45 A, n_refl.=22769 (all), 10.16 % free)------------| | | | r_work= 0.2741 r_free= 0.3045 coordinate error (max.-lik. estimate): 0.69 A | | | | x-ray target function (ml) for work reflections: 6.492710 | |-----------------------------------------------------------------------------| phenix.refine, strategy=none 1 macrocycle |--(resolution: 3.68 - 29.45 A, n_refl.=22769 (all), 10.16 % free)------------| | | | r_work= 0.2741 r_free= 0.3045 coordinate error (max.-lik. estimate): 0.69 A | | | | x-ray target function (ml) for work reflections: 6.492702 | |-----------------------------------------------------------------------------| gregers Professor Gregers Rom Andersen Department of Molecular Biology and Genetics Aarhus University Gustav Wiedsvej 10C DK8000 Aarhus C phone +45 871 55507 fax +45 861 23178 email gra(a)mb.au.dk -------------extract of log files-------- phenix.maps log Parameters to compute maps:: maps { input { pdb_file_name = "/u/gra/myproject/juli2014/mave/ref_01.pdb" reflection_data { file_name = "/u/gra/myproject/juli2014/mave/reflections.mtz" labels = "FP,SIGFP" high_resolution = None low_resolution = None outliers_rejection = True french_wilson_scale = True french_wilson { max_bins = 60 min_bin_size = 40 } sigma_fobs_rejection_criterion = None sigma_iobs_rejection_criterion = None r_free_flags { file_name = "/u/gra/myproject/juli2014/mave/reflections.mtz" label = "R-free-flags43" test_flag_value = 1 ignore_r_free_flags = False } } } =============================== Reflection data =============================== F-obs: /u/gra/myproject/juli2014/mave/reflections.mtz:FP,SIGFP Miller array info: /u/gra/myproject/juli2014/mave/reflections.mtz:FP,SIGFP Observation type: xray.amplitude Type of data: double, size=22776 Type of sigmas: double, size=22776 Number of Miller indices: 22776 Anomalous flag: False Unit cell: (168.063, 154.031, 78.988, 90, 90, 90) Space group: P 21 21 2 (No. 18) Systematic absences: 0 Centric reflections: 2864 Resolution range: 29.4462 3.67631 Completeness in resolution range: 0.992029 Completeness with d_max=infinity: 0.989401 Wavelength: 0.0000 Number of F-obs in resolution range: 22776 Number of F-obs<0 (these reflections will be rejected): 0 Number of F-obs=0 (these reflections will be used in refinement): 0 Refinement resolution range: d_max = 29.4462 d_min = 3.6763 R-free flags: /u/gra/myproject/juli2014/mave/reflections.mtz:R-free-flags43 Miller array info: /u/gra/myproject/juli2014/mave/reflections.mtz:R-free-flags43 Observation type: None Type of data: int, size=22776 Type of sigmas: None Number of Miller indices: 22776 Anomalous flag: False Unit cell: (168.063, 154.031, 78.988, 90, 90, 90) Space group: P 21 21 2 (No. 18) Systematic absences: 0 Centric reflections: 2864 Resolution range: 29.4462 3.67631 Completeness in resolution range: 0.992029 Completeness with d_max=infinity: 0.989401 Wavelength: 0.0000 Test (R-free flags) flag value: 1 Number of work/free reflections by resolution: work free %free bin 1: 29.4471 - 7.8747 [2434/2441] 2190 244 10.0% bin 2: 7.8747 - 6.2702 [2347/2348] 2103 244 10.4% bin 3: 6.2702 - 5.4834 [2297/2300] 2076 221 9.6% bin 4: 5.4834 - 4.9847 [2284/2286] 2053 231 10.1% bin 5: 4.9847 - 4.6289 [2272/2274] 2045 227 10.0% bin 6: 4.6289 - 4.3569 [2294/2295] 2066 228 9.9% bin 7: 4.3569 - 4.1393 [2240/2241] 1994 246 11.0% bin 8: 4.1393 - 3.9595 [2254/2255] 2027 227 10.1% bin 9: 3.9595 - 3.8074 [2277/2278] 2055 222 9.7% bin 10: 3.8074 - 3.6763 [2077/2241] 1853 224 10.8% overall 20462 2314 10.2% ------------------------------------------------------------------------------- Input model file: /u/gra/myproject/juli2014/mave/ref_01.pdb ============================== Scattering factors ============================= ----------X-ray scattering dictionary---------- Number of scattering types: 6 Type Number sf(0) Gaussians S 48 15.91 1 P 28 14.91 1 Mg 2 11.95 2 O 2498 7.97 1 N 2146 6.97 1 C 7880 5.97 1 sf(0) = scattering factor at diffraction angle 0. Number of scatterers: 12602 At special positions: 0 Unit cell: (168.063, 154.031, 78.988, 90, 90, 90) Space group: P 21 21 2 (No. 18) ------------------------------------------------------------------------------- Bulk solvent correction and anisotropic scaling: |--(resolution: 3.68 - 29.45 A, n_refl.=22769 (all), 10.16 % free)------------| | | | r_work= 0.2550 r_free= 0.2823 coordinate error (max.-lik. estimate): 0.60 A | | | | x-ray target function (ml) for work reflections: 6.433959 | |-----------------------------------------------------------------------------| phenix.reciprocal_space_arrays Default params:: hkl_file = None pdb_file = None f_obs_label = None r_free_flags_label = None remove_f_obs_outliers = True bulk_solvent_and_scaling = True hendrickson_lattman_coefficients_label = None output_file_name = None space_group = None unit_cell = None job_title = None |--(resolution: 3.68 - 29.45 A, n_refl.=22769 (all), 10.16 % free)------------| | | | r_work= 0.2741 r_free= 0.3045 coordinate error (max.-lik. estimate): 0.69 A | | | | x-ray target function (ml) for work reflections: 6.492710 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 29.4471 - 9.3567 0.99 1316 144 0.1750 0.1935 7.111 7.2567| | 2: 9.3567 - 7.4666 1.00 1244 147 0.1844 0.2442 6.8649 7.0955| | 3: 7.4666 - 6.5345 1.00 1243 135 0.2403 0.3183 6.6514 6.7683| | 4: 6.5345 - 5.9424 1.00 1221 136 0.2622 0.3386 6.5345 6.547| | 5: 5.9424 - 5.5195 1.00 1230 131 0.2482 0.3091 6.3934 6.5161| | 6: 5.5195 - 5.1959 1.00 1199 141 0.2741 0.2699 6.3987 6.4315| | 7: 5.1959 - 4.9370 1.00 1196 129 0.2528 0.2600 6.3987 6.4955| | 8: 4.9370 - 4.7230 1.00 1227 136 0.2747 0.3240 6.4448 6.5001| | 9: 4.7230 - 4.5418 1.00 1178 151 0.2867 0.3278 6.4205 6.5232| | 10: 4.5418 - 4.3856 1.00 1224 113 0.2871 0.2980 6.4246 6.5162| | 11: 4.3856 - 4.2489 1.00 1201 151 0.3209 0.4007 6.4221 6.5583| | 12: 4.2489 - 4.1278 1.00 1174 137 0.3552 0.3395 6.4274 6.4033| | 13: 4.1278 - 4.0194 1.00 1190 129 0.3917 0.3944 6.4059 6.366| | 14: 4.0194 - 3.9216 1.00 1184 149 0.3931 0.3915 6.3718 6.38| | 15: 3.9216 - 3.8326 1.00 1221 116 0.3952 0.3998 6.3442 6.3031| | 16: 3.8326 - 3.7512 1.00 1168 138 0.4077 0.3949 6.334 6.3252| | 17: 3.7512 - 3.6763 0.88 1040 130 0.4322 0.4220 6.3237 6.2334| |-----------------------------------------------------------------------------| ------------------------------- phenix.refine refine { strategy = individual_sites individual_sites_real_space rigid_body \ individual_adp group_adp tls occupancies group_anomalous main { number_of_macro_cycles = 1 ============================= updating all scales ============================= start: r_work=0.3857 r_free=0.4073 n_reflections: 22776 start: r_work=0.3857 r_free=0.4073 (reset all scales to undefined) bulk-solvent and scaling: r_work=0.2758 r_free=0.3049 remove outliers: r_work=0.2758 r_free=0.3049 correct solvent mask: r_work=0.2741 r_free=0.3045 final: r_work=0.2741 r_free=0.3045 n_reflections: 22769 overall anisotropic scale matrix: V0: 0.0014,6.7700,1.3003,-6.1473,-1.1440,0.3484 V1: -0.0036,-0.0045,-0.0442,0.0324,0.0082,0.0028 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work <Fobs> <Fmodel> kiso kani kmask 29.446-20.724 97.09 90 10 0.2436 1579.386 1497.822 1.000 2.341 0.338 20.553-17.465 100.00 91 10 0.2757 1238.791 1140.148 1.000 1.886 0.335 17.444-14.852 99.35 137 16 0.2182 1221.185 1176.515 1.000 1.685 0.327 14.833-12.617 98.73 210 23 0.1958 1278.964 1244.386 1.000 1.494 0.307 12.608-10.717 98.98 349 39 0.1500 1428.238 1389.811 1.000 1.395 0.300 10.715-9.108 99.84 547 62 0.1416 1410.502 1384.438 1.000 1.354 0.290 9.104-7.738 100.00 883 99 0.1789 1027.723 1002.711 1.000 1.233 0.290 7.736-6.574 99.94 1427 159 0.2385 682.594 646.245 1.000 1.076 0.290 6.573-5.586 99.88 2288 254 0.2567 515.856 486.005 1.000 0.892 0.270 5.586-4.747 99.90 3710 411 0.2654 489.477 455.553 1.000 0.818 0.220 4.746-4.033 99.95 5973 671 0.3225 441.426 390.526 1.000 0.817 0.170 4.033-3.676 96.99 4751 559 0.4048 366.235 296.284 1.000 0.848 0.170 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1939 b_overall=26.4160

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Fwd: real_space_refine
by George Devaniranjan 02 Aug '14

02 Aug '14

Hi I was wondering if there is a way to restrain the omega angles of the structure being refined to its starting values while allowing the phi and psi dihedral angles to vary? I was looking at omega_esd_override_value discard_omega in phenix.real_space_refine. Thank you, George

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Maximum Likelihood Method for Twinning
by Chris Fage 30 Jul '14

30 Jul '14

Hi All, Can anyone please direct me to a literature reference describing the maximum likelihood method for detection of twinning based on twin laws, as implemented in phenix.xtriage? Thank you! Best, Chris

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Use of NCS in Autosol
by Nick Huang 29 Jul '14

29 Jul '14

Dear All, Does autosol use NCS averaging in its density modification? I checked the log file for an Autosol run. It seemed Autosol used NCS in heavy atom refinement but not in the density modification procedure. But I might be wrong. If this is the case, is there a way to include NCS in autosol pipeline or do I just have to run density averaging afterward? Thanks. Nick Huang Hauptman-Woodward Institute

2 1

alternatives to RMSD
by Patrick. C 29 Jul '14

29 Jul '14

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real space refinement
by George Devaniranjan 28 Jul '14

28 Jul '14

Hi, I know this is going to sound blasphemous in phenix (my apology particularly to Pavel) but is there other s/w that does similar things to phenix.real_space_refine ? I used that already (works very well) but was wondering if there was anything similar out there to do a comparison. Thank you, George

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eLBOW / REEL and chirality
by L. Costenaro (IBB) 24 Jul '14

24 Jul '14

Dear all, I am making the restraints file (CIF) for a ligand with two chiral carbons, using eLBOW (AM1 QM, output: retain original chirality) from a SMILES description and obtain the following: Atom input_chirality input_smiles output_vol_sign output_R/S output_chirality_pdb C20 S C@H negative S S C37 R C@@H positive S S Although the volume_sign in the output cif file correspond to the input chiralities, the output pdb has the wrong chirality for the carbon C37: S instead of the desired R. I think the "retain original chirality" option is what I need to keep the input chirality, but apparently it doesn't. How should I proceed to get a pdb with the correct chiralities? Best regards, Lionel PS: phenix version 1.9-1692, linux X86_64 PS2: in REEL, the action "Find unique code" make phenix (not REEL) crash (all windows close) without error message

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SFALL in CCP4 and calculate F(model) in Phenix
by PC 24 Jul '14

24 Jul '14

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Re: [phenixbb] [External] RE: phenix.ligandfit does not recognize a list of SDF file names
by Terwilliger, Thomas Charles 22 Jul '14

22 Jul '14

Hi Jason, I fixed ligandfit so that it should now be able to take your list of sdf files and run each file sequentially. Starting with tomorrow's build, you should be able test it out with this regression test: phenix_regression.wizards.test_command_line_ligands test_ligand_list Thanks for pointing out the problem! Let me know if that does not do it. All the best, Tom T On Jul 21, 2014, at 7:11 PM, Phan, Jason wrote: > ________________________________________ > From: phenixbb-bounces(a)phenix-online.org<mailto:[email protected]> [phenixbb-bounces(a)phenix-online.org] on behalf of Phan, Jason [jason.phan(a)vanderbilt.edu] > Sent: Monday, July 21, 2014 4:32 PM > To: phenixbb(a)phenix-online.org<mailto:[email protected]> > Subject: [phenixbb] phenix.ligandfit does not recognize a list of SDF file names > > Hi All, > > I'm trying to fit a list of ligands in SD format with phenix.ligandfit using the ligand=ligand.dat (file containing the ligand file names in the same directory) and the file_or_file_list=file_with_list_of_files flag. It complained that the ligand does not exist. I tested a single ligand, ligand=ligand1.sdf, and it worked fine. I tested a list containing pdb file names and it worked fine. I think phenix.ligandfit does not recognize SD-formatted ligands from a list, although it is fine running as a single ligand. PDB format is fine single or list of names. Any suggestions other than converting SDF to PDB or writing a script to run one SDF at a time? Thanks. > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org<mailto:[email protected]> > http://phenix-online.org/mailman/listinfo/phenixbb

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B iso average versus B wilson
by Emily Golden 22 Jul '14

22 Jul '14

Dear All, I have a 1.12 A refined structure with and average B of 11.5 but the wilson B is 6. There are a couple of highly mobile loops and water molecules in the structure that are increasing the average B. What is an acceptable difference between wilson B and average B? Thank you, Emily

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phenix.ligandfit does not recognize a list of SDF file names
by Phan, Jason 22 Jul '14

22 Jul '14

Hi All, I'm trying to fit a list of ligands in SD format with phenix.ligandfit using the ligand=ligand.dat (file containing the ligand file names in the same directory) and the file_or_file_list=file_with_list_of_files flag. It complained that the ligand does not exist. I tested a single ligand, ligand=ligand1.sdf, and it worked fine. I tested a list containing pdb file names and it worked fine. I think phenix.ligandfit does not recognize SD-formatted ligands from a list, although it is fine running as a single ligand. PDB format is fine single or list of names. Any suggestions other than converting SDF to PDB or writing a script to run one SDF at a time? Thanks.

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CCTBX questions
by Morten Grøftehauge 22 Jul '14

22 Jul '14

Hi people, I notice that cctbx.python comes with phenix but as far as I can tell from when I run it, look at imported modules with dir(), and compare to the documentation on Sourceforge the version that comes with phenix is abridged. And possibly not the same version as the sourceforge one but they probably are the same. Will it cause any problems with Phenix if I install cctbx from sourceforge? Is it unnecessary? Second question: Is there any better documentation anywhere? I found James Stroud's wiki but that's mainly for structure factor manipulation. Cheers, Morten -- Morten K Grøftehauge, PhD Pohl Group Durham University

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Long Distant Restraints
by Bradley Hintze 18 Jul '14

18 Jul '14

Hey PHENIX, I am wondering if I can define a distant restraint longer that 3A in a custom restraint file? The conventional way of doing this is to provide : refinement.geometry_restraints.edits { C8_C1=chain C and resid 8 and name C1' D10_C1=chain D and resid 10 and name C1' bond { action = *add atom_selection_1 = $C8_C1 atom_selection_2 = $D10_C1 distance_ideal = 9.1 sigma = 0.02 slack = 0.5 } Obviously this is a distant and not bond restraint. 9.1 exceeds the allowed length of 3 for a bond. Is there a different type of restraint that allows longer distances? Thanks! -- Bradley J. Hintze Duke University PhD Candidate Department of Biochemistry

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Refinement cycles
by George Devaniranjan 17 Jul '14

17 Jul '14

Hi, I was wondering if there is a reason for setting the default number of refinement cycles to 3 in Phenix refine? is there a number of cycles at which point it becomes unacceptable to run so many ? Thank you, George

2 1

B factors too high for low resolution data refinement
by 李翔 15 Jul '14

15 Jul '14

Hi everyone, I am working on my low-resolution data (~6.5 A). When I was doing refinement with PHENIX, the B factors remain pretty high (~400, not sure whether it is normal for the data with such resolution.) And B factors further increased after group B factor refinement (~500). Does it mean the group B factors refinement not working or is there a way I can somehow define a limit for B-factors? (I read one previous topic a few years ago which indicates the B factor can not be controlled. Not sure whether it is available now). Thank you very much for your help! Sincerely, Xiang -- Li Xiang Department of chemistry, Purdue University Email：lixiang1642(a)gmail.com

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So what is unique?
by Kenneth A. Satyshur 15 Jul '14

15 Jul '14

There is some disagreement on terms used to deposit data. We need a definition and an algorithm for each definition. "Unique Reflections" My definition is all the possible reflections out to the highest resolution reported not related by symmetry. Where can I find this? The .mtz contains a list of all HKL calculated to the highest resolution. Usually, we are not able to measure all these diffraction spots due to limits of the detector, mechanical limits, crystal orientation, etc. 'Total reflections' The depositions server asks for total reflections. I assume it wants only those unique reflections we were able to collect, regardless of the sigma cut off. These are called 'observed'. The total we use in refinement will be a subset of the 'unique observed' that are cut on sigma. However, some crystallographers believe that we should not cut on sigma since some of the intensities may in fact be zero. Is this a question for the Refmac and Phenix people? Please give us some guidance and maybe a reference or two that we can use. thanks -- Kenneth A. Satyshur, M.S.,Ph.D. Senior Scientist University of Wisconsin Madison, Wisconsin 53706 608-215-5207

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cifs still in pdb v2
by Guenter Fritz 14 Jul '14

14 Jul '14

Dear Pavel and Nat, can you include in future phenix versions the FAD.cif, NAD.cif and data_NAI.cif / NAI.cif in pdb v3? Currently both are still pdb v2. I usually simply copy the cifs pdb v3 into the mon_lib directory , but sometimes I forget it and stumble over it. Thanks and best wishes, Guenter

2 1

Maximum-likelihood score calculation
by Jouko Virtanen 12 Jul '14

12 Jul '14

Hi all, I would like to calculate the maximum-likelihood score given an input structure and an mtz file. How can I do that? Thanks in advance. Best regards, Jouko

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