- phenixbb - phenix-online.org

Coot 3D for Geforce GTX 970 Graphics card on Windows 7 and Fedora
by Xiao Lei 25 Jan '16

25 Jan '16

Hi Phenixbb members, My lab has a desktop PC which has Windows 7 with Geforce GTX 970 Graphics card, is this card ok for the Coot 3D function with 3D monitor and Nvidia 3D kit? Do I need to do some settings before I can use the Coot 3D function? I'm also thinking installing Fedora 23 on the PC and use coot 3D, is there any settings in the Fedora environment before using coot 3D? Thanks ahead.

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Changing NCS groups
by Marie Elizabeth Fraser 25 Jan '16

25 Jan '16

Hello, I would like to edit the NCS information for a model with two chains. I've tried running find_ncs and editing the phil file, but I get an error when I try to use my edited file in the next cycle of refinement. I've tried using the utility to detect NCS groups, then edited in the little windows - also no success. How are other people defining NCS when they aren't content with the equivalences the program finds? Thank you for your insight, Marie

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Xtriage systematic results is not consistent with HKL2000
by Alex Lee 23 Jan '16

23 Jan '16

Dear All, I scaled a dataset of SG P2221 in HKL2000 and got systematic absence results as below, it seems clearly HKL2000 showed the data had systematic absence violations, but when I used the .sca file from HKL2000 as input in Xtriage, the result did not show any systematic violations. Which result should I rely on? HKL200 Results: Summary of reflections intensities and R-factors by shells R linear = SUM ( ABS(I - <I>)) / SUM (I) R square = SUM ( (I - <I>) ** 2) / SUM (I ** 2) Chi**2 = SUM ( (I - <I>) ** 2) / (Error ** 2 * N / (N-1) ) ) In all sums single measurements are excluded Shell Lower Upper Average Average Norm. Linear Square limit Angstrom I error stat. Chi**2 R-fac R-fac Rmeas Rpim CC1/2 CC* 50.00 5.60 2819.0 103.7 44.8 0.607 0.033 0.040 0.037 0.017 0.998 0.999 5.60 4.45 1801.5 63.8 28.1 0.914 0.043 0.050 0.048 0.022 0.997 0.999 4.45 3.88 1435.3 52.6 25.5 0.980 0.048 0.051 0.054 0.024 0.997 0.999 3.88 3.53 738.7 31.8 20.5 1.117 0.068 0.067 0.075 0.032 0.996 0.999 3.53 3.28 489.7 26.5 20.1 1.134 0.092 0.080 0.102 0.043 0.996 0.999 3.28 3.08 236.3 19.8 17.4 0.975 0.147 0.108 0.162 0.069 0.993 0.998 3.08 2.93 93.4 16.4 16.0 0.850 0.296 0.277 0.327 0.138 0.947 0.986 2.93 2.80 62.9 16.3 16.0 0.737 0.422 0.384 0.467 0.197 0.921 0.979 2.80 2.69 42.6 16.7 16.5 0.677 0.622 0.515 0.688 0.291 0.879 0.967 2.69 2.60 29.3 20.0 19.9 0.680 0.924 0.842 0.000 0.440 0.659 0.891 All reflections 798.1 37.4 22.6 0.873 0.064 0.050 0.068 0.031 Intensities of systematic absences h k l Intensity Sigma I/Sigma 0 0 3 -0.4 1.3 -0.3 0 0 5 10.4 3.0 3.5 0 0 7 11.4 3.9 2.9 0 0 9 8.7 4.3 2.0 0 0 11 18.6 6.4 2.9 0 0 13 182.9 17.1 10.7 0 0 15 3.0 7.8 0.4 0 0 17 11.9 9.2 1.3 0 0 19 30.0 14.3 2.1 0 0 21 7.4 11.1 0.7 0 0 23 54.2 15.6 3.5 0 0 25 43.1 16.1 2.7 0 0 27 12.5 18.9 0.7 0 0 29 -16.6 20.9 -0.8 0 0 31 31.0 25.4 1.2 0 0 33 3.4 29.2 0.1 0 0 35 -24.2 32.0 -0.8 0 0 37 50.9 42.5 1.2 0 0 39 -53.3 66.4 -0.8 0 0 41 65.8 50.6 1.3 0 0 43 -24.3 46.8 -0.5 0 0 45 -6.1 48.3 -0.1 0 0 47 -14.8 45.8 -0.3 0 0 49 1.1 53.5 0.0 0 0 51 -7.9 64.2 -0.1 Phenix Xtriage Results: ----------Space group identification---------- Analyses of the absences table indicates a number of likely space group candidates, which are listed below. For each space group, the number of systematic absence violations are listed under the '+++' column. The number of non-absence violations (weak reflections) are listed under '---'. The last column is a likelihood based score for the particular space group. Note that enantiomorphic spacegroups will have equal scores. Also, if absences were removed while processing the data, they will be regarded as missing information, rather then as enforcing that absence in the space group choices. ------------------------------------------------------------------------------------- | space group | # absent | <Z>_absent | <Z/sigZ>_absent | +++ | --- | score | ------------------------------------------------------------------------------------- | P 2 2 2 | 0 | 0.00 | 0.00 | 0 | 4 | 0.000e+00 | | P 2 2 21 | 0 | 0.00 | 0.00 | 0 | 4 | 0.000e+00 | | P 2 21 2 | 5 | 3.07 | 16.77 | 5 | 4 | 1.038e+01 | | P 2 21 21 | 5 | 3.07 | 16.77 | 5 | 4 | 1.038e+01 | | P 21 2 2 | 5 | 1.89 | 15.21 | 5 | 4 | 1.250e+01 | | P 21 2 21 | 5 | 1.89 | 15.21 | 5 | 4 | 1.250e+01 | | P 21 21 2 | 10 | 2.48 | 15.99 | 10 | 4 | 2.288e+01 | | P 21 21 21 | 10 | 2.48 | 15.99 | 10 | 4 | 2.288e+01 | ------------------------------------------------------------------------------------- ----------List of individual systematic absences---------- Note: this analysis uses the original input data rather than the filtered data used for twinning detection; therefore, the results shown here may include more reflections than shown above. P 2 2 2: no systematic absences possible P 2 2 21 (input space group): no absences found P 21 2 2 ( 5, 0, 0): i/sigi = 21.0 ( 7, 0, 0): i/sigi = 4.8 ( 9, 0, 0): i/sigi = 14.3 ( 11, 0, 0): i/sigi = 15.2 ( 13, 0, 0): i/sigi = 18.3 ( 15, 0, 0): i/sigi = 12.7 ( 17, 0, 0): i/sigi = 4.1 P 2 21 2 ( 0, 3, 0): i/sigi = 21.3 ( 0, 5, 0): i/sigi = 21.4 ( 0, 7, 0): i/sigi = 20.7 ( 0, 9, 0): i/sigi = 21.4 ( 0, 11, 0): i/sigi = 20.7 ( 0, 13, 0): i/sigi = 14.5 ( 0, 17, 0): i/sigi = 10.4 ( 0, 21, 0): i/sigi = 14.4 ( 0, 23, 0): i/sigi = 0.8 ( 0, 25, 0): i/sigi = 2.3 ( 0, 27, 0): i/sigi = 2.0 P 21 21 2 ( 0, 3, 0): i/sigi = 21.3 ( 0, 5, 0): i/sigi = 21.4 ( 0, 7, 0): i/sigi = 20.7 ( 0, 9, 0): i/sigi = 21.4 ( 0, 11, 0): i/sigi = 20.7 ( 0, 13, 0): i/sigi = 14.5 ( 0, 17, 0): i/sigi = 10.4 ( 0, 21, 0): i/sigi = 14.4 ( 0, 23, 0): i/sigi = 0.8 ( 0, 25, 0): i/sigi = 2.3 ( 0, 27, 0): i/sigi = 2.0 ( 5, 0, 0): i/sigi = 21.0 ( 7, 0, 0): i/sigi = 4.8 ( 9, 0, 0): i/sigi = 14.3 ( 11, 0, 0): i/sigi = 15.2 ( 13, 0, 0): i/sigi = 18.3 ( 15, 0, 0): i/sigi = 12.7 ( 17, 0, 0): i/sigi = 4.1 P 2 21 21 ( 0, 3, 0): i/sigi = 21.3 ( 0, 5, 0): i/sigi = 21.4 ( 0, 7, 0): i/sigi = 20.7 ( 0, 9, 0): i/sigi = 21.4 ( 0, 11, 0): i/sigi = 20.7 ( 0, 13, 0): i/sigi = 14.5 ( 0, 17, 0): i/sigi = 10.4 ( 0, 21, 0): i/sigi = 14.4 ( 0, 23, 0): i/sigi = 0.8 ( 0, 25, 0): i/sigi = 2.3 ( 0, 27, 0): i/sigi = 2.0 P 21 2 21 ( 5, 0, 0): i/sigi = 21.0 ( 7, 0, 0): i/sigi = 4.8 ( 9, 0, 0): i/sigi = 14.3 ( 11, 0, 0): i/sigi = 15.2 ( 13, 0, 0): i/sigi = 18.3 ( 15, 0, 0): i/sigi = 12.7 ( 17, 0, 0): i/sigi = 4.1 P 21 21 21 ( 0, 3, 0): i/sigi = 21.3 ( 0, 5, 0): i/sigi = 21.4 ( 0, 7, 0): i/sigi = 20.7 ( 0, 9, 0): i/sigi = 21.4 ( 0, 11, 0): i/sigi = 20.7 ( 0, 13, 0): i/sigi = 14.5 ( 0, 17, 0): i/sigi = 10.4 ( 0, 21, 0): i/sigi = 14.4 ( 0, 23, 0): i/sigi = 0.8 ( 0, 25, 0): i/sigi = 2.3 ( 0, 27, 0): i/sigi = 2.0 ( 5, 0, 0): i/sigi = 21.0 ( 7, 0, 0): i/sigi = 4.8 ( 9, 0, 0): i/sigi = 14.3 ( 11, 0, 0): i/sigi = 15.2 ( 13, 0, 0): i/sigi = 18.3 ( 15, 0, 0): i/sigi = 12.7 ( 17, 0, 0): i/sigi = 4.1 Thanks ahead

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Change of PHIL definitions in phenix.find_alt_orig_sym_mate
by R.D. Oeffner 22 Jan '16

22 Jan '16

I have changed the PHIL definitions in this program from AltOrigSymMates.moving_pdb to AltOrigSymMates.moving.pdb and from AltOrigSymMates.fixed_pdb to AltOrigSymMates.fixed.pdb. I'm not sure if it is being used elsewhere but let me know if you encounter an error due to this. Regards, Rob

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anomalous completeness from Phenix Xtriage result
by Alex Lee 22 Jan '16

22 Jan '16

Dear All, After check my data with Phenix Xtriage, I got a warning of "the anomalous completeness is 42.34%". I do not know if I need to pay attention to this? I did not do experimental phasing and I did not add heavy metal to my crystal nor there is selenium on my protein. I even don't know why I still get the anomalous signal. But from the detailed summary below I guess in my case it's not a problem? ----------Summary---------- File name: P2_rejoutput.sca Data labels: I(+),SIGI(+),I(-),SIGI(-) Space group: P 1 2 1 Unit cell: 72.255, 46.617, 134.086, 90, 90.052, 90 Data type: xray.intensity Resolution: 49.1682 - 2.5855 Anomalous: True Number of reflections (non-anomalous): 27184 Completeness (non-anomalous): 95.42% Number of reflections (all): 38285 Completeness (all): 69.98% Anomalous completeness: 42.34% Completeness (non-anomalous) is the completeness of the data after merging Friedel pairs. Completeness (all) is the completeness of the data before merging Friedel pairs. Completeness (anomalous) is the completeness of the anomalous data. The anomalous completeness is calcluated by dividing the number of measured acentric, Bijvoet mates by the total possible number of acentric indices. Completeness (non-anomalous) should be used to determine if there is sufficient data for non-anomalous purposes (refinement, model-building). A value greater than 90% is generally desired, while a value less than 75% is considered poor. Values in between will provide less than optimal results. Completeness (anomalous) should be used to determine if there is sufficient data for anomalous purposes (phasing, finding anomalous atoms, refinement of anomalous occupancies or scattering factors). A value greater than 80% is generally desired, while a value less than 50% is considered poor. Values in between will provide less than optimal results. Thanks.

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Specify a chain in Phenix Autobuild
by Xiao Lei 21 Jan '16

21 Jan '16

Hi Phenixbb members, I am using Phenix autobuild for a protein-DNA complex. There are three chains for protein (F, H, I) and two chains for DNA (A and B). I know Autobuild can only build one chain at a time and I'm only going to build chain F. In the autobuild GUI, I can find an option of Chain type "Auto", "protein" , "DNA" and "RNA". Is there a place in the GUI which I can specify only building protein chain "F"? Thanks ahead.

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ligand modification / combination in REEL
by andre.stiel 20 Jan '16

20 Jan '16

Hi, I have a phosphatidyl inositol ligand without an existing CIF file only smiles. When I construct the ligand from the smiles ELBOW regards the sugar as just an aromatic ring. So I see three possibilities how to end up with a proper constraints file for my ligand (that is: tails like in the smiles but with a proper sugar (chair) conformation on top): 1. Can I edit the aromatic ring in REEL in a way to push it into the desired boat/chair conformation? I did not find a command to that end although he can clearly „see“ this conformation as I know from another ligand. 2. Can I chop the sugar part from the .CIF of another ligand and somehow fuse it to my tails? 3. There is a sugar editor in REEL (which however crashes at the moment for me (Version 1-10-2155)) can I use this to construct the desired sugar and somehow fuse it to the rest… basically like option 2? I have not found a very extensive documentation on how to play such tricks with REEL. Or would I have to rebuild a complete ligand with this SCALES? Other suggestion how to get my ligand are also welcome. Thanks André Helmholtz Zentrum Muenchen Deutsches Forschungszentrum fuer Gesundheit und Umwelt (GmbH) Ingolstaedter Landstr. 1 85764 Neuherberg www.helmholtz-muenchen.de Aufsichtsratsvorsitzende: MinDir'in Baerbel Brumme-Bothe Geschaeftsfuehrer: Prof. Dr. Guenther Wess, Dr. Alfons Enhsen, Renate Schlusen (komm.) Registergericht: Amtsgericht Muenchen HRB 6466 USt-IdNr: DE 129521671

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N-acetylgalactosamine lacking amide planarity restraint
by Tristan Croll 20 Jan '16

20 Jan '16

Hi, I'm refining a structure that includes an O-linked N-acetylgalactosamine (NGA) residue, and from the way it's behaving the N-acetyl amide clearly has no restraints on its planarity. It's currently twisted almost 45 degrees from planar despite having no close contacts. Cheers, Tristan

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how not to refine residue X?
by Murpholino Peligro 19 Jan '16

19 Jan '16

Hi. How to tell phenix.refine to leave residue X during refinement? I already tried in the .eff >>> strategy = *individual_sites *individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous sites { individual = not (chain A and resid 97) <<< But resid 97 is being moved to another position. I am using phenix.refine_1.10.1-2155 Thanks

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phenix.sort_heteroatoms produced duplicated residue number
by luzuok 13 Jan '16

13 Jan '16

Dear phenixbb, When I use phenix.sort_hetero_atoms to resort my pdb, there are duplicated residue number of water and aa in the output pdb. Is this a bug? As there are many number gaps water, how can I fix it? Best wishes! Lu -- 卢作焜南开大学新生物站A202 Lu Zuokun, Ph.D. Candidate College of Life Science, Nankai University

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pdbtools model_statistics: average B-factors
by wtempel 12 Jan '16

12 Jan '16

Hello, are the mean B-factors in the "ADP statistics" table occupancy-weighted, or perhaps weighted in any other way? If so, please could you provide the formula. Thank you. Wolfram Tempel

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phenix.refine with reference model
by Falk, Sebastian 08 Jan '16

08 Jan '16

Hi! I am currently building a 3.3 A structure of a large protein. I do have a reference model at much better resolution that has 58% sequence identity and 77% similarity. The structures are quite similar, there are only a few regions with insertions. However, phenix.refine does ‘accept’ the reference model and thus creates no torsion restraints. I also tried to run ProSmart in CCP4 but there the cut-off for the reference model is 75% sequence identity. I could not find any threshold for phenix.refine though. I am happy for any suggestion or tip how to include the reference model even though the sequence identity is not as high. Thank a lot. Sebastian Sebastian Falk Max-Planck-Institute for Biochemistry Structural Cell Biology Am Klopferspitz 18 D-82152 Martinsried Germany sfalk(a)biochem.mpg.de

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Generate sequence files of homodimer protein or double strand DNA for phaser MR
by Alex Lee 08 Jan '16

08 Jan '16

Dear Phenixbb members, I am using Phaser MR for solving a homodimer DNA binding protein with dsDNA complex structure. I'd like to use sequence file rather then molecular weight in the component definition of ASU. As there are solved homodimer protein structures (amino acid identity 100%) on PDB, I can download seq file (fasta form) from PDB webpage, but the seq file is only for one protein chain. I also tried online tools like "make sequence from PDB file" (http://swift.cmbi.ru.nl/servers/html/soupir.html), when I put the protein dimer bound to dsDNA pdb into the online tool, the outtput pir sequence file only shows a single protein chain and dna which dose not seems like two strands, rather then just put two 23base dna together for a 46 base length single strand DNA. I am asking is there a way to generate sequence file for a homodimer and dsDNA? or I have to generate sequence file for each chain separately (there will be four sequence files in this case, two protein chains and two dna chains)? Thanks. Alex Alex

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coot generate symmetry mates like pymol
by Xiao Lei 08 Jan '16

08 Jan '16

Hi Phenixbb members, 1. Is there a function in coot which can generate symmetry mates like pymol (action--> generate symmetry mates)? I know in coot there is a "Draw---> Cell&Symmetry" function, but it seems the display results could not display my crystal packing like pymol. 2. In pymol, is there a button which just display structure in one unit cell? Thanks. Xiao

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unwanted N/Q/H flipping in PHENIX.REFINE
by Bernhard Loll 05 Jan '16

05 Jan '16

Dear all, I am currently refining a 1.9 A structure with PHENIX 1.10.1-2155. The problem I am facing is the following: Running the Molprobity server, it suggests me to correct a couple of N/Q/H flips. I perform the flips re-run PHENIX.REFINE with “Automatically correct N/Q/H errors” not ticked. The log file confirms the selection with nqh_flips = False. Nevertheless PHENIX.REFINE again flips these residues and the output PDB file has all previously flipped residues “re-flipped” in comparison to the input PDB file. I am very confident that the automatically flips performed by PHENIX.REFINE (REDEUCE) are wrong, since I have two metal binding sites. Why PHENIX.REFINE rotates side chains by 180 degree even though nqh_flips were set to false? Any help is appreciated. Cheers, Bernhard Dr. Bernhard Loll Freie Universitaet Berlin Fachbereich Biologie, Chemie, Pharmazie Institut fuer Chemie und Biochemie AG Strukturbiochemie Takustr. 6 D-14195 Berlin Germany Phone: +49 (0) 30 838-57348 Fax: +49 (0) 30 838-454936 Email: loll(a)chemie.fu-berlin.de Homepage: http://www.bcp.fu-berlin.de/chemie/bc/ag/agwahl/

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Project info lost after a disk crash
by hli 04 Jan '16

04 Jan '16

Hi, The hard drive of our major Linux computer crashed recently. After installing a new disk and recovering all the data in the damaged disk I lost all the project information in PHENIX GUI home page. I noticed that under .phenix directory there are files like project_db.pkl, but do not know how to retrieve the old project info into the GUI. Thanks in advance for your help. Huiying Dept. MB&B UC Irvine

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Re: [phenixbb] Modifications for Ca-binding site
by Nigel Moriarty 30 Dec '15

30 Dec '15

Jacob Once again Boaz is leading you in the correct direction. You did send me a *.metals.edits file. You just need to change the ideal distances in this file. On another point, I ran a refinement with your inputs and the values don't seem a long way off. However, I'd wait for Pavel to take a look because the density around the Calcium ion itself seems unusual. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, 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 On Wed, Dec 30, 2015 at 6:27 AM, Boaz Shaanan <bshaanan(a)bgu.ac.il> wrote: > Hi Jacob, > > My guess is that answer (or hint) is here (taken from this link : > https://www.phenix-online.org/documentation/faqs/refine.html#targets-and-re…): > > > *I have ions very close to water molecules/protein atoms, and > phenix.refine keeps tring to move them apart. How can I prevent this?* > > Use phenix.ready_set or *phenix.metal_coordination* to generate custom > bond (and optionally, bond angle) restraints, which will be output to a > parameter file ending in ".edits". If you are using the PHENIX GUI, there > is a toolbar button for ReadySet in the phenix.refine interface, which will > automatically load the output files for use in phenix.refine. > > I have not used it myself but I assume that the sigmas for the restraints > would be in the *.edits files that you'll generate. > > Hope this helps. > > Boaz > > > > > > > > > > *Boaz Shaanan, Ph.D. Dept. of Life > Sciences Ben-Gurion University of the > Negev Beer-Sheva > 84105 > Israel > E-mail: > bshaanan(a)bgu.ac.il <bshaanan(a)bgu.ac.il> Phone: 972-8-647-2220 Skype: > boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 * > > > > > > ------------------------------ > *From:* Keller, Jacob [kellerj(a)janelia.hhmi.org] > *Sent:* Wednesday, December 30, 2015 4:09 PM > *To:* Nigel Moriarty > *Cc:* בעז שאנן; phenixbb(a)phenix-online.org > *Subject:* RE: [phenixbb] Modifications for Ca-binding site > > How does one change the ideal bond length/sigma in Phenix? > > > > JPK > > > > *From:* Nigel Moriarty [mailto:[email protected]] > *Sent:* Tuesday, December 29, 2015 10:12 AM > *To:* Keller, Jacob > *Cc:* Boaz Shaanan; phenixbb(a)phenix-online.org > *Subject:* Re: [phenixbb] Modifications for Ca-binding site > > > > Jacob > > > > Boaz has some sage advice. I recommend not excluding the Ca-O coordination > but changing the ideal to better reflect the distances in your files. > > > > PS I'd also like the PDB files, directly, so as not to put noise on the > list. > > > Cheers > > > > Nigel > > > > --- > > Nigel W. Moriarty > Building 33R0349, 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 > > > > On Tue, Dec 29, 2015 at 5:49 AM, Keller, Jacob <kellerj(a)janelia.hhmi.org> > wrote: > > Well, I think it's more of a data-vs-geometry battle, with the geometry > dragging in the side chains towards the calciums, and the data pulling them > out. When I real-space refine them in Coot, some of the Ca-O distances are > pretty different from the "ideal" values. Maybe I could just exclude them > from xyz refinement in Phenix after making sure they're correct in Coot? > I'll give that a shot. > > Kol tuv, > > Jacob > > > > > > -----Original Message----- > From: Boaz Shaanan [mailto:[email protected]] > Sent: Tuesday, December 29, 2015 7:52 AM > To: Keller, Jacob; phenixbb(a)phenix-online.org > Subject: RE: Modifications for Ca-binding site > > Hi Jacob, > > Sucking-up neighboring residues into the Calcium (or other heavier atoms) > density is a known issue. Turning-off the Ca-O or other distance restraints > around the Calcium is the last thing you want to do, in my experience. > You'd better check those distance restraints and verify that they're > compatible with the distances in other (preferably high resolution, of > course) structures with calcium binding sites similar to yours and then > make sure they're given the appropriate weight during refinement. That's my > view but Pavel will give you more advices I'm sure. > > Cheers, > > Boaz > > > Boaz Shaanan, Ph.D. > Dept. of Life Sciences > Ben-Gurion University of the Negev > Beer-Sheva 84105 > Israel > > E-mail: bshaanan(a)bgu.ac.il > Phone: 972-8-647-2220 Skype: boaz.shaanan > Fax: 972-8-647-2992 or 972-8-646-1710 > > > > > > ________________________________________ > From: phenixbb-bounces(a)phenix-online.org [ > phenixbb-bounces(a)phenix-online.org] on behalf of Keller, Jacob [ > kellerj(a)janelia.hhmi.org] > Sent: Tuesday, December 29, 2015 4:44 AM > To: phenixbb(a)phenix-online.org > Subject: [phenixbb] Modifications for Ca-binding site > > I am getting a lot of problems with my calcium binding sites--there is > clear density for the calciums and the protein side chains, but Phenix > keeps sucking the side chains out of their density towards the calciums and > also the calciums show some positive difference density, perhaps due to > too-high b-factors (or potentially partial occupancy by Na?). I think what > might work best is to turn off the Ca-O bond length restraints somehow, but > don't see where/how to do that. I tried releasing them from geometrical > restraints, but that made things worse, since things went haywire in the > sidechains themselves. > > Is it possible to make Phenix ignore the Ca-O bond distance restraints? > > JPK > > ******************************************* > Jacob Pearson Keller, PhD > Looger Lab/HHMI Janelia Research Campus > 19700 Helix Dr, Ashburn, VA 20147 > email: kellerj(a)janelia.hhmi.org > ******************************************* > > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > Unsubscribe: phenixbb-leave(a)phenix-online.org > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > Unsubscribe: phenixbb-leave(a)phenix-online.org > > >

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Modifications for Ca-binding site
by Keller, Jacob 30 Dec '15

30 Dec '15

I am getting a lot of problems with my calcium binding sites--there is clear density for the calciums and the protein side chains, but Phenix keeps sucking the side chains out of their density towards the calciums and also the calciums show some positive difference density, perhaps due to too-high b-factors (or potentially partial occupancy by Na?). I think what might work best is to turn off the Ca-O bond length restraints somehow, but don't see where/how to do that. I tried releasing them from geometrical restraints, but that made things worse, since things went haywire in the sidechains themselves. Is it possible to make Phenix ignore the Ca-O bond distance restraints? JPK ******************************************* Jacob Pearson Keller, PhD Looger Lab/HHMI Janelia Research Campus 19700 Helix Dr, Ashburn, VA 20147 email: kellerj(a)janelia.hhmi.org *******************************************

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RSRZ in Phenix?
by Keller, Jacob 30 Dec '15

30 Dec '15

Dear Crystallographers, Is there any place in Phenix where RSRZ or a similar measure is shown? All the best, Jacob Keller ******************************************* Jacob Pearson Keller, PhD Looger Lab/HHMI Janelia Research Campus 19700 Helix Dr, Ashburn, VA 20147 email: kellerj(a)janelia.hhmi.org *******************************************

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Coot add DNA base or mutate DNA base
by Xiao Lei 25 Dec '15

25 Dec '15

Hi All, I'm using coot to build DNA, when I click "add residue" to one end of DNA, coot automatically add an "A" base to it, but I'd like to add "G" base, is it a way to mutate the A base to G base, I know coot can mutate amino acid residue, is is a way to mutate DNA residue in coot GUI? Thanks ahead. Xiao

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Trouble refining following molecular replacement
by Tyler Liban 22 Dec '15

22 Dec '15

Hello all, We are currently working with a dataset for a trimeric protein complex at 3A that is giving us some issues. The space group seems to be P21 ( 59.5, 61.6, 99.6 , 90, 98, 90) and the Mathews coefficient (2.6) suggests 2 copies of this 35kDa complex in the ASU. We are using a homolog as the search model that is 80% identical, and Phaser is able to find 2 molecules in P21 when searching in the same point group and gives good TFZ scores (TFZ = 9 or 10). However, these solutions do not refine well following Phaser (Rfree ~.50), and after removing parts of the model that look incorrect the Rfree still stays between .46 and .50. We ran the data through Xtraige and saw no signs of twinning based on the L-test, and the Patterson map has one small off-origin peak that is only 5%, indicating that there is no significant pseudotranslation. We have also tried finding MR solutions in P1, but haven’t had much luck. Any ideas on where to go from here would be greatly appreciated. Tyler

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command line for reflection file editor
by Zheng Zhou 22 Dec '15

22 Dec '15

Dear phenix experts, How do I combine Rfree from one dataset with the new dataset under command line? I can do this using reflect file editor GUI easily. But I tried to look up the documentation for phenix.reflection_file_converter and could not find a solution. I am trying to write a script to handle several datasets scaled from HKL2000. I could do this easily in ccp4, but looks like Ctruncate's French&Wilson made the completeness worse than scale.log. Thanks for your help in advance. Best, Zheng

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mmCIF file must contain at least one data block
by Ursula Schulze-Gahmen 18 Dec '15

18 Dec '15

I am getting this thie error message mmCIF file must contain at least one data block when trying to run readyset or phenixrefine I cannot find anything wrong wqith my input files. What is the problem? Ursula -- Ursula Schulze-Gahmen, Ph.D. Project Scientist UC Berkeley, QB3 360 Stanley Hall #3220 Berkeley, CA 94720-3220 (510) 643 9491

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remove old phenix version but keep the processed data
by Xiao Lei 17 Dec '15

17 Dec '15

Hi Phenixbb member, As I updated Phenix version on my Macbook pro (OS X 10.10), I found the newer version phenix did not automatically replace the old versions. Is there a way to remove the old version Phenix safely and only keep the newer version, but at the same time keep the processed data (data from phenix refine and xtriage)? Thanks ahead. Xiao

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ML with Twinning?
by Keller, Jacob 16 Dec '15

16 Dec '15

Is Phenix able yet to use the ML target function with twinned data? Is it in the works? All the best, Jacob Keller ******************************************* Jacob Pearson Keller, PhD Looger Lab/HHMI Janelia Research Campus 19700 Helix Dr, Ashburn, VA 20147 email: kellerj(a)janelia.hhmi.org *******************************************

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