- phenixbb - phenix-online.org

hydrogen nomenclature
by Patrick Loll 23 Oct '12

23 Oct '12

Hi, I'm trying to sort out some monomer libraries for a high-resolution refinement involving non-canonical amino acids, but now I've become side-tracked with a hydrogen nomenclature issue that seems to affect even canonical amino acids. I will use the example of L-leucine to illustrate: In the CCP4 monomer library LEU.cif, the two hydrogens on CB are named HB1 and HB2. However, if I look at the LEU entry on the RCSB PDB site, these two hydrogens are named HB2 and HB3. Looking at pdbe.org is not too helpful, since it lists those two hydrogens as HB2 and HB3, but includes alternate "PDB names" of HB1 and HB2. Similar situations pertain for other atoms and other residues. Presumably I need to stick with the nomenclature found in the monomer library in order for refinement to work properly; but will this come back to bite me later when I submit coordinates to the PDB? Any insights welcome. Thanks, Pat

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Durandal clustering applied to homology models
by Quentin Delettre 22 Oct '12

22 Oct '12

Dear Phenix users, I am new to phenix and the Durandal tool, i would like to know if Durandal is an appropriate way to cluster many homology models of a protein. And if so, what is the syntax of the output ? The man page does not provide any information beside inputs commands. Thanks.

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problem installing Phenix 1.8.1 on Fedora16
by Marianna Biadene 22 Oct '12

22 Oct '12

Dear all, I am trying to install Phenix 1.8.1-1168 on my Linux 64bit, Fedora 16. If I try to install it in the default directory (/usr/local) I have no problem, but when I try to install it in /usr/local/bin using the command written in the documentation (http://www.phenix-online.org/documentation/install.htm) ./install --prefix=</usr/local/bin> I got the following error message: -bash: syntax error near unexpected token `newline' I am not a super expert in Linux and I have tried to search in Internet for a solution but I am lost. Any idea of how could I solve this problem? Thanks a lot, Marianna -- Dr. Marianna Biadene Division of Biological Chemistry - Group Prof. Scheffzek Biocenter Medical University Innsbruck Innrain 80 / 4 6020 Innsbruck Austria Phone: +43 512 9003 70336

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xyz and adp weight optimisation
by Alex Theodossis 19 Oct '12

19 Oct '12

Dear bb, I have made use of the target weight optimisation feature with great results. The question is, having optimised these weighting terms, how can I use the optimised values in subsequent runs without having to keep the optimisation option switched on? In the last round of refinement I get: Best XYZ weight: 9.000 Best ADP weight: 0.695 But the output .eff file does not seem to have saved these values for use in subsequent refinements: target_weights { optimize_xyz_weight = True optimize_adp_weight = True wxc_scale = 0.5 wxu_scale = 1 wc = 1 wu = 1 fix_wxc = None fix_wxu = None Is it appropriate to enter the optimised values in the fix_wxc and fix_wxu fields? Thanks in advance

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Re: [phenixbb] Metal Coordination and symmetry operation
by Pavel Afonine 18 Oct '12

18 Oct '12

Hi Alex, thanks for the file - I will have a closer look. Did you mean the restraint did not work or it worked but you wanted something else? (I'm just trying to understand if this is a Phenix problem that we need to fix). Pavel On 10/18/12 10:30 PM, Alex Theodossis wrote: > Hi Pavel, > > thanks for the info. With it I was able to correctly define the > symmetry-related links as per this example: > > refinement.geometry_restraints.edits { > bond { > action = *add > atom_selection_1 = name ZN and chain C and resname ZN and resseq > 1 > atom_selection_2 = name NE2 and chain A and resname HIS and altid > A and resseq 39 > symmetry_operation = -x+1,y+1/2,-z+1/2 > distance_ideal = 2.030000 > sigma = 0.050 > } > > Unfortunately, this didn't have the desired result. Instead, the > addition of riding hydrogens fixed the problem. > I've also attached the relevant fragment of the refined model as > requested. > > Cheers, > > Alex > > > > On 17 October 2012 13:04, Pavel Afonine <pafonine(a)lbl.gov > <mailto:[email protected]>> wrote: > > Hi Alex, > > Nigel is the best person to reply, so he may provide more > comments. My understanding is that phenix.metal_coordination > command (or whatever the equivalent click in the GUI is) should > account for symmetry related atoms. If not you can fix it > manually. First create edits file using phenix.metal_coordination > and then add symmetry related bonds as described here: > > http://www.phenix-online.org/documentation/refinement.htm#anch353 > > Also, could you please send me the PDB file or its portion > containing relevant to your question atoms and I will have a > closer look? > > Pavel > > > On 10/16/12 6:33 PM, Alex Theodossis wrote: >> >> Dear bb, >> >> I am trying to refine a Zn ion coordinated by symmetry >> related residues. To avoid groups being pushed away. I have >> use phenix.metal_coordination to >> generate the necessary link edits. However only non-symmetry >> related interactions are accounted for. Is there a relevant >> option I can switch on? >> Alternatively, does anyone have an example of the syntax >> required to define the necessary symmetry operations in the >> elbow.edits file? >> >> Thanks in advance. >> >> >> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org <mailto:[email protected]> >> http://phenix-online.org/mailman/listinfo/phenixbb > >

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Re: [phenixbb] Metal Coordination and symmetry operation
by Alex Theodossis 18 Oct '12

18 Oct '12

> > Dear bb, > > I am trying to refine a Zn ion coordinated by symmetry related residues. > To avoid groups being pushed away. I have use phenix.metal_coordination to > generate the necessary link edits. However only non-symmetry related > interactions are accounted for. Is there a relevant option I can switch on? > Alternatively, does anyone have an example of the syntax required to > define the necessary symmetry operations in the elbow.edits file? > > Thanks in advance. >

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Re: [phenixbb] Table 1 stastics
by Nathaniel Echols 18 Oct '12

18 Oct '12

On Thu, Oct 18, 2012 at 8:45 AM, Katherine Sippel <katherine.sippel(a)gmail.com> wrote: > Part of the problem could lie in whether he input the original mtz as > intensities or not. In older versions of phenix some intensities were > dropped if they were below the cutoff and particularly for high res data the > completeness would go down significantly. I know you have implemented the > French and Wilson conversion in the newer versions but if he comes from a > lab like my old one and is refining off of intensities that could be the > culprit. This is a good point, but it depends on the version of Phenix, the type of input data, and how the data file was processed. I checked my code for Table 1 and if the input data are intensities, the negative observations should *not* be discarded. The same goes for phenix.refine, among other programs. However, if amplitudes were used as input for Table 1, and had previously been filtered through a program that does not perform the French & Wilson treatment, they may be missing some data (most of which will probably be at high resolution). One caveat: the reflection file editor in Phenix has an option to convert intensities to amplitudes, but this will not run F&W, which is perhaps a bug... -Nat

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Table 1 stastics
by Andrew Waight 18 Oct '12

18 Oct '12

Hi All, Thanks for Phenix! Anyway quick question, I tried out the "generate Table1" utility for fun and noticed that my I/SigI and completeness do not match what is found in my XSCALE file. From Table 1 Completeness (%) 98.62 (90.57) Mean I/sigma(I) 7.39 (1.59) Wilson B-factor 59.78 R-sym R-factor 0.2006 (0.3275) R-free 0.2241 (0.3739) From XSCALE SUBSET OF INTENSITY DATA WITH SIGNAL/NOISE >= -3.0 AS FUNCTION OF RESOLUTION RESOLUTION NUMBER OF REFLECTIONS COMPLETENESS R-FACTOR R-FACTOR COMPARED I/SIGMA R-meas CC(1/2) Anomal SigAno Nano LIMIT OBSERVED UNIQUE POSSIBLE OF DATA observed expected Corr 20.00 313 69 72 95.8% 3.6% 4.6% 313 30.88 4.3% 99.9* 8 0.725 54 10.00 2174 471 471 100.0% 3.9% 4.8% 2174 28.71 4.4% 99.8* 34* 0.972 382 6.00 8195 1983 1992 99.5% 4.7% 5.3% 8160 20.70 5.4% 99.8* 12* 0.913 1299 5.00 8055 1818 1820 99.9% 7.0% 6.9% 8051 17.73 7.9% 99.5* 7 0.892 1337 4.50 7207 1634 1636 99.9% 6.0% 6.2% 7207 20.06 6.8% 99.6* -1 0.824 1163 4.00 9603 2479 2521 98.3% 6.8% 6.7% 9536 17.05 7.9% 99.4* -2 0.819 1369 3.60 13641 3141 3156 99.5% 9.6% 9.5% 13621 13.71 11.0% 99.1* -2 0.799 2073 3.20 22112 4948 4951 99.9% 16.5% 16.6% 22083 8.82 18.8% 98.1* 4 0.810 3383 3.00 14155 3550 3579 99.2% 27.8% 27.7% 14058 5.45 32.1% 94.6* -1 0.742 1875 2.80 19676 4584 4611 99.4% 44.9% 46.2% 19604 3.71 51.2% 88.5* 3 0.740 2750 2.60 26749 6192 6202 99.8% 76.3% 78.4% 26686 2.20 87.2% 71.8* 1 0.717 3598 2.40 33999 8339 8388 99.4% 130.9% 132.7% 33810 1.26 150.6% 48.5* 1 0.671 4170 2.30 22347 5332 5348 99.7% 198.4% 206.4% 22276 0.85 227.7% 31.5* 0 0.623 2685 total 188226 44540 44747 99.5% 9.0% 9.4% 187579 7.09 10.3% 99.8* 2 0.755 26138 How does Phenix compute these parameters? Obviously my I/sigI has gotten much better (1.59 versus 0.85) but the scaling statistics should be the correct ones. Thanks, Drew

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close contact and torsion angle
by hchxia＠ujs.edu.cn 12 Oct '12

12 Oct '12

Hi, There are some close contacts (hydrogen bonds) in my refined model. Can I just ignore it, delete it or what? I added hydrogen for refinement since the resolution is 1.47 A. Should I remove all these added hydrogens and refine again? Second question is there are several outilers of torsion angles (6 from Ramachandran plot in coot ). But 16 are outside expected Ramachandran regions from the validation report from PDB bank(ADIT) . What is the cause? And should I re-refine to correct them? Or just go ahead to deposit it? Thanks! chuan

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how to continue an aborted phenix.refine
by hchxia＠ujs.edu.cn 11 Oct '12

11 Oct '12

Hi! I aborted a run of phenix.refine due to linux problem. Is there a way to continue from the aborted point to finish the run? or I have to start from 0 to rerun it ? Thanks a lot! chuan

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OS X 10.8 Mountain Lion
by Alexander Batyuk 10 Oct '12

10 Oct '12

Dear all, Could anybody confirm that Phenix does or does not run on OS X 10.8 Mountain Lion, please? Best wishes, Alex -- Alex Batyuk The Plueckthun Lab www.bioc.uzh.ch/plueckthun

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labelit and latest mosflm
by "Weiergräber, Oliver H." 04 Oct '12

04 Oct '12

Hello, the labelit.index executable provided with phenix 1.8.1 has a problem with the latest mosflm (7.0.9, as included in ccp4 6.3.0): "MosflmVersionError: mosflm versions after 7.0.8 not supported" Is there any reason to believe that mosflm 7.0.9 has really become incompatible with labelit? If not, can the version check be overridden as a temporary fix? Best, Oliver ================================================ PD Dr. Oliver H. Weiergräber Institute of Complex Systems ICS-6: Structural Biochemistry Tel.: +49 2461 61-2028 Fax: +49 2461 61-9540 ================================================ ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Kennen Sie schon unsere app? http://www.fz-juelich.de/app

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automr
by Shya Biswas 02 Oct '12

02 Oct '12

Hi all, I was wondering if anyone knows how to change the packing clash distance in Automr gui. Thanks, Shya

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changes from 1.8.1-1161 to official 1.8.1?
by Eric Williams 02 Oct '12

02 Oct '12

Where any major bugs fixed between the 1161 nightly build and the official 1.8.1 release? I have a large batch job running that uses 1161. If the squashed bugs are big enough, it might be worth stopping the job to install the new release. Otherwise, I'll just let it run to completion. Thanks. :) Eric

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Phenix version 1.8.1 released
by Paul Adams 01 Oct '12

01 Oct '12

The Phenix developers are pleased to announce that version 1.8.1 of Phenix is now available. Binary installers for Linux, Mac OSX, and Windows platforms are available at the download site: http://phenix-online.org/download/ Some of the new features in this version are: Graphical interface: ==================== - New GUIs: phenix.find_alt_orig_sym_mate General: ======== - Multiple bug fixes - New commands: phenix.erraser, phenix.merging_statistics - Added geometry restraints for over 400 non-standard amino acid entries Refinement: =========== - Overall B-cart now applied to individual atomic B-factors (restores pre-1.8 behavior) - Improvements to torsion NCS rotamer correction - Real-space refinement (including rotamer fitting) for twinned data New command: ============ - phenix.erraser: - New method from Fang-Chieh Chou and Rhiju Das (Stanford) combining Rosetta nucleic acid rebuilding with phenix.refine (requires separate installation of Rosetta 3.4 or more recent) Molecular Replacement: ====================== - Phaser updated to version 2.5.2: - Scattering from HETATM records that represent modified amino acids (e.g. MSE/SeMet) included so that maps no longer show holes for these HETATM records in the model; occupancies will not be reset. - Packing test was incorrectly applied to reoriented molecules where there was PTNCS Experimental Phasing and Model Building: ======================================== - AutoSol: - Scale of derivative in SIR (for RIP phasing) can be set with keyword "derscale" - AutoBuild: - Unassigned chains are now given the segid of "UNK" and are normally given chain ID="U" Ligands: ======== - eLBOW: - New option, --multiple-planes, to generate planes around double bonds - Saturated rings now have dihedral restraints to maintain chair conformation - REEL: - View relationships between ligands using PubChem fingerprint and tanimoto score. Miscellaneous: ============== - phenix.real_space_correlation: - Simplified command-line behavior - phenix.merging_statistics (new command): - Calculate statistics for unmerged data in a variety of formats, including <I/sigmaI>, R-merge, R-meas, R-pim, CC1/2 - References: Diederichs K & Karplus PA (1997) Nature Structural Biology 4:269-275 Weiss MS (2001) J Appl Cryst 34:130-135. - phenix.kinemage: - Improvements to handling of alternate conformations. - phenix.combine_models: - Combine two models, taking the best parts of each to create a new model For a full list of changes see: http://www.phenix-online.org/documentation/CHANGES Please note that this publication should be used to cite use of Phenix: PHENIX: a comprehensive Python-based system for macromolecular structure solution. P. D. Adams, P. V. Afonine, G. Bunkóczi, V. B. Chen, I. W. Davis, N. Echols, J. J. Headd, L.-W. Hung, G. J. Kapral, R. W. Grosse-Kunstleve, A. J. McCoy, N. W. Moriarty, R. Oeffner, R. J. Read, D. C. Richardson, J. S. Richardson, T. C. Terwilliger and P. H. Zwart. Acta Cryst. D66, 213-221 (2010). Full documentation is available here: http://www.phenix-online.org/documentation/ There is a Phenix bulletin board: http://www.phenix-online.org/mailman/listinfo/phenixbb/ Please consult the installer README file or online documentation for installation instructions. Direct questions and problem reports to the bulletin board or: help(a)phenix-online.org and bugs(a)phenix-online.org Commercial users interested in obtaining access to Phenix should visit the Phenix website for information about the Phenix Industrial Consortium. The development of Phenix is principally funded by the National Institute of General Medical Sciences (NIH) under grant P01-GM063210. We also acknowledge the generous support of the members of the Phenix Industrial Consortium. -- 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 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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point-n-click installer is bjorking OS X Dock
by Scott Classen 26 Sep '12

26 Sep '12

Hello, After running the OS X point-n-click installer for the 1.8.1-1160 nightly build, the dock becomes unresponsive and I can no longer command+tab to switch between applications. I've reproduced this on 2 Macs. One running 10.8.2 and the other running 10.7.5 Relaunching Finder does not fix the proton dock/app switching Logging out and then logging back in fixes the problem. Scott

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den refinement with multiple reference files
by Andreas Förster 26 Sep '12

26 Sep '12

Dear all, I've started DEN refinement on a structure obtained by MR from data optimistically going to 3.8A. There are several chains of two kinds in the structure. High-resolution structures exist for both. How do I use two reference files for DEN refinement, and how do I assign which chain corresponds to which reference? (Currently, I'm using reference_file = None.) Thanks. Andreas -- Andreas Förster, Research Associate Paul Freemont & Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk

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Phenix cut out density labels choice
by Mikalai Lapkouski 21 Sep '12

21 Sep '12

Hello, I have a following issue with running Phenix.cutout density either on command line or in GUI. I have multiple columns in the mtz.file and I want to choose map coefficients FOFCWT_d1-8,PHFOFCWT_d1-8 for the difference map to be cut around pdb selection. I run a command: phenix.cut_out_density model.pdb my.mtz cutout_fix_position=True cutout_model_radius=10 cutout_type=model \ map_coeff_labels=FOFCWT_d1-8,PHFOFCWT_d1-8 Problem: The output cutout.mtz has FWT and PHWT (which I did not have at all in the input) and not my difference map coefficients, and obviously the map is not my difference map. In GUI is the same problem, I choose columns I need but it outputs FWT and PHWT again. Please, let me know what I am doing wrong. Thank you very much! Mikalai

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Combine map labels
by Mikalai Lapkouski 21 Sep '12

21 Sep '12

Hello, I have a following question. I have generated several Fo-Fc sa omit maps (FOFCWT, PHFOFCWT) for different portions of a DNA molecule. Now that I have each omit map as a separate file to display the whole DNA omit map I have to load them in coot one by one. Is there a way of how to combine all this maps into one file and have a single name for label columns so that the whole map will open at once? I managed to put them all in one file but column labels are separate: FOFCWT_1, PHFOFCWT_1 FOFCWT_2, PHFOFCWT_2...... Can they all go under FOFCWT, PHFOFCWT? Thank you very much for any suggestion Mikalai

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Specifying union of two chains in pdb_atom_selection
by Francis E Reyes 20 Sep '12

20 Sep '12

Hi all, I issue the following command to pdb_atom_selection but I get 0 atoms selected at the end? $ phenix.pdb_atom_selection refine_to_submit.pdb "chain X and chain B" refine_to_submit.pdb Monomer Library directory: "/usr/local/phenix-1.8-1069/chem_data/mon_lib" Total number of atoms: 3817 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 1800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1800 Classifications: {'RNA': 84} Modifications used: {'rna3p_pyr': 26, 'rna2p_pur': 5, 'rna3p_pur': 44, 'rna2p_pyr': 9} Link IDs: {'rna3p': 70, 'rna2p': 13} Chain: "X" Number of atoms: 1800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1800 Classifications: {'RNA': 84} Modifications used: {'rna3p_pyr': 26, 'rna2p_pur': 5, 'rna3p_pur': 44, 'rna2p_pyr': 9} Link IDs: {'rna3p': 70, 'rna2p': 13} chain X and chain B 0 atoms selected Thanks! F --------------------------------------------- Francis E. Reyes PhD 215 UCB University of Colorado at Boulder

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Scaling for Isomorphous Difference Maps
by Michael Thompson 20 Sep '12

20 Sep '12

Hello All, I'm currently using the GUI to calculate some Fo-Fo isomorphous difference maps. From looking at the Phenix documentation, it hasn't become apparent to me if the tool that performs this calculation automatically scales the two sets of amplitudes to one another, or if the input mtz files need to be scaled together elsewhere before running the map utility. Any info would be appreciated! Thanks, Mike -- Michael C. Thompson Graduate Student Biochemistry & Molecular Biology Division Department of Chemistry & Biochemistry University of California, Los Angeles miket(a)chem.ucla.edu

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Two versions of TFZ, molecular replacement
by 赵岩 19 Sep '12

19 Sep '12

Hi everyone, I am trying to solve a structure though molecular replacement and I have obtained a suspected solution. The header of the solution as follows, REMARK TITLE [no title set] REMARK Log-Likelihood Gain: 238.884 REMARK RFZ=10.9 TFZ=13.9 PAK=2 LLG=235 TFZ==5.0 LLG=239 TFZ==5.0 REMARK ENSEMBLE 1 EULER 15.53 0.10 344.54 FRAC -0.499 -1.000 -0.499 At first sight, the solution has no problem(TFZ>8), but the second and third TFZ are very low. For a correct solution, the later TFZs always higher than the first TFZ. So I don't konw how to understand the later TFZs and what extent I can refer to them. Thanks a lot! --

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advice for speeding up cif_as_mtz
by Eric Williams 19 Sep '12

19 Sep '12

I'm currently running cif_as_mtz and model_vs_data on the whole PDB as part of my dissertation. Time has become a critical concern, and cif_as_mtz (dev-1141) is running very, very slowly (1-4 minutes per entry). Here's how I'm calling it: phenix.cif_as_mtz <sf_cif_fn> --ignore-bad-sigmas --merge --remove-systematic-absences --map-to-asu --symmetry=<pdb_model_fn> --output-file-name=<sf_mtz_fn> I'm hoping that perhaps someone could help me determine which command line argument(s) could be removed to provide maximum speed-up. Thanks. :) Eric

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B-iso vs. B-aniso
by Yuri 18 Sep '12

18 Sep '12

Dear community, The protein model I am refining has 400 amino acids (3320 atoms). Some real quick calculations tell me that to properly refine it anisotropically, I would need 119,520 observations. Given my unit-cell dimension and space-group it is equivalent to about a 1.24 A complete data set. However, I have had a couple of cases where anisotropic B-factor refinement significantly improved R-work and R-free, while maintaining a reasonable R-gap, for lower resolution models (1.4-1.5 A, around 70,000 reflections). What is the proper way of modelling the B-factors? Any thoughts/opinions/call-outs from the community are welcome. Cheers, -- Yuri Pompeu

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Monitoring MR_ROSETTA progress on a cluster
by Dmitry Rodionov 17 Sep '12

17 Sep '12

Hi Tom, How are you doing? Sorry to bother you again. I got my hands on a login to local cluster (MOAB) and started MR_rosetta there as well. Problem is, I have hard time figuring out what it is doing at this moment and if everything is under control. All I see in the queue are the original submission and a process it spawned less then a minute later. While a day ago there were 30 processes (that's how much I can have). All mr_rosetta.log files end with a list of methods to be run. MR_ROSETTA_1/GROUP_OF_PLACE_MODEL_1/LIST_OF_JOBS_RUNNING says: /sb/home/drodionov/MR_ROSETTA_1/GROUP_OF_PLACE_MODEL_1/RUN_1 /sb/home/drodionov/MR_ROSETTA_1/GROUP_OF_PLACE_MODEL_1/RUN_FILE_1.log MISSING FINAL COUNT: 0 But the file happily exists : GROUP_OF_PLACE_MODEL_1/RUN_FILE_1.log .... Starting job 1000...Log will be: /sb/home/drodionov/MR_ROSETTA_1/GROUP_OF_PLACE_MODEL_1/RUN_1/REBUILD_IN_SETS_1/RUN_FILE_1000.log And that job successfully finished a while ago. Is everything ok with the run? Am I just being impatient? Thanks! Best regards, Dmitry

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