- phenixbb - phenix-online.org

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 07 Aug '14

07 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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