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Re: [phenixbb] phenixbb Digest, Vol 117, Issue 9
by Cesar Santiago 27 Aug '15

27 Aug '15

Hi Mark! Anybody for the 24th trip to Alba? I'll be away from the 1st - 16th of September but I can still arrange the trip before leaving. César. ------------------------------------------------------------------ Cesar Santiago, Ph. D. Dept. of Macromolecules Structure at CNB, CSIC. X-ray Crystallography Facility. Campus Universidad Autónoma. Madrid, 28049 csantiag(a)cnb.csic.es On Aug 27, 2015, at 6:42 AM, phenixbb-request(a)phenix-online.org wrote: > Send phenixbb mailing list submissions to > phenixbb(a)phenix-online.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://phenix-online.org/mailman/listinfo/phenixbb > or, via email, send a message with subject or body 'help' to > phenixbb-request(a)phenix-online.org > > You can reach the person managing the list at > phenixbb-owner(a)phenix-online.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of phenixbb digest..." > > > Today's Topics: > > 1. Re: phenix.refine automatic linking options (Engin ?zkan) > 2. external passive 3D monitor with macbook pro or imac for coot > and pymol stereo view (Xiao Lei) > 3. Rank-scaled map (Jianghai Zhu) > 4. Re: Rank-scaled map (Pavel Afonine) > 5. Re: on the starting mtz file for phenix refine (Pavel Afonine) > 6. Ligand addition in COOT for later refinement in Phenix.refine > (Manoj saxena) > 7. Re: Ligand addition in COOT for later refinement in > Phenix.refine (Oleg Sobolev) > 8. Computational Crystallography Newsletter - Volume 6, Number 2 > (Nigel Moriarty) > 9. Starting structure as reference model - crashing in 1.10-2142 > (Tristan Croll) > 10. Re: Starting structure as reference model - crashing in > 1.10-2142 (Pavel Afonine) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 20 Aug 2015 15:41:31 -0500 > From: Engin ?zkan <eozkan(a)uchicago.edu> > To: Billy Poon <bkpoon(a)lbl.gov> > Cc: PHENIX user mailing list <phenixbb(a)phenix-online.org> > Subject: Re: [phenixbb] phenix.refine automatic linking options > Message-ID: <55D63B7B.6000707(a)uchicago.edu> > Content-Type: text/plain; charset="utf-8"; Format="flowed" > > Dear Billy and Nigel, > > Thank you. Phenix.refine GUI in the latest nightly/release candidate no > longer has the master enable/disable button, and so the problem is resolved. > > Engin > > On 8/13/15 11:28 AM, Billy Poon wrote: >> Hi Engin, >> >> Thanks! We updated that part of the GUI so that it should be more >> intuitive. There is now a button that lets you apply automatic linking >> to all the components and a button that disables all automatic >> linking. You can, of course, still pick which components to enable by >> checking the specific boxes. >> >> On Tue, Aug 11, 2015 at 7:40 AM, Engin ?zkan <eozkan(a)uchicago.edu >> <mailto:[email protected]>> wrote: >> >> Dear Developers, >> >> Using the latest phenix nightly, I observed something odd in the >> phenix.refine UI, and I thought I should report it. If one >> unchecks Automatic ligand linking, this seems to not override its >> options, as the instructions in the Options window suggest. >> Specifically, if "Automatic Ligand Linking" is unchecked, but the >> "Link metals" is checked within its Options window, metal link >> restraints are still created. >> >> I checked the .geo file to confirm this. >> >> Thanks, >> Engin >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org <mailto:[email protected]> >> http://phenix-online.org/mailman/listinfo/phenixbb >> Unsubscribe: phenixbb-leave(a)phenix-online.org >> <mailto:[email protected]> >> >> >> > >

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Starting structure as reference model - crashing in 1.10-2142
by Tristan Croll 27 Aug '15

27 Aug '15

Hi, When I attempt to run a refinement in Phenix 1.10-2142 using the starting structure as a reference model, it crashes with the complaint that the reference (actually, the error states NCS - despite no NCS being present or enabled. I guess internally it's using the same code?) is too dissimilar to the model, and a calculated RMSD of >90 (degrees? I'm using torsion-angle restraints in any case). The same settings work without complaint on the same structure in dev-2006. I'm running from the GUI, checking "Reference model restraints" in the main phenix.refine window, and then "use starting model as reference" under "All parameters... Reference model restraints...". Thanks, Tristan

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Computational Crystallography Newsletter - Volume 6, Number 2
by Nigel Moriarty 25 Aug '15

25 Aug '15

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. July 2015 <http://www.phenix-online.org/newsletter/CCN_2015_07.pdf> Articles - A context-sensitive guide to RNA & DNA base-pair & base-stack geometry <http://www.phenix-online.org/newsletter/CCN_2015_07.pdf#page=22> Short Communications - New Phaser-MR search panel in Phenix <http://www.phenix-online.org/newsletter/CCN_2015_07.pdf#page=7> - Quantum chemical techniques for minimising ligand geometries in the active site <http://www.phenix-online.org/newsletter/CCN_2015_07.pdf#page=10> - 13 typical occupancy refinement scenarios and available options in *phenix.refine* <http://www.phenix-online.org/newsletter/CCN_2015_07.pdf#page=12> Fitting tips #10 – How do your base pairs touch and twist? <http://www.phenix-online.org/newsletter/CCN_2015_07.pdf#page=3> 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

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Ligand addition in COOT for later refinement in Phenix.refine
by Manoj saxena 25 Aug '15

25 Aug '15

Greetings I am trying to place a ligand (CIT) in a protein model that already have some citrate ligands placed. I am doing this using Coot's option "get monomer", and after the fitting of ligand in the density I tried to refine the model using the ligand and the protein pdb as input models. Refinement did not start and I got an error message in Phenix- "Number of groups of duplicate atom labels:....." Could someone please explain how could I get past this error message and what is the correct way to add a ligand to a model that already has some of the ligands of the same type. Many thanks in advance Regards Manoj Saxena

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on the starting mtz file for phenix refine
by Smith Lee 22 Aug '15

22 Aug '15

Dear All, In the on-line phenix document, there is, "Should I use the MTZ file output by phenix.refine as input for the next round of refinement? The only time this is necessary is when you refined against a dataset that did not include R-free flags, and let phenix.refine generate a new test set. In this case, you should use the file ending in "_data.mtz" for all future rounds of refinement. You do not need to update the input file in each round, as the actual raw data (and R-free flags) are not modified". When we have phenic adding R-free flgas in the first time we process the mtz data by phenix.refine, besides the *data.mtz, phenix also create a *.mtz. In the future phenix.refine, can I refine by always using the *.mtz created in the R-free flag adding step, rather than refine by always using the *data.mtz created in the R-free flag adding step? What is the difference between that *data.mtz and that *.mtz? And what is the side-effect if in the future steps I refine by always using the *.mtz created in the R-free flag adding step? Best regards. Smith

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Rank-scaled map
by Jianghai Zhu 22 Aug '15

22 Aug '15

Hi, I know PHENIX can calculate a rank-scaled density map. Could anyone inform me which program in PHENIX actually does this? Thanks. Best, --Jianghai

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external passive 3D monitor with macbook pro or imac for coot and pymol stereo view
by Xiao Lei 21 Aug '15

21 Aug '15

Dear phenixbb members, I'm thinking to view stereo 3D structure on coot and pymol with passive 3D monitor, does anyone have experience of doing this with a macbook pro or imac and a external passive 3D monitor connected using HDMI port? If mac does not support this, should I buy a PC and a passive 3D monitor to do it? Thanks ahead. Xiao

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phenix.refine automatic linking options
by Engin Özkan 21 Aug '15

21 Aug '15

Dear Developers, Using the latest phenix nightly, I observed something odd in the phenix.refine UI, and I thought I should report it. If one unchecks Automatic ligand linking, this seems to not override its options, as the instructions in the Options window suggest. Specifically, if "Automatic Ligand Linking" is unchecked, but the "Link metals" is checked within its Options window, metal link restraints are still created. I checked the .geo file to confirm this. Thanks, Engin

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Phenix on Mageia
by Marie Elizabeth Fraser 20 Aug '15

20 Aug '15

Hello, We are having a problem getting the display of the cycles of Phenix running on our Linux machines. I am running Mageia 4, but the problem first appeared when I added a new student and he started to run Phenix on Mandriva. When I changed to Mageia 4, I had to do a clean install, so everyone got new home directories. Then the problem appeared for all of us. This has gone in as a bug report (and I can send the message if that would help). The response was that we were using a character like “é” in the filename or directory. I do not think that we are. However, at the bottom of the bug report it does say "LATIN CAPITAL LETTER A WITH RING ABOVE = Ã…”, which sounds like the symbol for Angstrom. Has anyone else seen a similar problem and been able to fix it? Thank you, Marie

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planarity between atoms of neighboring residues
by Agnieszka Kiliszek 20 Aug '15

20 Aug '15

Dear All, I would like to add restrains between two residues. I was trying to use geometry restrains planarity but I don't know how to select atoms from two different residues. I mean, I have: chain A resid 1 atoms: C5' C' and O1' chain A resid 2 atom: N1' I would like all 4 atoms to be planar. I found example only for atoms from the same residue. Can you help me? Agnieszka

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