December 2015 - phenixbb - phenix-online.org

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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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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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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