- phenixbb - phenix-online.org

Refinement of perfect twined data of P31/P32
by miyatake 23 Apr '13

23 Apr '13

Hello, Phenix users, Now I'm triying to refine almost perfect twining data (mixing of P31 and P32). It has a twining operation of (h, k, l) = (-h, -k, l), detected by the xtriage program. The data qualigy seems to be good, deflacting to 1.6A resolution with Rmerge ~ 5%. When I refined the MR structures with phenix.refine, however, the model geometries have been worse as over the 20% residues fall into disallowed Ramachandran region, and Rfree stacked around 30%. I tried many options such as real space refinement, SA, bad rotamer fixation, NCS restrain,,.., but they seem to be not so effective as usual twininig cases.. One molecule consists of 202 residues, and three molecules are inolved in AU. Of course, I used the twin option (-h, -k, l) during the refinement. Manual collection of the models could not improve the model anymore. Would anyone please advise me how should I refine the twinned data? Sincerely, Hideyuki, M.

3 2

Turn off non-bonded interactions to measure distance in case of unknown interaction
by Edward A. Berry 23 Apr '13

23 Apr '13

I have a phenix-specific question and a general chemistry question. In a ligand-bound structure, S in an aromatic ring (substituted thiophene) may be H-bonding NH1 of arginine guanidino group. The general question is whether thiophene S can act as H-bond acceptor (assuming one lone pair is in the aromatic pi system for a total of 6 e, the other lone pair is available as H-bond acceptor?). The phenix-specific question involves whether non-bonded interactions will push the atoms apart during refinement, and how to turn off the nonbonded interaction between these two atoms to allow the xray data to determine the position. Under geometry_restraints.edits I define a bond, but give a very large sigma of 1A. Will this effectively remove non-bonded interactions between these two atoms?

4 8

dummy atom v.s. model with zero occupancy.
by Jinzhong Lin 22 Apr '13

22 Apr '13

Dear PHENIX users, In phenix, in order to improve bulk solvent model when the model is not complete, you can add dummy atom and set "refinement.mask.ignore_zero_occupancy_atoms=False". My question is that can I just put a model ( I know the approximate position for the model) there instead of dummy atoms and set all atoms in the model zero occupancy and keep the same setting. Will I get the same result? I suspect that model will still be used to calculate the Fc even though the occupancy is zero, so the map will be severely model biased. Lithlin

3 6

Re: [phenixbb] how to fix a side chain not to be refined?
by Rongjin 20 Apr '13

20 Apr '13

Hi Nat, You are right. By turning off the "fix rotamers" the Arg does not move any more. Best Rongjin ------------------ Original ------------------ From: "Nathaniel Echols"<nechols(a)lbl.gov>; Date: Apr 20, 2013 To: "PHENIX user mailing list"<phenixbb(a)phenix-online.org>; Subject: Re: [phenixbb] how to fix a side chain not to be refined? On Fri, Apr 19, 2013 at 2:14 PM, Rongjin <guanrj(a)foxmail.com> wrote: > I have an Arg with flexible side chain, close to an iodide ion. Every time > I refine it, the side chain of Arg will push the iodide ion away, even I > selected The syntax below looks correct to me, although you should probably do the same thing for the ADP selection, but it's a little disturbing that it's doing this. Do you have rotamer correction turned on? That may be the problem, if it is trying to fit to the difference density (I don't think it's very aware of nearby atoms). -Nat > the Arg not to be refined: > > refine { > strategy = *individual_sites individual_sites_real_space rigid_body \ > *individual_adp group_adp tls *occupancies group_anomalous > sites { > individual = "not (chain A and resid 40)" > } > } > > > The residue 40 in Chain A is that Arg close to the Iodide. Is this selection > correct? > How to fix the side chain of Arg in refinement? > > I attached two pictures, one before and one after refinement, the local area > of the Arg > and the iodide. The iodide is bound to an Asn residue of one symmetric > molecule. > > Thank you > Rongjin Guan > > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb .

2 1

how to fix a side chain not to be refined?
by Rongjin 20 Apr '13

20 Apr '13

Hello I have an Arg with flexible side chain, close to an iodide ion. Every time I refine it, the side chain of Arg will push the iodide ion away, even I selected the Arg not to be refined: refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous sites { individual = "not (chain A and resid 40)" } } The residue 40 in Chain A is that Arg close to the Iodide. Is this selection correct? How to fix the side chain of Arg in refinement? I attached two pictures, one before and one after refinement, the local area of the Arg and the iodide. The iodide is bound to an Asn residue of one symmetric molecule. Thank you Rongjin Guan

3 2

Unusually low B factors
by Brennan Bonnet 18 Apr '13

18 Apr '13

Hi all, I have produced xenon derivatives for SAD phasing of several standard proteins by placing them under xenon gas pressure and then immediately flash freezing in liquid nitrogen. Everything has worked out nicely as far as successful phasing, nice models, and low R factors. Now I've noticed that the B values have decreased from initial processing values. Several rounds of manual changes and phenix.refine have caused B values to decrease each round of refinement to values of around 10 (I guess 20 is a more common value). Does anyone know why this is happening or what the explanation might be? I'm not sure what other information to include so please contact to discuss further. Thanks! ~Brennan

3 5

Exclude atoms from refinements
by Simon Kolstoe 17 Apr '13

17 Apr '13

Hi, I want to exclude some atoms from refinement altogether in phenix.refine. Googling this I came up with the following link: http://phenix-online.org/pipermail/phenixbb/2011-December/018020.html however was wondering how you implement this sort of thing in the GUI? Thanks, Simon --------------------------------------------------------------- Dr. Simon Kolstoe Honorary Senior Research Associate Laboratory for Protein Crystallography Wolfson Drug Discovery Unit University College London Rowland Hill Street, London, NW3 2PF http://www.ucl.ac.uk/~rmhasek ---------------------------------------------------------------

3 4

Pause phenix runs
by Mark J van Raaij 13 Apr '13

13 Apr '13

Just wondering if being able to pause a phenix run would be something useful. Currently, it appears one can only abort. Currently doing refinement of a large structure, and doing several simultaneous runs with different options is slowing down the computer too much. Individual runs take about 72 hrs, so o/n is not an option (o/weekend will be...) (or is it possible and I have missed it?) if the FPLC can do it, why not phenix? Seriously, I don't know how easy or difficult it would be to implement, or if paused runs would still take up too many resources, but it seems like something that might be useful - i.e. set several long runs running, and temporarily interrupt them for other jobs on the same computer (like watching youtube movies, as some people seem to think I do all day...) Mark J van Raaij Lab 20B Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij

5 4

Problem with MR-Rosetta
by Marta Sanz Gaitero 13 Apr '13

13 Apr '13

Hi to everyone, I've have a little problem running MR-Rosetta in Phenix. Some weeks ago, I tried to solve some data which didn't have very much identity with any PDB model using MR-Rosseta. The program started running but after a few hours it stopped suddenly. To check if the problem was that it was not possible to solve my data because they were very complicated or if something was going wrong with MR-Rosetta, I decided to run it using model data. I runned it using the mtz of a protein we had already solved in the lab, its sequence, and its own PDB file, generated after solving it. After 10 minutes, the program stops when it's starting the rebuild step. I think the program shouldn't have any problem to solve this data, since the model used for molecular replacement is exactly the same protein in the mtz, so I wonder if i'm doing something wrong. If someone could gave me any idea which helped me to solve the problem i would be very grateful. I attatch a snapshot of the error. Thank you in advance, Regards, Marta

2 1

Re: [phenixbb] base stacking
by Ed. Pozharski 11 Apr '13

11 Apr '13

I wonder whether something simple like restraining a model to that of an ideal dna (a la den refinement) would do the trick with existing tools. -------- Original message -------- From: Nathaniel Echols <nechols(a)lbl.gov> Date: 04/10/2013 7:27 PM (GMT-05:00) To: PHENIX user mailing list <phenixbb(a)phenix-online.org> Subject: Re: [phenixbb] base stacking On Wed, Apr 10, 2013 at 4:09 PM, jp d <yoyoq(a)yahoo.com> wrote: is there a way to do base stacking in phenix ? If you mean restraints on base stacking, no, we don't have anything like this right now. The only implementation of this anywhere, as far as I know, is the one from your (Noller) lab, but (aside from the lack of an explicit license) the fact that it's derived from CNS makes me very reluctant to even look at the code. However, if anyone has the derivation for the restraint energy function, we'd be happy to consider adding this to Phenix - we need to make a lot of changes to how we handle base-pairing anyway. -Nat

2 1