- phenixbb - phenix-online.org

alternate side chains conjugated with water molecules
by Jorge Iulek 31 May '15

31 May '15

Dear all, I have a 1.70 A resolution dataset in which I observe, with certain confidence, that some (few) side chains are alternated with waters. Though managing to tie occupancies of each alternate side chain with a water molecule to give an overall occupancy of 1.00, phenix refine still pushes them (water from side chain) apart as if there were bumping restraints (but their occupancies sum up to no more than 1.00). The closest to this I could find is: http://www.phenix-online.org/pipermail/phenixbb/2009-May/013354.html But I could not find how to turn off specific bumping restraints. I would be thankful if someone could point me to the recipe to do this. Jorge

2 2

Low resolution refinement - rotamers and Ramachandran
by mohamed noor 29 May '15

29 May '15

Dear developers I am refining a low resolution structure (3.8 A). After I fix most of the outliers (red bars) in Coot, phenix.refine is causing my structure to be worse than the start with 13 % Ramachandran outlier and 13 % rotamer outlier. Secondly, when I used phase_and_build to build my model, my R/Rfree is around 30/35 with atoms from some residues missing. When I fill them in with Coot, fix the outliers above and re-refine, R/Rfree jumps to 36/42 and the rmsd angles are too high (2.9). I have already used weight optimization and NCS. Am I doing something wrong? Thanks.

3 5

reference model restraints by segid
by jp d 28 May '15

28 May '15

Hi,I am having trouble getting phenix to used segid's in reference model restraints when my reference and target pdbs both don't use chain ID's.phenix quits with this message: *** Adding Reference Model Restraints *** Sorry: chain ' ' in /home/path/removed/agnref2.pdb contains one or more errant TER cards. Please remove and try again. my definition file looks like this:refinement { main { reference_model_restraints = True } reference_model { file = two.pdb } } refinement.reference_model.reference_group { reference = segid A16S selection = segid A16S } (above about 50 more times) this was on versions 1.9-1692 , dev-2016 and dev-2056 any suggestions ?thanksjpd

4 4

riding hydrogen model
by Filip Qbukarski 27 May '15

27 May '15

Dear phenix community I am currently refining a 1.75A structure and wanted to usethe riding hydrogen model in pehnix.refine. From what I found in the manual andprevious discussions on the mailing list and if I understand well, using ridingHs is advised for every resolution and the way of doing this in phenix.refine is notRefmac-like but instead I should 1) put Hs using ReadySet, 2) select the‘riding’ option for Hs and 3) use the PDB containing the H coordinates fordeposition, even though they were not individually refined. In this case theircontribution to scattering is also taken into account (which makes sense),which is a different way of treating riding Hs compared to Refmac, if Iunderstand well. Would it be possible to comment on this and in case I got thingswrong, correct?In fact for my structure, after adding the Hs prior to refinement using ReadySet and using theriding option, I actually got Rfree dropping by 1% (from 19.5 to 18.5) and better clash score (~0.5 according to Molprobity). Thanks in advancebestFilip

2 1

Re: [phenixbb] Refinement
by Pavel Afonine 26 May '15

26 May '15

Hi Mohamed, > How do tell phenix.refine to not move my HEM ligand around? yes, you can exclude selected atoms from refinement of coordinates in Phenix refinement GUI: Refinement settings -> Modify selection for: XYZ coordinates -> Edit -> type atom selection in "Edit selected" field (under XYZ refinement) like "chain A and resseq 1" or "chain A and resname ATP" However, I would rather find why correct geometry is not preserved. > I have a cif file describing the ligand but in my case, I can see > clear density of it not following the ideal geometry. If you send me files (off mailing list of course!) I will see if I can explain it.. You can copy to Nigel too as chances are that if you choose to send files I will be talking to him anyway. > As an example, I have attached a screenshot from Coot. It's hard to infer what's going on from a static image.. > In fact, the C atom is covalently linked to the nearest Cys, so the > HEM side chain should be 'moved' into the density and the green blob > shouldn't be there. Is this link defined anywhere in restraints used in refinement? Pavel

5 7

Fw: on the convergence of phenix refine
by Smith Liu 25 May '15

25 May '15

Dear All, For the meaning of non-convergence here, I mean in the whole 30 macro-cycles, both the Rwork and Rfree curves were in zigzag format, which I never met before. I am looking forward to getting an explanation from you. Smith -------- Forwarding messages -------- From: "Smith Liu" <smith_liu123(a)163.com> Date: 2015-05-26 09:26:23 To: phenixbb(a)phenix-online.org Subject: [phenixbb] on the convergence of phenix refine Dear All, Recently I have done a phenix refine, I find even I have 30 macro-cycles, the refine did not converge well. For example, for the last 5 cycles refine, the Rwork can still fluctuate between o.21 and 0.22, although both the final Rwork and Rfree decreased in comparison with the start Rwork and Rfree. What is wrong for my map and refine strategy? Smith

2 1

on the convergence of phenix refine
by Smith Liu 25 May '15

25 May '15

Dear All, Recently I have done a phenix refine, I find even I have 30 macro-cycles, the refine did not converge well. For example, for the last 5 cycles refine, the Rwork can still fluctuate between o.21 and 0.22, although both the final Rwork and Rfree decreased in comparison with the start Rwork and Rfree. What is wrong for my map and refine strategy? Smith

1 0

on B-factor refine of the phenix.real_space_refine
by Smith Liu 23 May '15

23 May '15

Dear Pavel, For the input, the last line of PDB is as followng, ATOM 21953 HH22 ARG H 295 53.862 115.032 84.116 1.00100.56 H For the run=ADP of the phenix.real_space_refine, the last line of the first model of all states pdb is, ATOM 21953 HH22 ARG H 295 53.862 115.032 84.116 1.00194.44 H and the last line of the second model of all states pdb is ATOM 21953 HH22 ARG H 295 53.862 115.032 84.116 1.00164.47 H. Clearly in each PDB of each model of the all states pdb produced, the b-factor is different, and they are different with the b-factors of the input pdb. Thus will you please explain why there are 2 states pdbs which seems both are refined pdbs? In addition, is it normal that the single state refined pdb cannot be opended? Next, will you please explain based on what of the mrc file, the phenix.real_space_refine run=ADP function got the b-factors? Further, I have noticed that the phenix.real_space_refine run=ADP gave a resolution which is different from the mrc general resolution given by relion or some other software. Will you please explain base on what the phenix.real_space_refine run=adp gives the resolution? Best regards. Smith -------- Forwarding messages -------- From: "Pavel Afonine" <pafonine(a)lbl.gov> Date: 2015-05-23 00:48:00 To: "Smith Liu" <smith_liu123(a)163.com>,"phenixbb(a)phenix-online.org" <phenixbb(a)phenix-online.org> Subject: Re: Fw:Re: [phenixbb] on B-factor refine of the phenix.real_space_refine For the all states PDB, it contains the input pdb for the phenix.real_space_refine and the real spaced refined PDB Yes I think so.. Is it not? Pavel

2 1

Fw:Re: on B-factor refine of the phenix.real_space_refine
by Smith Liu 22 May '15

22 May '15

Dear Pavel, It looks work. But for the refined PDB, it seems it was in read-only format, which I cannot copy. For the all states PDB, it contains the input pdb for the phenix.real_space_refine and the real spaced refined PDB, am I right? Smith -------- Forwarding messages -------- From: "Pavel Afonine" <pafonine(a)lbl.gov> Date: 2015-05-21 14:44:30 To: "Smith Liu" <smith_liu123(a)163.com>,phenixbb(a)phenix-online.org Subject: Re: [phenixbb] on B-factor refine of the phenix.real_space_refine I have a EM map (.mrc), with fitting and based on a crystal structure I got the fitted PDB file. I convert the mrc map to the CCP4 map， no need to convert .mrc into .ccp4 (isn't it the same thing?). Anyways, phenix.real_space_refine can use both. and I run phenix.real_space_refine model.pdb map.mtz run=adp, with phenix-dev-2034, in order to get my own b-factors for my fitted PDB based on my EM map. However after the above phenix.real_space_refine, I checked the refined PDB, and I find phenix.real_space_refine neither change the coordinates, nor change the b-factors for each atom. I need to see the files to be able to comment. If you share the files (off list and not sending directly via email but using things like Dropbox instead) then I will be happy to have a look. Thus will you please introduce to me how can I get my own b-factors for my fitted PDB in order to deposit my map and fitte pdb to the EM database? phenix.real_space_refine model.pdb map.mtz run=adp should just do what you want. If it didn't - see above (I need to see the files). Pavel

2 1

metal-ligand distances, and Optimize X-ray/stereochemistry weights
by Emilia C. Arturo (Emily) 21 May '15

21 May '15

I'm refining a model at 2.9 A, where four chains are in the ASU, and each active site has an iron with a few ligands; the configuration of this active site is the topic here. Currently the iron-ligand distances are not ideal (according to CheckMyMetal and the ideal distances generated by phenix.metal_coordination), but they are within a range observed previously for structures of truncated versions of this enzyme; furthermore, the more the metal-ligand distances change towards ideal distances, the more positive and negative density I observe in the Fo-Fc, so it appears that this deviation from the 'ideal' is supported by the data. However, when I use the 'Optimize X-ray/stereochemistry weights' option during refinement, the metal-ligand distances change (the metal appears to do most of the moving), getting closer to ideal, and this generates more positive and negative density in the Fo-Fc map). However, clearly it's nice that optimizing the X-ray/stereochemistry weights reduces R-free (and keeps the R-f/R-work ratio fine as well). So what is the most appropriate approach here, in order to keep the metal-ligand distances that best support the data, but still reap the benefits of the optimized stereochemistry weights? Some details of the structure and refinement are these: The iron in each of the four chains in the ASU is coordinated with atoms from two histidines, a glutamate, and a water (so four ligands per Fe) and there remains un-modeled density in the iterative build comp OMIT map used for modeling (because resolution is 2.9A and adding more water (which is my best guess, given what truncated structures at higher resolution show coordinating the Fe) does nothing to the Rf). I am working with an .edits file generated by phenix.metal_coordination. After some experimentation, I've left the sigma values (for Fe-O and Fe-N) at default values, and added a restraint for Fe-O (water), using an ideal distance of 2.3 and a sigma value of 0.1. Emily.

3 6