Search results for "look through"

Re: [phenixbb] multiple ligand conformations

by Pavel Afonine

Hi Len, sorry for delayed reply - somehow I managed to overlook your email... > One of the groups here has run into a problem in the refinement of > their structure or more specifically a ligand bound to the structure. > Through a series of other experiments they know that a photo reaction > occurs to the compound when exposed to high flux as found at your > everyday synchrotron source. The exposure changes the bonding such > that there are two conformations with a bit in between obviously. > They collected 360 degrees worth of data and if the data is split you > can model the two conformations depending which half of the data you > use. They are trying to refine with all of the data and modeling of > the ligand into the two conformations. In refmac they can model this > with no problem but in Phenix the ligand adopts a chemically wrong > conformation, sort of a halfway point between the two chemically > relevant conformations. They have used Phenix to do similar > refinements on other structures but it appears either the last release > or the latest release is causing problems. They have started out with > everything from 50% occupancy to shifting it towards on one > conformation or the other and the ligand always ends up in the > chemically wrong position. Data is in the 1.4-1.5 ang. range. It's hard to tell what's causing this without looking at actual files. But I'm pretty sure it must be something easy to fix. If you send me an example: a fraction of PDB file containing atoms in question, and explain how you expect their occupancies to be refined, then I will send you back a working example and explain why it did not work before. I will look into it immediately once I have the files. Pavel P.S.: Please send the files to my email, not to the whole mailing list.

13 years, 7 months

Re: [phenixbb] Discrepancy between R-factors from phenix.refine vs phenix Generate "Table 1"

by Jon Schuermann

Sorry if this is a little long, but I saw that more than one person was having a similar problem. First, I agree with everything Nat has said, but I will explain a little bit more. Twinning and/or pseudosymmetry can be a hairy issue to deal with. In some cases, NCS can be a real pain. I have seen many cases where just pseudosymmetry is present, but people assume it is twinned as well. To be fair, it is very easy to come to that conclusion, especially at the early stages. Let me just set the stage with a hypothetical example... You collect a 2.5A dataset that processes well in P622 with an Rsym=0.11 (overall). The intensity statistics look normal, which I won't go into right now because it is complicated (even though Nat eluded to it with the 'L-test'). You perform MR with a search model that has 60% sequence identity and get a solution with 1 molecule in the AU in P6522. The solvent content is 0.6. You run the solution through rigid-body, followed by positional and B refinement with simulated annealing. The resulting R=0.35, Rfree= 0.40. You look at the maps and the density does not look good. You can see density for most of the main-chain but almost all of the side-chain density is not present. You go about trying to build in the density but the R/Rfree do not drop much. What is your next step? Some would go to Se-Met or heavy atom soaks to solve by SAD or MIR, but the results are the same... Now What? Most people would say, its hexagonal where merohedral twinning is possible so it must be twinned. You rescale the data in P6, P312, P321, and even P3 (tetartohedral twinning) and the Rsym is about the same in all the subgroups with P6 and P3 being the lowest with Rsym=0.08. You perform MR in P65 and get a solution with 2 molecules in the AU. To 'check' if it is twinned, you run refinement twice from the same starting model; first, twin refinement specifying the 'twin law' (from XTRIAGE), and second regular refinement and then compare the results. You think the results speak for themselves... with the twin refinement, the R=0.24, Rfree=0.28 with the twin fraction refining to 0.49 (nearly perfect twinning). The maps look great! The regular refinement (without specifying the 'twin law') refines to R=0.30, R-free=0.32 and the maps look better than P6522, but not as good as the maps from the twin refinement. You think, 'This has to be twinned!' But here is the kicker, IT'S NOT TWINNED!!! How could this be??? When you input the 'twin law' in refinement and the twin fraction refines to >0.4, Phenix detwins using the proportionality rules. This method uses the model in the detwinning process which WILL introduce model bias in the maps, so they look great. Even if your model is NOT correct, the maps will still look good, because of the model bias. For this reason, you should calculate several 'omit maps' over different regions of your structure and inspect them, or look at maps calculated from refinement when you did NOT specify the 'twin law'. As for the R-factor being lower, the calculated twin R-factor is usually lower than the standard R-factor since the equations are NOT the same. So, a drop in R-factor at this early stage is not necessarily conclusive that your data is twinned. There are a couple of papers explaining this (which Nat eluded to and I believe I reference below). I have seen many people get 'itchy finger' and try to use the twin refinement too early. As Nat mentioned, you don't want to run it unless you are at the end of model building and ready for deposition, but the R-factor is still too high. Then it may be necessary to run refinement with the 'twin law' included to see if the R-factor drops 'significantly'. To summarize, if you suspect an issue with twinning and/or pseudosymmetry since the maps don't look as good as they should for a given resolution and the R-factor is too high, rescale/reprocess your data in lower symmetry SG's and rerun MR. When you get a solution, refine it WITHOUT specifying 'twin law' and look at the maps. A)If they look much better than the solution in the higher symmetry SG, continue your model building and refinement (WITHOUT 'twin law') cycles in this lower symmetry SG until the model building is complete and you would be ready to deposit the structure in the PDB. If the R-factor is still too high, then run refinement including the 'twin law' with the twin operator from Xtriage. If you see an appreciable decrease in R-factor, then you probably have twinning. If the R-factor dropped, but is still not low enough, then either your model is still not completely correct or you have something else going on as well (see end of B below). B) If the maps still do not look any better than the higher symmetry SG, try MR in another lower symmetry SG and repeat. I sometimes go down to P1, if I have enough data. If the maps still look bad (assuming you have a complete dataset and MR solution), then you may not have a SG issue at all, but something else. I would look into other issues including anisotropy, pseudo-translational symmetry, order-disorder, missing molecules, etc. I will usually scroll through the images to see if I see something obvious. Reprocess the data more carefully looking for things like extra spots not predicted, or predicted spots that aren't actually there, etc. Here are a few references to papers that explain some of these issues more in depth with examples: Acta Crystallogr. (2008), D64, 99-107. Acta Crystallogr. (2012), D68, 1541-1548. Acta Crystallogr. (2006), D62, 83-95. I hope this helps some people... Jon -- Jonathan P. Schuermann, Ph. D. Beamline Scientist, NE-CAT Argonne National Laboratory, 436E 9700 S. Cass Ave. Argonne, IL 60439 Email: schuerjp(a)anl.gov Tel: (630) 252-0682 On 05/30/2013 09:26 AM, Nathaniel Echols wrote: > On Thu, May 30, 2013 at 7:09 AM, Heather Condurso <condurso(a)bc.edu> wrote: >> I have a similar issue. My data is nearly perfectly twinned so Xtriage usually fails to find any twin law. However when I solve the structure in the lower symmetry space group with twinning my maps look beautiful. In the higher symmetry space group, only 3 of the 6 monomers fit into nice looking density. I simply use generate table 1 and uncheck the box so it won't regenerate R factors. The discrepancy between the R-factors is however much more significant than 2%. From refine I get 18/22 and from table1 28/31. > That's actually a little surprising that Xtriage wouldn't work - would > you be willing to send us the data? Keep in mind that if you have > perfect twinning and refine with the twin law, I think the maps will > look beautiful pretty much by definition, because of the model bias. > (Which doesn't mean that you did it wrong - the R-factors sound > realistic - you just need to be very careful and make lots of omit > maps.) > > It helps to have actual examples when warning against the dangers of > twin refinement and model bias in general, so here's one (attached). > This map isn't beautiful, but it matches the model very closely, > including the complete lack of sidechains. Another Phenix user got > this result by accident with a mostly-if-not-entirely incorrect MR > solution - fortunately the combination of missing sidechain density > and relatively high R-free (~40%) prompted him to email us. I suspect > that if we searched the PDB we'd find an actual published example > (especially considering how many spurious ligands have been found > there). > > (Sorry to sound like a broken record here, but this keeps coming up in > emails and workshops - perhaps we need better validation tools.) > > -Nat > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb

12 years, 1 month

[phenixbb] Reduce NQH

by jp d

hi, we were going through the logs recently and see something odd during Reduce N/Q/H analysis the log file looks like this: ================================== NQH flips ================================== r_work=0.3047 r_free=0.3518 Analyzing N/Q/H residues for possible flip corrections... segID AL01 renamed chain A for Reduce N/Q/H analysis segID AL02 renamed chain B for Reduce N/Q/H analysis ... segID AL29 renamed chain Y for Reduce N/Q/H analysis segID AL30 renamed chain Z for Reduce N/Q/H analysis segID AL32 renamed chain a for Reduce N/Q/H analysis segID AL33 renamed chain a for Reduce N/Q/H analysis segID AL34 renamed chain b for Reduce N/Q/H analysis segID AL35 renamed chain b for Reduce N/Q/H analysis ... segID BL28 renamed chain z for Reduce N/Q/H analysis segID BL31 renamed chain z for Reduce N/Q/H analysis segID BL13 renamed chain AA for Reduce N/Q/H analysis segID BL29 renamed chain AB for Reduce N/Q/H analysis ... we noticed that the lower case chain letters start to duplicate themselves and are not unique to each segid. when it starts the two letter chain, everything seems unique again. forgive me if that is expected, it just seems kind of strange this was seen in mutlple log files and we are using version Version: 1.8.4 Release tag: 1496 if you need our files or more details, let me know thanks jpd

11 years, 6 months

Re: [phenixbb] Missing plotting libraries

by Nathaniel Echols

On May 4, 2009, at 10:14 AM, Leigh Allen wrote: > ERROR: > > Reading package lists... Done > Building dependency tree > Reading state information... Done > E: Couldn't find package lapack3 > > Thanks for your help. I've tried installing lapack and/or lapack3 > through apt-get and synaptic... and I can't find it. I'll continue > looking and potentially ask the Ubuntu people since this is not a > Phenix problem. Well, we try to distribute packages that will work without any extra tinkering or compilation. . . which is sometimes difficult on Linux, but the lapack3 error should be avoidable (we don't actually need to link to it, it's just difficult to disable this behavior if it's present on the build system). To access lapack3 in Ubuntu, you need to have enabled the "universe" repositories. I think I did this manually by editing /etc/apt/ sources.list, but in Synaptic, you can do it via the menu item Settings-->Repositories. Searching for "lapack" then finds it - it will probably also come up with the BLAS libraries, which I recommend installing just to be safe. -Nat ------------------- Nathaniel Echols Lawrence Berkeley Lab 510-486-5136 NEchols(a)lbl.gov

16 years, 1 month

Re: [phenixbb] phenix refinement question

by Nathaniel Echols

On Mon, Nov 15, 2010 at 1:09 PM, Katarina Moravcevic <katarinm(a)mail.med.upenn.edu> wrote: > Hi all, > I have only started using PHENIX and have made an interesting observation. > If I run my model through PHENIX refine (individual sites, individual ADPs, > occupancies, optimized X-ray/stereochemistry weight, optimized X-ray/ADP > weight options selected) I obtain R/Rfree 0.15/0.18 and very nice geometry > values (data is to 1.7A). However, if I now take this refined model and run > it through Refmac (without any refinement) I obtain R/Rfree of 0.19/0.21. > Can anyone explain why is there such a big difference? Will this be an issue > during PDB submission? Take a look at what phenix.refine reports for the number of reflections used for refinement in the logfile - I believe it will discard reflections that are flagged as suspicious (can't remember the reference, I think it's one of Randy Read's papers), and unless you're using a very recent version, it may also be ignoring reflections where F=0. There are probably a half-dozen other reasons why the programs disagree, but these are less obvious and potentially much harder to detect. If you're concerned about reproducibility, run phenix.model_vs_data with the reflections and PDB file, and make sure that the statistics it reports agree with what you're sending to the PDB. The program is well-documented and mostly open-source, and is a good sanity check for data in the PDB. The PDB is using a much more primitive method to check R-factors, and after they process your structure you'll get an email that includes something like this: Structure factor validation High_Res Low_Res Compl Num_Ref R_obs R_work R_free Corr(Fo-Fc) Reported PHENIX 2.500 20.005 81.28 15118 0.2183 0.2150 0.2884 N/A SFCHECK without TLS 2.50 19.64 87.9 8004 0.2850 0.2850 N/A 0.8546 REFMAC without TLS 2.500 67.386 87.609 8937 0.234 0.2336 0.0000 0.918 The lack of TLS in their validation means that they'll even overestimate the R-factors of most structures refined by REFMAC! (Although in this case I think I left the ANISOU records in the deposited PDB file, so I'm not sure what they're doing wrong.) They will never complain about this, in my experience, so it's not something you need to worry about. -Nat

14 years, 7 months

Re: [phenixbb] Rfree refuse to come down

by Nathaniel Echols

On Thu, Mar 1, 2012 at 11:36 PM, Vellieux Frederic <Frederic.Vellieux(a)ibs.fr> wrote: > And I'd certainly start refinement using the NCS present, to relax it > (restraints) as the refinement proceeds (smoothly) and possibly not use any > NCS in the final stages of the refinement. You may need to carry out > annealing initially and so forth. Fred is correct, you absolutely want to use NCS at this resolution - if you use the torsion NCS parameterization (get a new-ish build for this), you probably will not need or want to turn off the restraints. The other thing to try is optimizing the X-ray/stereochemistry weight. This can take quite a long time (unless you have a large multi-core system), but it almost always yields a better result. You might also want to turn off the real-space refinement, sometimes it behaves weirdly. At 2.4A with an R-free of 0.32 you can probably start running the ordered solvent update, which will help a little bit. A more general suggestion is to look through the log file and identify where the R-factors begin to explode. This will give you a better idea where you need to change your strategy. Final suggestion: make sure you're running at least version 1.7.3, since there have been many improvements to refinement of more marginal cases. -Nat

13 years, 4 months

Re: [phenixbb] Clashes problem

by Karolina Michalska

Hi, Basically I have the same observation. My structure looks good (1.7A, R=19.6 free=22.5; strategy=individual_sites+individual_adp+tls; twin fr. 0.47) with nice geometry and density, but the clashscore in Molprobity is terrible. Almost all residues form clashes. It is improved only slightly if I add hydrogens at riding positions. So I am also curious where the problem is... Karolina Dnia 11-02-2008, pon o godzinie 13:02 +0000, Simon Kolstoe napisał(a): > Dear Phenix community, > > I am using phenix.refine version 2007_08_18_1856 to refine a 2.65A > structure (with individual_sites, group_adp, TLS & NCS, > wxc_scale=0.1). After refinement I am running the pdb file through the > Molprobity server. Molprobity gives a clash score of 33.78 indicating > the number of steric clashes (within 0.4A) per 1000 atoms. > > I am slightly concerned that a refinement program seems happy to allow > such clashes. Is this a problem with the version of phenix.refine I am > running, or is there a more obvious explanation that I have missed? > > Thanks, > > Simon > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb

17 years, 4 months

Re: [phenixbb] Selecting ellipsoid of data

by Frank von Delft

Hi Ralf Yeah, I figured. So if I want to use cctbx, where do I start? Just a pointer to a) package and b) function where I'll see the syntax. So equation for ellipsoid is x^2/a^2 + y^2/b^2 + z^2/c^2 = 1; so I imagine I take each reflection, convert each of h,k,l to 1/reso, and with a = 1/res(a*), I just check whether the above is < 1. The main thing I still need is to convert h,k,l into orthogonal coordinates.... or do I? I suppose I don't, as what I care for is not whether it's "really" an ellipsoid, only whether it cuts through miller index space anisotropically. Hmmmm... I may be able to do it in sftools; but if you can in <1minute give me a link to where to look to get started in cctbx, that would be awesome. (Thanks for listening :) > Hi Frank, > > >> Hi, is there a tool in phenix that allows me to select an ellipsoid of >> data -- specified e.g. by the highest resolutions in three reciprocal >> lattice directions. (Yes, I'm playing with anisotropy, "playing" being >> the operative word.) >> > I'm not aware of such a tool. > > Ralf > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb >

14 years, 11 months

[phenixbb] DNA covalent bond angles deviate from PDB standard dictionary

by Scott Classen

Hello, I'm running into validation problems with DNA when validating on PDB website. the validation report indicates that the refined value is significantly different that the PDBs standard dictionary. Deviation Residue Chain Sequence AT1 - AT2 - AT3 Bond Dictionary Standard Name ID Number Angle Value Deviation ------------------------------------------------------------------------------------------- 2.2 DG D 6 N9 - C1' - O4' 110.5 108.3 0.3 2.6 DC D 7 N1 - C1' - O4' 110.9 108.3 0.3 2.3 DC D 8 N1 - C1' - O4' 110.6 108.3 0.3 3.0 DT D 9 N1 - C1' - O4' 111.3 108.3 0.3 I've looked through a few of these in the .geo file and it appears that phenix.refine is using different values. for example, angle pdb=" O4' DG D 6 " pdb=" C1' DG D 6 " pdb=" N9 DG D 6 " ideal model delta sigma weight residual 108.40 110.18 -1.78 3.00e+00 1.11e-01 3.52e-01 ideal is specified as 108.4º so clearly my refinement has converged, but it has NOT converged on the RCSBs accepted value of 110.5º What to do? Who is "right" phenix or RCSB? Thanks, Scott

14 years, 5 months

Re: [phenixbb] Phenix.refine on coordinate-optimised structures

by Dorothee Liebschner

Hi, The strategy depends also on the resolution of the data, so if you could tell us that, we can give suggestions. Also the type of data, I guess X-ray diffraction? Out of curiosity, how do model quality metrics look like (clashscore, ramachandran, etc) at this point? If you keep coordinates fixed, they won't improve in refinement. Best wishes, Dorothee On Fri, Aug 7, 2020 at 2:52 PM Joey Farrell <jpfarrell(a)uchicago.edu> wrote: > Hello, > > > > I am trying to design a set of input parameters that I will be passing > through the phenix.refine function. The structures > > that I am working with have already had their X,Y, and Z orthogonal Å > coordinates optimised via separate protocol. > > I am looking for advice on which strategies and parameter values to use > with phenix.refine to improve the crystallographic R-factors > > of such structures while preserving their earlier optimisation in real > space. > > > > I have been having some success using “strategy = > tls+individual_adp+occupancies” (where tls = “chain A”, tls = “chain B”, > etc.) as > > well as adjusting the wxu_scale value until R-work and R-free are > minimised. Are there other strategies or phenix.refine functionalities > > that may also prove helpful with this end in mind? I believe there may be > ways to further improve R-work and R-free with this software > > that I am not yet aware of. > > > > Thank you for your help! > > > > Best, > > Joey > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > Unsubscribe: phenixbb-leave(a)phenix-online.org -- Project Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 Fax: (510) 486-5909 Web: https://phenix-online.org

4 years, 10 months

Search results for query "look through"