Re: [ccp4bb] Different conformation of chains

2021-10-20 Thread Pavel Afonine
Hi, if I understood your question correctly, then one of 13 scenarios described here: fits your situation and you should be able to handle it in refinement all right. For more specific advice please

Re: [ccp4bb] AI papers in experimental macromolecular structure determination

2021-08-03 Thread Pavel Afonine
One more: BraggNet: integrating Bragg peaks using neural networks B. Sullivan, R. Archibald, J. Azadmanesh, V. G. Vandavasi, P. S. Langan, L. Coates, V. Lynch and P. Langan J. Appl. Cryst. (2019). 52, 854-863 Pavel On Tue, Aug 3, 2021 at 4:53 AM Thorn, Dr. Andrea <>

Re: [ccp4bb] AI papers in experimental macromolecular structure determination

2021-08-03 Thread Pavel Afonine
Andrea, you may want to include this one: Using support vector machines to improve elemental ion identification in macromolecular crystal structures. Morshed N, Echols N, Adams PD Acta Cryst. D71, 1147-58 (2015). Pavel On Tue, Aug 3, 2021 at 4:53 AM Thorn, Dr. Andrea <

Re: [ccp4bb] writing coordinates of full biomol into one (PDB) file

2021-05-25 Thread Pavel Afonine
Hi Frank, phenix.pdb.biomt_reconstruction command should do it. Pavel On Tue, May 25, 2021 at 12:44 PM Frank von Delft <> wrote: > Hello all - this presumably has a really simple solution: > > For a PDB file with a (correct) biomolecular assembly record (REMARK >

Re: [ccp4bb] phenix refinement for bent DNA

2021-03-29 Thread Pavel Afonine
Hi Dhiraj, I have structure with bent DNA. I am trying to refine the structure > using phenix. do I need to turn off the DNA secondary structure restraints > during refinement? > probably not, unless you have reasons to do so otherwise. P.S.: There is a Phenix mailing list for Phenix

Re: [ccp4bb] Student Question--Negative Difference Density in some Histidine side chains in Iron Coordination complex in 2XGF T4 Phage Model Structure

2021-02-22 Thread Pavel Afonine
Hi, as others pointed out electron rich elements tend to amplify imperfections visible in Fo-Fc maps. Consider: - refining occupancy of Fe, the site may be partially occupied; - refining f' and f'' if data are anomalous; - surrounding histidines may 'see' this Fe as a nonbonded interaction and

Re: [ccp4bb] increased Rfree after ligand fitting refinement

2021-01-20 Thread Pavel Afonine
Hi Wajahat, first off, there is a dedicated mailing list for Phenix specific questions ( You need to run more than one refinement cycle before you try making sense of R factors. Pavel On Wed, Jan 20, 2021 at 10:05 AM Wajahat ali khan wrote: > Dear all, > > > I

Re: [ccp4bb] Rama-Z, Ramachandran plot validation in PDB-REDO

2021-01-19 Thread Pavel Afonine
Rama-Z is implemented in CCTBX meaning it is available to CCP4 and Phenix. Also it is reported in validation and refinement in Phenix (you get the number every time you run real- or reciprocal-space refinement!). Pavel On Mon, Jan 18, 2021 at 1:58 PM Boaz Shaanan wrote: > Hi, > Will it be

Re: [ccp4bb] how to swap chain IDs

2020-12-07 Thread Pavel Afonine
Hi Christian, you can do it in Phenix PDBTools: GUI->Model Tools-> load files then Options->Other modifications look for Rename chain ID. Pavel On Mon, Dec 7, 2020 at 9:49 AM Christian GALICIA <> wrote: > Hello, > I'm trying to swap the chain IDs of a

Re: [ccp4bb] Phenix refine distorting a sidechain despite correct density

2020-12-02 Thread Pavel Afonine
Hi Folmer, I would choose to not do the real space refinement in phenix.refine during > the last rounds of refinement of a model, when sidechain positions are > essentially correct. > by design it is supposed to place and fit side chains as good as possible, satisfying both map fit and geometry

Re: [ccp4bb] over-fitting? over-refinement?

2020-10-19 Thread Pavel Afonine
Hi Sam, > Hi, the question may be a bit weird, but how do you define 'over-fitting' > in the context of structure refinement? From users' perspective the > practical aspect is to 'fit' the model into the density. So there comes > this question from our juniors: fit is fit, how is a model

Re: [ccp4bb] Tyr pushed out during refinement

2020-10-19 Thread Pavel Afonine
Hi All, there was a bug at some point that could potentially lead to this. This all should be fixed in current Phenix nightly builds: If not, get back to us (phenixbb or Phenix help lists or reply directly to me). Pavel On Mon, Oct 19, 2020

Re: [ccp4bb] Protein-DNA covalent bond refinement

2020-07-06 Thread Pavel Afonine
Hi Cristina, in Phenix it is: Refinement settings -> Select Atoms -> Custom Geometry Restraints : you can define bonds, angles, torsions, planes, etc... Pavel On Thu, Jul 2, 2020 at 8:11 AM Cristina Machon wrote: > Dear all, > > I am writing regarding a problem we are facing with the

Re: [ccp4bb] Heavy atom vs light atoms density

2020-06-12 Thread Pavel Afonine
Hi Vito, many of us have probably experienced that, in the > diffraction of protein ligands containing heavy atoms (cisPt, I3C, etc), > the overwhelming electron density of the metal can totally flatten that of > the light atoms around (or rather make it look insignificant). > I

Re: [ccp4bb] visual mask editor - why

2020-05-29 Thread Pavel Afonine
Hi Bernhard, "Like comparing these map regions, excluding intrusion of a solvent mask, etc.": You didn't say much about the context.. So I'd say Polder map approach comes to mind first based on these keywords. Next is "map comparison" ( If none of

Re: [ccp4bb] How to compare between electron density maps?

2020-05-11 Thread Pavel Afonine
phenix.match_maps can overlay model B and map B onto model A and map A. A and B can be any symmetry and box (unit cell) dimensions. Model A and map A stay in its original frame of reference. Let me know should you have questions. Pavel On Mon, May 11, 2020 at 3:19 PM Murpholino Peligro wrote:

Re: [ccp4bb] [3dem] Which resolution?

2020-03-06 Thread Pavel Afonine
Randy Read's paper in latest Acta D: Measuring and using information gained by observing diffraction data seems very relevant to this discussion! Pavel On Fri, Mar 6, 2020 at 8:44 AM James Holton wrote: > Thank you Kay, > > Very

Re: [ccp4bb] Hydrogens in PDB File

2020-03-02 Thread Pavel Afonine
Clearly, it is a good idea to keep hydrogens: Not sure why this keeps coming up as a topic given how much it was said about it in the past, all the MolProbity arguments, etc.. Issue of missing side chains and loops is tricker indeed. Pavel

Re: [ccp4bb] [3dem] [ccpem] Which resolution?

2020-02-12 Thread Pavel Afonine
Interesting conversation! I see the 2017 paper is on bioRxiv. I wonder if it ever made into a peer reviewed journal (couldn't find quickly)? @Tim Gruene : have a look at d_model in which is sort of along similar lines of what you are hinting here.

[ccp4bb] Phenix workshop at ACA 2020 (San Diego)

2020-02-12 Thread Pavel Afonine
Dear Colleagues, please make a note of upcoming Phenix workshop focusing on crystallography and Cryo-EM tools for structure solution, August 2nd 2020 in San Diego, California. This is a day-long satellite workshop prior to ACA meeting. For schedule and registration see ACA 2020 web site:

Re: [ccp4bb] refinement of 0.73A data in shelxl

2020-02-03 Thread Pavel Afonine
Hi Matthias, did you use correct model parameterization and optimal refinement strategy for the resolution? Such as: - Add H atoms; - Refine all but H atoms with anisotropic ADPs; - Model alternative conformations (that one'd expect many at this resolution); - Add solvent (water, crystallization

Re: [ccp4bb] Examples of EM models at 4.0Å or better with serious modelling errors?

2019-12-10 Thread Pavel Afonine
Dear Gerard, a possible programmatic approach may be a loop over all (model, map, resolution) or (model, map, half_map1, half_map2, resolution) from PDB/EMDB and calling phenix.validation_cryoem model. resolution=value > .log or phenix.validation_cryoem model.

Re: [ccp4bb] TLS parameters

2019-11-19 Thread Pavel Afonine
Dear Eleanor, Phenix reads and writes TLS records, both PDB and mmCIF format. It can also read (but not write) TLS records in REFMAC and BUSTER format. In ATOM records Phenix outputs complete B factors, which includes both individual and TLS components (this is why they have ANISOU). Phenix

Re: [ccp4bb] Calculating RMSD of a loop

2019-09-17 Thread Pavel Afonine
Yet another way is: phenix.superpose_pdbs fixed.pdb moving.pdb selection_fixed="chain A and and resseq 1:10 and name CA" selection_moving="chain B and resseq 1:10 and name CA" or using the GUI. Pavel On Tue, Sep 17, 2019 at 8:06 AM Folmer Fredslund wrote: > Dear Kyle, > > As other non-CCP4

Re: [ccp4bb] I am doing phenix refinement now. Is it a problem if the r-work and r-free values are equal?

2019-08-30 Thread Pavel Afonine
for obvious issues like this one! Pavel On Fri, Aug 30, 2019 at 7:59 AM Pavel Afonine wrote: > Please send me log file off-list and that may be a start. -Thanks! > Pavel > > On Fri, Aug 30, 2019 at 6:48 AM Tung Thanh Dinh wrote: > >> After phasing with phenix, i clicked on the

Re: [ccp4bb] I am doing phenix refinement now. Is it a problem if the r-work and r-free values are equal?

2019-08-30 Thread Pavel Afonine
Please send me log file off-list and that may be a start. -Thanks! Pavel On Fri, Aug 30, 2019 at 6:48 AM Tung Thanh Dinh wrote: > After phasing with phenix, i clicked on the phenix.refine ribbon. Since > then for every macrocycle of refinement, r-work and r-free values are > always the same. Is

Re: [ccp4bb] How to include in refinement high resolution shells with VERY low completeness ?

2019-08-07 Thread Pavel Afonine
Hi Ivan, > My conclusion is that "no fill-in" option might be tried at some > stages, but with caution, especially for datasets with poor low res > completeness. > I'm guessing you really meant *high*, not low. More or less repeating what others said already.. Correcting for low res

Re: [ccp4bb] How to include in refinement high resolution shells with VERY low completeness ?

2019-08-06 Thread Pavel Afonine
For the record, phenix.refine always produces two versions of 2mFo-DFc maps, with and without filling in missing Fobs. The one that opens in Coot by default is the "filled" map, but you can always load the other one for comparisons. Pavel On Tue, Aug 6, 2019 at 8:34 AM Ivan Shabalin wrote: >

Re: [ccp4bb] Fo-Fc density close to cysteine residue

2019-07-09 Thread Pavel Afonine
Hard to see from a static image, but could it be an alternative conformation? Pavel On Tue, Jul 9, 2019 at 2:32 AM Lumbini Yadav wrote: > Dear all, > > > > We have found a huge Fo-Fc density close to cysteine residue (see attached > image) in the structure with resolution of 1.2A. In the

Re: [ccp4bb] resolution

2019-07-04 Thread Pavel Afonine
Hi Sam Tang, Sorry for a naive question. Is there any circumstances where one may wish > to refine to a lower resolution? For example if one has a dataset processed > to 2 A, is there any good reasons for he/she to refine to only, say 2.5 A? > yes, certainly. For example, when information

Re: [ccp4bb] Phenix / Coot neutron queries.

2019-06-22 Thread Pavel Afonine
Hi Jonathan, send me files off list and I will have a look. From your description it isn't clear to me what the problem is. You need to add H or D or H and D only once (and phenix.ready_set is the right tool to do it!), then just do refinement and all should work. Coot indeed may not play well

Re: [ccp4bb] Disulphide occupancies.

2019-05-26 Thread Pavel Afonine
Hi Jonathan, this may also be a result of too strong SS bond restraints or/and inaccurate SS bond restraints parameters or/and disorder (in some fraction of unit cells there is no SS bond). More on the topic: "Disulfide bond restraints" here:

Re: [ccp4bb] On estimating Unit Structure Factor distribution

2019-05-15 Thread Pavel Afonine
Hi Andre, here is the link to cctbx-based code that computes Uhkl according to your formula below, using model mean B and F000 that accounts for atomic model and bulk-solvent: I leave it up to you to read and understand

Re: [ccp4bb] On estimating Unit Structure Factor distribution

2019-05-15 Thread Pavel Afonine
Hi Andre, > - Is there any macromolecular crystallography software that can compute > Uhkl as above, or equivalent? > I estimate this can take about 10 minutes to script in CCTBX. I can write a script for you, if interested, and send off list. > - If not, would it be more correct to use the

Re: [ccp4bb] On estimating Unit Structure Factor distribution

2019-05-15 Thread Pavel Afonine
Hi Andre, - How can F(000) be best estimated from the final model, which is not > necessarily always the most complete or best refined? Should we simply add > together the number of electrons for all the atoms refined in the > asymmetric unit (protein + ligands + solvent)? > the text here

Re: [ccp4bb] “Bound ligand” versus “modified residue”

2019-04-24 Thread Pavel Afonine
Hi Ian, perhaps there are as many answers to this as many subscribers to this list, but personally "Cysteine with attachment" seems more logic and clear to me than calling the whole thing a different name. Although I would also understand arguments like if it is a CYS with an attachment it is not

Re: [ccp4bb] High Rfree in last Shell

2019-04-18 Thread Pavel Afonine
Also, values in parentheses (high-res shell) depend on how you (the program you use) do binning. Different programs do it differently and so these values can vary quite substantially. With a little of trial-and-error effort choosing the binning one can make these values farther or closer to

Re: [ccp4bb] Question about the electron density maps (.ccp4) in PDBe

2019-03-05 Thread Pavel Afonine
P.S.: while on the topic, it might be helpful to you to have a look at this article ("On the analysis of residual density distributions on an absolute scale", page 43) available here: Pavel On Tue, Mar 5, 2019 at 10:02 AM Pavel Afon

Re: [ccp4bb] Question about the electron density maps (.ccp4) in PDBe

2019-03-05 Thread Pavel Afonine
Hi Sen, As Pavel mentioned, phenix.f000 will give you F(0,0,0) value, but I don't > see that information stored and easily calculated from .ccp4 data. > phenix.f000 requires atomic model (PDB or mmCIF file) as input, not a map. If you want bulk-solvent to be added, then you need to give it mean

Re: [ccp4bb] Question about the electron density maps (.ccp4) in PDBe

2019-03-04 Thread Pavel Afonine
Hi, > Unfortunately not all structure > factor programs will give you that F000. > phenix.f000 will give you F(0,0,0) value based on atomic model alone or atomic model plus bulk-solvent. Pavel To unsubscribe from the

Re: [ccp4bb] Electron scattering factors for SHELXL

2019-03-04 Thread Pavel Afonine
Hi, > Or, alternatively, if anyone has used a different program to refine small > molecule structures determined by ED, we would be happy to hear about that > program too. > phenix.refine has an option to use electron scattering factors. I can provide further assistance off-list or on phenix

Re: [ccp4bb] Turning off the bulk solvent modelling in Refmac5 to generate Polder maps?

2019-02-08 Thread Pavel Afonine
Hi, this is why Polder map tool also includes analysis of the map in question to determine whether it looks like bulk-solvent or something else, as described in paragraph 5 here: This analysis tells you in plain English what you are

Re: [ccp4bb] [offtopic for ccp4bb] Real space vs reciprocal refinement

2019-02-05 Thread Pavel Afonine
Hi Mahesh, In the current version of phenix.refine contains the separate option for > refinement: xyz (reciprocal space) and xyz (real space ). What does it > mean and how it differs from the previous versions which had xyz and real > space instead. > All the same, different name. One refines

Re: [ccp4bb] Experimental phasing vs molecular replacement

2018-12-06 Thread Pavel Afonine
Hi, > Any time you do a thought experiment you make a fake-data data set, the > "true" phases and "true" amplitudes become the ones you put into the > simulation process. This is by definition. Is there potential for > circular reasoning? Of course! But you can do controls: > this is so

Re: [ccp4bb] Polder or FEM

2018-11-26 Thread Pavel Afonine
Hi Markus, I can only guess without seeing files (and link to files seems to be broken).. So my guess is that the ligand density is weak enough so FEM treats it as "near noise" and it wipes it. Polder decides it is likely ligand because it uses correlations, and so even of two maps are weak but

Re: [ccp4bb] high SOLVENT content low RESOLUTION and a LIGAND to be found

2018-11-21 Thread Pavel Afonine
Hi Almudena, I wonder to which extent I can trust the positive blobs or polder maps that > I am generating... > the answer to this question is given in corresponding paper that describes Polder map: Based on the analysis described

Re: [ccp4bb] VERY old mtz file..

2018-11-09 Thread Pavel Afonine
Now I see the value of storing data in plain text files even more (mind Shelx or X-plor formats, for example) -;) On Fri, Nov 9, 2018 at 9:47 PM Clemens Vonrhein wrote: > Hi Eleanor, > > You could try running the oldest MTZ2VARIOUS binary you can find - > e.g. > > wget

Re: [ccp4bb] transform NMR ensemble with pdbset

2018-11-08 Thread Pavel Afonine
Perhaps phenix.pdbtools model.pdb rotate=... translate=... which should work with any PDB or mmCIF file. Pavel On Thu, Nov 8, 2018 at 11:36 PM Tim Gruene wrote: > Dear Kaushik, > > you could try moleman2 from the Uppsala Software Factory, > - maybe

Re: [ccp4bb] CC work / free

2018-11-08 Thread Pavel Afonine
Clément, I'm guessing this is because it isn't clear what CCwork/CCfree can tell you that Rwork/Rfree can not. Needless to say we all more or less have a good idea about what the ok values for Rwork, Rfree and Rfree-Rwork (as function of resolution) while it is much less clear (to me at least)

Re: [ccp4bb] Issue with high Rfree (0.25) for a high-resolution dataset (1.05 Ang)

2018-10-10 Thread Pavel Afonine
Hi Tony, I always feel some people are too "greedy" with the resolution they want to > achieve. I mostly find that extremely high density is a pain to work with > as it's usually accompanied by many dual, triple conformers, a lot of noise > in the solvent phase that is often difficult to

Re: [ccp4bb] structure with missing density

2018-10-10 Thread Pavel Afonine
Hi Deepanshu, how complete the data set? What's completeness across resolution zones? Systematically missing reflections can have systematic impact in real space (maps). I've seen entire ligands or domains disappear due to missing low-resolution data. Just another check-point to consider.. Good

Re: [ccp4bb] collective term for hydrogen bonds and salt bridges

2018-09-17 Thread Pavel Afonine
Nonbonded interactions? (if you approach this from classic geometry restraints used in refinement programs) Pavel On Mon, Sep 17, 2018 at 2:09 PM Joel Tyndall wrote: > Hi, > > > > Polar interactions seems to make the most sense. This is what Pymol uses > as I don’t think it differentiates > >

Re: [ccp4bb] Electron density maps for Cryo-EM structures.

2018-09-09 Thread Pavel Afonine
P.S.: all questions are welcome of course, no labeling. It's just some of them are so orthogonal to common sense that answers my be such as well. Best, Pavel On Sun, Sep 9, 2018 at 9:38 PM Pavel Afonine wrote: > Hi, > > Is there any sever available to create electron density maps fo

Re: [ccp4bb] Electron density maps for Cryo-EM structures.

2018-09-09 Thread Pavel Afonine
Hi, Is there any sever available to create electron density maps for cryo-em > structures? > The questions are nonsensical. Here is why: 1) In cryo-EM maps are not electron density maps but surfaces representing electric potential. 2) Creating such a map is essentially carrying on from cryo-EM

Re: [ccp4bb] cryo-EM

2018-08-31 Thread Pavel Afonine
Hi Xavier, > is there some kind of general trend if not consensus as how to refine > cryo-EM structures? > Not really consensus, but my clearly biased contribution to the topic: I'd say basic common sense for refinement applies: - optimally sharpen the map (

Re: [ccp4bb] Can H-clashes be ignored ?

2018-08-22 Thread Pavel Afonine
Hi, also, it helps to keep in mind that some clashes may actually be valid interactions that are labeled as 'clashes' by validation software that is simply not sophisticated enough to distinguish between bad steric clashes and chemically/physically favorable valid interactions. For an example,

Re: [ccp4bb] Normalization of B-factors

2018-08-09 Thread Pavel Afonine
> I (personally) think the best answer from these was to look at the > TLS-subtracted residuals (ie. total B-factor - TLS component) — can’t > remember who sent it, off the top of my head. > TLS is just an approximation, sometimes good and sometimes not. If TLS parameters are refined along with

Re: [ccp4bb] identifying bound ions

2018-07-31 Thread Pavel Afonine
There is an option in phenix.refine to do this, described here: Automated identification of elemental ions in macromolecular crystal structures. Echols N, Morshed N, Afonine PV, McCoy AJ, Miller MD, Read RJ, Richardson JS, Terwilliger TC, Adams PD Acta Cryst. D70, 1104-1114 (2014). Pavel On

Re: [ccp4bb] wwpdb validation

2018-07-27 Thread Pavel Afonine
Phenix has its own way to do it which is "Comprehensive validation" available from the GUI. This includes validation of model, data and model-to-data fit. It is data-specific: there is one for crystallography (X-ray or neutron) and one for Cryo-EM. For best results, you need the latest version

Re: [ccp4bb] Help with omit map

2018-07-24 Thread Pavel Afonine
As others suggested, you can use Polder map: - how-to video tutorial can be found here: - background is described here: Pavel On Tue, Jul 24, 2018 at

Re: [ccp4bb] R-flag choose

2018-07-10 Thread Pavel Afonine
It's important to remember that free-R reflections are not only used to calculate Rfree, but also are used in calculation of m and D scales in 2mFo-DFc and mFo-DFc maps, as well as in likelihood-based refinement targets. The fact is that you need to have a sufficient amount of free-R reflections

Re: [ccp4bb] Clear segid

2018-07-06 Thread Pavel Afonine
This should work in latest nightly builds: phenix.pdbtools model.pdb clear_seg_id=true If it doesn't please report a bug (on appropriate Phenix lists). Good luck! Pavel On Thu, Jul 5, 2018 at 4:33 AM, Eugene Osipov wrote: > Hello everyone, > is there any simple way in CCP4 to clear segid

Re: [ccp4bb] disulfate bond ?

2018-07-04 Thread Pavel Afonine
More re disulfide bonds: Pavel On Tue, Jul 3, 2018 at 11:26 PM, 张士军 <> wrote: > Hi all > > I got a structure which has COA in it, and the SH in the tail of COA > is very close to the SH side chain of

Re: [ccp4bb] B-factor standardization

2018-04-05 Thread Pavel Afonine
> If I am not wrong, I remember that someone proposed to standardize > B-factors of protein atoms as “BS = B - Bave”, where Bave is the average > B-factor of the protein. This will make some of BS negative (if B

Re: [ccp4bb] (arcane) How to generate complete set of indices at low res

2018-04-05 Thread Pavel Afonine
Just in case you find it helpful, you can get 100% complete set of reflections (Fcalc) in specified resolution range using phenix.fmodel model.pdb high_res=2.5 low_res=15 or if you leave out low_res it will go all the way up to theoretical limit of low resolution. If you have/use cctbx then I

Re: [ccp4bb] Looking at an EM map..

2018-03-15 Thread Pavel Afonine
This is discussed, for example, here: Also, here I calculated the distribution of map values (scaled in r.m.s.) for four groups of atoms: main-chain atoms, side-chain oxygen atoms of ASP and GLU (negatively charged OD1, OD2, OE1, OE2), side chain atoms of

Re: [ccp4bb] building into EM map

2018-01-23 Thread Pavel Afonine
> I am new to building into an EM map, and I wonder if I could get a > recommendation for some standard routine for programs to use. I tried "find > helixes and strands" tool in phenix, it found some secondary structure > elements, however, it seems that there is more that could be done >

Re: [ccp4bb] new ContaMiner features

2017-11-23 Thread Pavel Afonine
It's amusing how a seemingly innocent ad for a new tool can ignite a rather prickly thread.. I see two keys to this. Firstly, for those who are not familiar with the issue the add could be better structured by providing a clearer statement of what the problem is or why it is important (with

Re: [ccp4bb] [Off-topic] Comparison of the same structure built by many people

2017-11-21 Thread Pavel Afonine
Perhaps this can be automated: Software doesn't get tired or bored, and thus potentially can try more and produce more plausible interretations. Then one can hire a number of people of various expertise to choose "best" result according to

Re: [ccp4bb] High R/Rfree

2017-11-13 Thread Pavel Afonine
Hi Radhika, R-factor value is almost useless unless you know the resolution (which you did not tell us): 26% is ok for 3A resolution and is nonsense for 1A, for example. The Rfree-Rwork gap is obviously large, suggesting sub-optimal refinement strategy. Try optimizing weights, let program update

Re: [ccp4bb] question about resolution bins in deposition

2017-11-06 Thread Pavel Afonine
See Table 1 and corresponding discussion here: Hope that hints you the answer. If not get back to me with questions. All the best, Pavel On Mon, Nov 6, 2017 at 7:18 PM, Eze Chivi wrote: > Hi, my PDB file

Re: [ccp4bb] another unknown density problem

2017-11-03 Thread Pavel Afonine
If by "it was truncated at 5A for clarity" you really mean you truncated all low-resolution data from 5A and lower then I am not surprised you see funny densities all over or don't see density where it is expected. Why? Consult a textbook for the answer. All the best, Pavel On Fri, Nov 3, 2017

Re: [ccp4bb] efresol download?

2017-10-26 Thread Pavel Afonine
Johan, core functionality described in that paper is implemented in cctbx. Re the stand-alone program -- I'm cc'ing to the author. Pavel On Thu, Oct 26, 2017 at 8:39 AM, Hattne, Johan wrote: > Dear all; > > Would anybody know where I can find efresol (as detailed in

Re: [ccp4bb] model bias

2017-10-11 Thread Pavel Afonine
A round of refinement with simulated annealing followed by minimization should address your concern. Pavel On Wed, Oct 11, 2017 at 4:48 PM, Karsten Dreifus wrote: > Dear all, > I have a 120 aa protein. Matthews coefficient indicates 3 mol in asu. > Molrep (template with

Re: [ccp4bb] How to deal with the bad omega angles?

2017-10-10 Thread Pavel Afonine
And I should add this works just great! (given we are on the same page defining 'great'). I used this for Cryo-EM model challenge; Nigel added this functionality at that time to make this possible. Pavel On Wed, Oct 11, 2017 at 2:17 AM, Nigel Moriarty wrote: > Since you

Re: [ccp4bb] RMSD between superposed structures without moving

2017-08-28 Thread Pavel Afonine
Or using cctbx: from scitbx.array_family import flex import iotbx.pdb def run(): xyz_1 = iotbx.pdb.input(file_name="file_1.pdb").atoms().extract_xyz() xyz_2 = iotbx.pdb.input(file_name="file_2.pdb").atoms().extract_xyz() print flex.mean(flex.sqrt((xyz_1 - xyz_2).dot())) if (__name__

Re: [ccp4bb] normalization of B-factor values from different crystal structures

2017-08-02 Thread Pavel Afonine
Hi, also keep in mind that the total model structure factor used in refinement and anywhere where model-to-data agreement needs to be evaluated (such as maps or R factors) is: Fmodel = ktotal * (Fcalc_atoms + F_bulk_solvent + F_something_else) where ktotal ~ scale * exp(-h*Uoverall*h_transpose)

Re: [ccp4bb] refmac output

2017-08-02 Thread Pavel Afonine
Hi Ed, your suggestion makes perfect sense to me, and it's trivial to add an option to do what you want. This will be available in next Phenix nightly build (clearly not tomorrow given today's power outage). Command line: use "write_map_coefficients_only=True" (by default is is False).

Re: [ccp4bb] refmac output

2017-07-31 Thread Pavel Afonine
> > I know space is cheap these days, but is there a reason for Refmac to > generate all those extra columns in the output mtz file? Refmac (as well > as phenix.refine and buster-tnt) output mtz file is almost always used for > only one purpose - look at the map in coot. You only need 4 columns

Re: [ccp4bb] resolution limits

2017-07-26 Thread Pavel Afonine
Andrew, phenix.refine may not use reflection-outliers (Read, R. J. (1999). Acta Cryst. D55, 1759–1764.). Typically this is just a few reflections. If you have a good reason to disable this, then use xray_data.outliers_rejection=false. P.S.: There is Phenix mailing list for Phenix-related

Re: [ccp4bb] Chain ID number limit!

2017-07-24 Thread Pavel Afonine
Hi Lijun, it's not a problem if you use mmCIF or PDB with two-letter chain ID (both supported in Phenix). Pavel On Mon, Jul 24, 2017 at 5:09 PM, Lijun Liu wrote: > Hi: this must be an old problem but I would like to know if there are > other ideas to make things easier.

Re: [ccp4bb] Total occupancy of two conformations of one nucleotide is over 1.0? Need help!

2017-07-21 Thread Pavel Afonine
Hi Wei, thanks for sharing the data (off-list). I did some detective work and yes, Clemens is correct: what you see is the effect of bulk-solvent. After adjusting the solvent contribution (mask) in regions occupied by altlocs A and B the positive density mostly disappears. Pavel On Fri, Jul 21,

Re: [ccp4bb] Questionable Data collection and refinement statistics for 5XQL

2017-06-29 Thread Pavel Afonine
I agree with Dominika, I can't see major problems with this entry (I also did some quick refinement and briefly looked at maps). Reported R factors match re-calculated values using data from PDB, which is good. Smaller issues I see are: - no solvent (water) in the model, while density suggests

Re: [ccp4bb] Problem with Mg2+ binding site refinement

2017-06-15 Thread Pavel Afonine
Hi Mubinur, try without "metal restraints" and see if that helps. As others suggested, make sure 2+ is present in rightmost column of PDB file. The side may be partially occupied, so refining occupancy of Mg2+ is not a bad idea. Pavel On Wed, Jun 14, 2017 at 2:44 PM, Mohammad Rahman


2017-05-19 Thread Pavel Afonine
Yes, that is what I have been doing. Build one subunit and assemble into > tetramer before realspace refinement (with "ncs" constraints). I used > tetramer for refinement because I want the distances between the inter > subunits interaction partners to be considered. The problem is, whenever I >


2017-05-18 Thread Pavel Afonine
Just use P1 and "ncs" constraints. What's the problem? Or just keep entire map and have only symmetry independent copy to work with until finishes, then make the whole molecule. For real-space refinement it's totally irrelevant whether you have whole molecule or 1/Nth of it. So.. it isn't clear

Re: [ccp4bb] Using Coot and CCP4 program for cryoEM data

2017-05-17 Thread Pavel Afonine
Hi, 2. How do I convert cryoEM map file to MTZ file? > While technically you can do it, normally there is absolutely no need to do it. In cryo-EM the map is your data, not reflection data (structure factors!). So no need to 'massage' your data (the map) by converting it into "Fobs" and storing

Re: [ccp4bb] very high B-factor

2017-05-04 Thread Pavel Afonine
Hi, I'm working on a crystal structure with resolution of 2.2A. At the final > step, I use different strategies to refine the structure, they are: > no4: strategy=individual_sites+individual_adp+tls / set_b_iso=20 > results: Rwork/free=0.2052/0.2658 b-factor=11.4/136.8/48(min/max/average) > >

Re: [ccp4bb] peroxy-glutamate?

2017-05-03 Thread Pavel Afonine
Dear Gerard, I am sure others > are certain to propose a cooler name for that very same type of map > some day ;-) . > a free tip: how about DDM (Decarboxylation Detector Map)? All the best, Pavel

Re: [ccp4bb] CH-bond length discrepancies

2017-04-29 Thread Pavel Afonine
Also, see figure 4 here: that illustrates the difference. Pavel On Fri, Apr 28, 2017 at 10:33 AM, Bernhard Rupp wrote: > Dear Fellows of the Bond, > > > > when validating a QM refined homology model with Molprobity, I

Re: [ccp4bb] CH-bond length discrepancies

2017-04-28 Thread Pavel Afonine
Note, Molprobity has an option to use longer (neutron) X-H distances. Pavel On Fri, Apr 28, 2017 at 11:46 AM, Tristan Croll wrote: > I believe the reason for the discrepancy here is that MolProbity by > default places the hydrogens according to the centroid of the electron >

Re: [ccp4bb] NCS difference

2017-04-24 Thread Pavel Afonine
I suspect most (if not all) refinement software now have a nice way to deal with NCS in refinement locally. Technically, this means you can use NCS restraints at any resolution and software should be able to be careful and not wipe out local differences between NCS copies. In phenix.refine this is

Re: [ccp4bb] NCS difference

2017-04-24 Thread Pavel Afonine
Minimizing a red bar may be tricky.. Have you tried to make it less red (blue or may be green)? Otherwise Rw/Rf~20/25 is just fine at 2.2A resolution. What exactly your worry is about? Pavel On Mon, Apr 24, 2017 at 12:48 AM, Vipul Panchal wrote: > Hi all, > > I am solving

Re: [ccp4bb] software or tool for Individual residue in a Ramachandran plot graph?

2017-03-25 Thread Pavel Afonine
Except that Procheck is now ages behind the standard, with Molprobity being the standard. I'm not sure even if Coot uses the latest libraries. Those I quoted in example below come from latest Molprobity (Phenix that is) and are the latest. Pavel On Fri, Mar 24, 2017 at 2:55 PM, Edward A. Berry

Re: [ccp4bb] software or tool for Individual residue in a Ramachandran plot graph?

2017-03-24 Thread Pavel Afonine
phi and psi? for > example : > A 2 ASN:56.93:-60.58:141.19:Favored:General alpha helix > A 3 ASN:48.44:-119.25:125.15:Favored:General alpha helix > > On Fri, Mar 24, 2017 at 1:09 PM, Pavel Afonine <> wrote: > >> Trivial using command

Re: [ccp4bb] Ramachandran statistics and referee responsibility

2017-03-08 Thread Pavel Afonine
Hi Evette, (1) best practices in refining against lower resolution data (~4 angstrom) > to achieve the best model, > obtain a model that fits data best under requirement that it has zero geometry violations (Ramachandran, Cbeta deviations, rotamers, CABLAM, etc..). Note, a geometry outlier

Re: [ccp4bb] Removing TLS component of B factor of deposited PDB files to input to refmac

2017-03-08 Thread Pavel Afonine
Normally, these days at least, a model that is result of TLS refinement contains total B factor in ANISOU records and its TLS component in TLS records (REMARK3), with Btotal = Btls+Bresidual. If TLS matrices are available, it's trivial to calculate Btls from TLS matrices in REMARK3 and subtract

Re: [ccp4bb] Estimating the amount of missing electron density for a model

2017-02-22 Thread Pavel Afonine
Hi, Is there a straight-forward way to estimate the amount of missing electron > density that a particular protein structure is missing based on the > difference between Fo and Fc? > Any refinement or map calculation software that uses likelihood-based approach does this routinely. In

Re: [ccp4bb] Composit omit map vs. ligand

2017-02-16 Thread Pavel Afonine
er > economical in its acknowledgment of "prior art" - a notion that surely > has to be recognised as existing outside the confines of standard, > neatly packaged, immediately quotable Acta D publications :-) . > > > With best wishes, > > Gerard. > > -- > On Th

Re: [ccp4bb] Composit omit map vs. ligand

2017-02-09 Thread Pavel Afonine
In addition to excellent Kay's reply.. Also make sure to check refined B factors. Note, if the ligand is not there then that volume is likely filled with bulk-solvent. Now low occupancy in combination with very large B factors may approximate bulk-solvent quite well. The Polder map along with

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