Re: [ccp4bb] Resolution discrepancy between MTZ file and Refinement

Hi, every time you run phenix.refine it may exclude some reflections from refinement per Read 1999 (Acta Cryst. (1999). D55, 1759-1764). Usually the number of reflections omitted ranges from none to just a few, however, this may be just enough to make the resolution statistics look slightly

Re: [ccp4bb] About Staraniso

Dear All, What follows below is not very specific to the particular program (STAIRSANISO) nor the original questions, but nonetheless, I believe it is relevant. In the past, performing any adjustments to the diffraction data intended for solving and refining atomic models was more or less

Re: [ccp4bb] program to complete (or to change) side chains to specific rotamers

Hi Jorge, it'd take about 1 hour of my time to put together a cctbx-based script to do that, or about 2 hours to make an end-user program in Phenix that'll be available in tomorrow's build. But I'm not sure how of general interest this might be to warrant investing time into this. So here is an

Re: [ccp4bb] Identify mysterious density in CryoEM map

Hello Jan, you can convert your cryo-EM problem into crystallographic one by FT'ing your map into a set of structure factors "Fobs" and then giving the atomic model and MTZ with these "Fobs" to CheckMyBlob. If it's cool enough, it should not make much difference if your "Fobs" come from X-ray or

Re: [ccp4bb] Resolution Discrepancy in Data Set

Hi Liliana, a few things to consider: 0) There is a Phenix mailing list for Phenix specific questions (phenixbb); 1) Bin completeness depends on (obviously) how binning is done (number of reflections per bin or number of bins or binning in d^2 or d^3 spacing or log-binning etc etc etc) -- all

Re: [ccp4bb] Poor correlation coefficient of model to cryo-EM map.

Hi Ketul, CCmask evaluates the cross-correlation between your experimental map and the map that is calculated from the model. If you look at the formula, the map calculated from the model involves, among other things, atomic coordinates, B factors, and occupancies. This means that even if the

Re: [ccp4bb] Can Refmac5 refine temperature factor residue by group?

Hi All, I believe it depends on the resolution. At sufficiently low resolution, it may not be too unreasonable to assume that the main chain atoms of a residue have the same B factors, and its side chain atoms also share the same B factor (different from the main chain). Why? Simply because your

Re: [ccp4bb] nearestcell

Hi Kay, to address "(...) not elsewhere (...)", in Phenix GUI go to Tools then down to "Search PDB symmetry...". I've never used it myself nor do I know who added it in Phenix but from the description it looks like what you're looking for. Let us know if you have any problems with it. All the

Re: [ccp4bb] Occupany refinement protocol amd best practices

Hi Matt, Im wondering about occupancy refinements - both what's going on under the > hood and what are best practices. > since you are quoting Phenix I suggest this bit of reading that is somewhat relevant to your questions:

Re: [ccp4bb] skewness in a good EM map?

Hi Rob, the fundamental property of crystallographic or cryo-em maps -- the presence of high density points -- is what skewness depicts. So I can't see why the idea of using skewness to quantify maps would be any different for x-ray vs cryo-em. I've just downloaded a cryo-EM map for this (PDB:

Re: [ccp4bb] Occupancy Refinement limitation

Hi Matt, I believe figure 3 here: https://www.nature.com/articles/s41467-018-06957-w is relevant to your question. Pavel On Tue, Sep 5, 2023 at 11:32 AM Matt McLeod wrote: > Hi all, > > I am trying to get some insight in the accuracy/precision of occupancy > refinements. I have done some

Re: [ccp4bb] quantifying electron density

Hi Jon, not really the answer to your question but.. This may be very tricky to do because what you look at is not an electron density map but its Fourier image of finite resolution phased by crystal model (that has errors), plus experimental errors, and missing F000 (which is not measured as part

Re: [ccp4bb] Refinement of ligand with alternate chemical structure

Hi Stuart, the answer, I think, is here: https://phenix-online.org/phenixwebsite_static/mainsite/files/newsletter/CCN_2015_07.pdf#page=12 Pavel On Wed, Feb 15, 2023 at 8:37 AM Stuart McQuarrie < 974c6ca32bc4-dmarc-requ...@jiscmail.ac.uk> wrote: > I fit a large cyclic ligand cA6 (cylic

Re: [ccp4bb] Future Diffraction Methods

Nukri, IMO, the idea of cross-discipline meetings is great conceptually, at least for reasons you pointed out, but utopical in practice. When we attend our field-specific meetings we meet colleagues we know, we talk to collaborators from the past or find new ones, we have things in common that we

Re: [ccp4bb] Map superposition!

Hi Rams, phenix.match_maps will superpose maps and models. Totally general: target/moving boxes (unit cells) and symmetry can be different, gridding can be different too. I can help off list should you need any assistance! Pavel On Wed, Jan 25, 2023 at 6:30 AM Subramanian, Ramaswamy wrote:

Re: [ccp4bb] outliers

> > This is best illustrated by Ramachandran "outliers", > which are perfectly supported by electron density. > Indeed, and 3NOQ is one of my favorite examples of that, an outlier isn't necessarily equates to wrong! However, I think torsion angles (eg, phi/psi) are much more flexible than

[ccp4bb] ISO model with large groups of atoms in alternative conformations

Dear community, I’m looking for an example of a crystal structure where a large group of atoms (as large as a whole chain or even a domain) have more than one distinct conformation that would require modeling of such chain/domain as more than one individual copy, with each copy having partial

Re: [ccp4bb] Quantifying electron density inside of a given volume

Hi James, - Where exactly inside the blob of density do you place these dummy atoms? > > Where? At the peaks. > Peaks? This means you need to have atomic resolution data and also blobs representing ordered atoms, so you actually have peaks! > What I usually do is pick peaks, put atoms at the

Re: [ccp4bb] Quantifying electron density inside of a given volume

Hi James, I like your approach with dummy atoms and occupancy refinement. Dealing with actual maps sounds like hell to me indeed (especially given that we deal with weighted Fourier maps!). Reading this as someone who immediately translates this into a computer code (in my mind), a few things

Re: [ccp4bb] How to cut fragment of map

Hi, this can be a start: http://cci.lbl.gov/docs/cctbx/doc_maps_boxing/ There are a lot of boxing options: with and without masking (with many masking options: smooth masks, etc), around atom selection, per NCS etc.. Pavel On Fri, Aug 5, 2022 at 2:30 AM Evgenii Osipov wrote: > Dear CCP4

Re: [ccp4bb] Help with One dimensional electron density calculation

For some perhaps relevant discussion please see Appendix B here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6096492/pdf/d-74-00531.pdf Pavel On Sat, Jul 16, 2022 at 6:17 AM Marcin Wojdyr wrote: > On Thu, Jul 14, 2022 at 3:15 AM Pavel Afonine wrote: > > > Map values are calc

Re: [ccp4bb] Help with One dimensional electron density calculation

Hi Ravikumar, next nightly build of Phenix (dev-4661 and up, likely becomes available tomorrow) found in the usual place https://phenix-online.org/download/nightly_builds.cgi?show_all=1 will contain the new command line program called phenix.map_values_along_line. The program inputs the map

Re: [ccp4bb] Help with One dimensional electron density calculation

Hi Ravikumar, this can be easily done in CCTBX, but requires knowing CCTBX and Python scripting. I can write a script-example for you, if interested, or feel free to give it a try yourself and let me know if you need any help. Pavel On Wed, Jul 13, 2022 at 11:19 AM Ravikumar wrote: > > Dear

Re: [ccp4bb] Regarding File conversion

Hi, Phenix has a collection of tools like this: phenix.cif_as_mtz phenix.cif_as_pdb phenix.pdb_as_cif phenix.mtz_as_cif Pavel On Tue, Apr 19, 2022 at 7:52 AM Marcin Wojdyr wrote: > Plenty of options. I'll add one maintained by me. Type: > gemmi convert file.cif file.pdb > or use it here: >

Re: [ccp4bb] Coot 1

It's April 1st today, isn't it? -;) On Fri, Apr 1, 2022 at 3:15 AM Paul Emsley wrote: > Coot 1 > > 18 years after the release of Coot 0 it's time that I actually released > Coot 1. > > Coot 1 is a major change beyond Coot 0. It has required a lot of writing > and rewriting [1] > and has been

Re: [ccp4bb] Ligand occupancy refinement

For the record, occupancy refinement scenario you're looking for is described here: https://phenix-online.org/phenixwebsite_static/mainsite/files/newsletter/CCN_2015_07.pdf#page=12 Cheers, Pavel On Thu, Mar 3, 2022 at 7:09 AM Jon Cooper < 488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote: >

Re: [ccp4bb] Phenix/refmac incompatibility?

Hi All, who produced this file? If phenix.refine added water with chain S given that protein chains named S were already in that model, then it is a bug that I need to fix. Cheers, Pavel On Thu, Dec 30, 2021 at 11:05 AM Eleanor Dodson < 176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote: > I

Re: [ccp4bb] Validation of structure prediction

Hi Reza, If you think about it this way... Validation is making sure that the model makes sense, data make sense and model-to-data fit make sense, then the answer to your question is obvious: in your case you do not have experimental data (at least in a way we used to think of it) and so then of

Re: [ccp4bb] Different conformation of chains

Hi, if I understood your question correctly, then one of 13 scenarios described here: http://phenix-online.org/phenixwebsite_static/mainsite/files/newsletter/CCN_2015_07.pdf#page=12 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

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 < andrea.th...@uni-hamburg.de>

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

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

Hi Frank, phenix.pdb.biomt_reconstruction command should do it. Pavel On Tue, May 25, 2021 at 12:44 PM Frank von Delft < frank.vonde...@cmd.ox.ac.uk> 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

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

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

Hi Wajahat, first off, there is a dedicated mailing list for Phenix specific questions ( http://phenix-online.org/). 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

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

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 < christian.galicia.diaz.sant...@vub.be> wrote: > Hello, > I'm trying to swap the chain IDs of a

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

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?

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

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: http://phenix-online.org/download/nightly_builds.cgi 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

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

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

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" ( https://doi.org/10.1107/S1399004714016289). If none of

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

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?

Randy Read's paper in latest Acta D: Measuring and using information gained by observing diffraction data http://journals.iucr.org/d/issues/2020/03/00/ba5308/index.html 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

Clearly, it is a good idea to keep hydrogens: http://phenix-online.org/presentations/hydrogens.pdf 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?

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 https://www.ncbi.nlm.nih.gov/pubmed/30198894 which is sort of along similar lines of what you are hinting here.

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

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

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?

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. emdb_.map resolution=value > .log or phenix.validation_cryoem model. emdb_.map

Re: [ccp4bb] TLS parameters

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

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?

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?

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 ?

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 ?

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

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

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.

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.

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

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: https://www.dropbox.com/sh/g7sp7pqxst4ldj0/AAD1whlVD2mvAGoRa5jOF-fla?dl=0 I leave it up to you to read and understand

Re: [ccp4bb] On estimating Unit Structure Factor distribution

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

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”

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

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

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: http://phenix-online.org/newsletter/CCN_2012_07.pdf Pavel On Tue, Mar 5, 2019 at 10:02 AM Pavel Afon

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

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

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

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?

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: http://journals.iucr.org/d/issues/2017/02/00/ba5254/ba5254.pdf This analysis tells you in plain English what you are

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

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

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

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

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: http://journals.iucr.org/d/issues/2017/02/00/ba5254/ba5254.pdf Based on the analysis described

Re: [ccp4bb] VERY old mtz file..

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

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, > http://xray.bmc.uu.se/usf/moleman2_man.html - maybe

Re: [ccp4bb] CC work / free

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)

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

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

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.

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.

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

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 ?

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] identifying bound ions

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

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

As others suggested, you can use Polder map: - how-to video tutorial can be found here: http://www.phenix-online.org/documentation/reference/tutorial_channel.html - background is described here: http://journals.iucr.org/d/issues/2017/02/00/ba5254/ba5254.pdf Pavel On Tue, Jul 24, 2018 at

Re: [ccp4bb] R-flag choose

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

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 ?

More re disulfide bonds: http://www.phenix-online.org/newsletter/CCN_2015_01.pdf#page=13 Pavel On Tue, Jul 3, 2018 at 11:26 PM, 张士军 <21620150150...@stu.xmu.edu.cn> 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

> 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

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..

This is discussed, for example, here: http://www.pnas.org/content/114/12/3103 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

> 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

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

Perhaps this can be automated: https://www.phenix-online.org/papers/wd5073_reprint.pdf 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

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

See Table 1 and corresponding discussion here: http://journals.iucr.org/d/issues/2013/04/00/dz5273/dz5273.pdf 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

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?

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

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