[ccp4bb] Quest for resolution-sensitive substructure determination cases

the number of examples too much! If you email me directly, I’ll post a summary to the BBs. Thanks! Randy Read - Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: +44 1223 336500 The Keith Peters Building

[ccp4bb] Postdoc position: posted on behalf of Julia Shifman and Joel Sussman

= Shifman lab in the Hebrew University of Jerusalem is looking for a postdoctoral scholar to study evolution of protein-protein interactions. Our lab has pioneered computational and experimental methodology for mapping changes in binding affinity due to thousands of

[ccp4bb] Interesting article on the synchrotron data deluge...

…with lots of familiar names! https://physicstoday.scitation.org/do/10.1063/PT.6.2.20200925a/full/ Randy Read - Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: +44 1223 336500 The Keith Peters Building

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] Best protocols to advance a low resolution twin

ins > <288da93ae744-dmarc-requ...@jiscmail.ac.uk> wrote: > > Hi Randy, > >> On 14 Sep 2020, at 12:09, Randy Read wrote: >> >> Unfortunately, it looks like this is one of the few options that isn’t yet >> available from the ccp4i2 interface! > &g

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] Best protocols to advance a low resolution twin

interface! I’d probably try a number like 20 A^2 as a guess. If this doesn’t work, then it’s probably worth cutting out the density and treating it as a real-space MR problem, using the phased translation target at the translation step of the search. Best wishes, Randy Read - Randy J

Re: [ccp4bb] taking information from a deposited structure

the authors of the entry. Best wishes, Randy Read - Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: +44 1223 336500 The Keith Peters Building Fax: +44 1223 336827 Hills Road

Re: [ccp4bb] Homology modeling

/10.1002/prot.25767. You’ll find a variety of good tools described there. The one we’ve been playing with, in terms of local assessment of model quality for MR, is ProQ3D, which has an online server: http://proq3.bioinfo.se. Best wishes, Randy Read - Randy J. Read Department of Haematology

Re: [ccp4bb] Phaser Warning Message

serious clashes are found in P6122. Thanks for sharing the log file so we could see what is going on! Best wishes, Randy Read - Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: +44 1223 336500 The Keith Peters Building

[ccp4bb] Update on COVID-19 Open Structures initiative

) and to the CASP organisers (c...@predictioncenter.org). Either Massimo or I will add you to the team, upload the target data, links and other information and send an alert to everyone who has registered. Best wishes, Randy Read === The Covid-19 crisis is bringing out the best

[ccp4bb] Covid-19: open science to harness synergies in structure prediction and structure solution

hat others can build on them. Best wishes, Randy Read (in cooperation with the CASP organisers) - Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: +44 1223 336500 The Keith Peters Building Fax

Re: [ccp4bb] Se SAD phasing map becomes worse after refinement

the NCS, which would help a great deal in map improvement. Tom Terwilliger might answer this in more detail (perhaps on the Phenix-BB), but I don’t think you can build protein and nucleic acid in the same job, so you should look at the documentation to see how to do that. Good luck! Randy Read

Re: [ccp4bb] Error running Phaser-MR

. If neither of these explain the problem, please send the offending sequence file to me (off-list) and I’ll see if I can find out what’s wrong. Best wishes, Randy Read - Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: +44 1223

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

Hi Alexis, A brief summary of the relevant points in the paper that Pavel mentioned (https://journals.iucr.org/d/issues/2020/03/00/ba5308 ): The paper is about how to estimate the amount of information gained by making a diffraction

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

Dear Colin, Over the last few years we've been implementing measures of information gain to evaluate X-ray diffraction data in our program Phaser. Some results in a paper that has been accepted for publication in the 2019 CCP4 Study Weekend special issue are relevant to this discussion.

Re: [ccp4bb] Shipping samples for neutron diffraction

Hi Gloria, While we're confessing to minor economies with the truth, I never travelled to the Photon Factory in Japan with crystals of pertussis toxin: they were crystals of Bordetella pertussis ADP-ribosyltransferase. Randy > On 20 Feb 2020, at 02:47, Gloria Borgstahl wrote: > > Actually

Re: [ccp4bb] Dead link

It looks like someone at CCP4 will have to fix the link to their local copy of the wikidump, but the Phaserwiki link gives you a direct link to all of our documentation. Best wishes, Randy Read > On 18 Dec 2019, at 20:29, David J. Schuller wrote: > > On this CCP4 documenta

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] 1 out of 2 proteins in asymmetric unit does not fit density

? Having the data (which we would only use for this purpose) would be best, if you could send that off-line. If you don't feel able to share the data, then sample log files from an unsuccessful run and the eventual successful run might give us some hints. Best wishes, Randy Read > On 16 Dec 2

Re: [ccp4bb] Figure of merit in refinement

are actually true P1, just close enough to satisfy the high symmetry rules .. > but this is getting a bit philosophical I know .. > > Jan Dohnalek > > > > > On Wed, Oct 16, 2019 at 6:24 PM Randy Read <mailto:rj...@cam.ac.uk>> wrote: > James, > > Where

Re: [ccp4bb] Figure of merit in refinement

n FOM-weighted > map. > > Is there a way to "change up" the statistical distribution that assigns FOMs > to hkls? Or are we stuck with this systematic error? > > -James Holton > MAD Scientist > > On 10/4/2019 9:31 AM, Randy Read wrote: >> Hi James, &

Re: [ccp4bb] Figure of merit in refinement

he average will generally be close to the expected value. Best wishes, Randy Read > On 4 Oct 2019, at 16:38, James Holton wrote: > > I've done a few little experiments over the years using simulated data where > I know the "correct" phase, trying to see just how accurate FOMs are.

Re: [ccp4bb] One protein, two data sets

in the native Patterson map? If that's true, the two crystal forms could be closely related. Best wishes, Randy Read > On 8 Sep 2019, at 12:15, Prerana G. wrote: > > Dear all, > > We have two data sets of a protein with the following parameters: > 1. Space group P212121 a=61.0,

Re: [ccp4bb] Another difficult MR case

or in the wrong orientation) explains some feature of the data, i.e. the modulation caused by tNCS. I'd be happy to look at the log file for you if you find it hard to interpret. Best wishes, Randy Read > On 29 Aug 2019, at 17:24, Phil Jeffrey wrote: > > Are you *sure* there's no tran

Re: [ccp4bb] higher older tNCS

ot;Other settings". In the "Translational NCS" section of the popup, set "Number of molecules or complexes related by translation vector" to 3. And for completeness, if you're writing a command-line script, the command is "TNCS NMOL 3". Best wishes, Ran

Re: [ccp4bb] Does ncs bias R-free? And if so, can it be avoided by special selection of the free set?

Dear Ian, I think the missing ingredient in your argument is an assumption that may be implicit in what others have written: if you have NCS in your crystal, you should be restraining that NCS in your model. If you do that, then the NCS-related Fcalcs will be similar (especially in the

Re: [ccp4bb] High Rfree in last Shell

Hi, No-one else seems to have said this, but just from the data in that table, if I were a referee I would almost certainly be asking why you seem to have discarded useful data at higher resolution than 3.1A! Best wishes, Randy Read > On 16 Apr 2019, at 20:59, Jan van Agthoven wr

Re: [ccp4bb] Deposition requirement of anomalous pairs?

I’d be with you, Graeme, as a good compromise between merged data and raw diffraction images. Though it does seem to be getting more practical to make image data available… Randy - Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research

Re: [ccp4bb] help with TNCS + MR

Dear Almu, We have a discussion on the Phaser Wiki about some of the possibilities for tNCS, what you should look for, and what Phaser can handle: http://www.phaser.cimr.cam.ac.uk/index.php/Molecular_Replacement#Translational_Non-crystallographic_Symmetry. As it explains, if you have one

Re: [ccp4bb] Change dimer assembly in ASU

y copy that you want to make the master copy). Best wishes, Randy Read - Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical ResearchTel: +44 1223 336500 Wellcome Trust/MRC Building Fax: +44 1223 336827 Hill

Re: [ccp4bb] visualising anis B factors

Hi Eleanor, It’s easy in coot. Load in the PDB with ANISOU records, then select Draw -> Anisotropic atoms… -> tick box labelled “Show Anisotropic Atoms”! Best wishes, Randy - Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical ResearchTel:

Re: [ccp4bb] translational NCS & twinning

ol in CCP4. >> >> Dealing with potential complications from combinations of twinning and >> pseudosymmetry is one of the more challenging aspects of crystallography, >> but it's a good learning experience. Good luck! >> >> Randy Read >> >>> On 10 Jan 2

Re: [ccp4bb] translational NCS & twinning

of crystallography, but it's a good learning experience. Good luck! Randy Read > On 10 Jan 2019, at 22:38, Donghyuk Shin wrote: > > Dear all, > > Thank you very much for all of your suggestions and sharing experiences. > As many of you commented, the current small unit cell C

[ccp4bb] CCP4 Study Weekend: late addition and last chance to register

programme and to find registration information, please go to the meeting website: http://www.cvent.com/d/sgq8q6/6X. Best wishes, Isabel Usón, Ronan Keegan and Randy Read -- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: + 44

Re: [ccp4bb] preparing ellipsoidally truncated data for PDB deposition

ring the deposition process. Perhaps someone from one of the wwPDB sites, or someone who has gotten as far as depositing such data, can comment! Best wishes, Randy Read - Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical ResearchTel: +44 1223 33

[ccp4bb] CASP13 conference info

presentations. Detailed program of the meeting will be available in mid-November, 2018. Assessment of predictions: * High accuracy models - Randy Read (Cambridge University, UK) * Model topology - Matteo Dal Peraro (EPFL, Lausanne, Switzerland) * Contact prediction - Andras Fiser (Albert

Re: [ccp4bb] tCNS and space group determination

the counts for the rejections vs the ones being ignored. There are data sets where nearly half of the reflections end up being ignored, so I wouldn’t worry about that for this data set. Best wishes, Randy Read - Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute

Re: [ccp4bb] tCNS and space group determination

solution (e.g. in Zanuda) and see whether it obeys any higher symmetry than P1. Good luck! Randy Read > On 7 Aug 2018, at 10:35, Marcelo Liberato wrote: > > Dear CCP4 members, > > I need your help to figure out what is going on with my data. > I've integrated my data set in s

[ccp4bb] Call for targets (not-yet-released structures) for CASP13 modelling experiment

Posted on behalf of the CASP organizing committee: NB: There are only two weeks left to collect new targets for CASP13, so your contributions would be very gratefully received! Request for protein structures to test modeling methods - CASP13 CASP community experiments aim to

[ccp4bb] Software Engineer position to work with Phaser team in Cambridge

/BKS034/software-engineer). The text of the job description is appended, if you'd like to look at that before clicking on one of the links! Best wishes, Randy Read = We are looking for a graduate Software Engineer to join the group of Prof Read in the Cambridge Institute

Re: [ccp4bb] Predicting self-rotation function peaks from coordinates?

MMA 40 70 180 INPUT CCP4 ALPHA BETA GAMMA 90 90 90 OUTPUT CCP4 PHI PSI KAPPA END eof Best wishes, Randy > On 11 Jun 2018, at 13:33, Randy Read wrote: > > Dear Liang, > > Thanks, that looks like that will do the job very well starting from a list > of NCS rotations! &

Re: [ccp4bb] Predicting self-rotation function peaks from coordinates?

gt; and output all the angles related by the crystallographic symmetry. > Hopefully this will help with what you need to do. I attach a script and > print file as examples. > > > best regards > Liang Tong > Columbia University > > > > On Mon, Jun 11, 2018 at 4

[ccp4bb] Predicting self-rotation function peaks from coordinates?

-rotation function from the Fcalcs is another option to prove that the structure agrees with the self-rotation function computed from the data, but it would sometimes be helpful to be able to say which pair of molecules led to a particular peak. Thanks! Randy Read -- Randy J. Read

Re: [ccp4bb] [ccp4bb] tNCS problem

the detection of twinning, and sometimes a crystal has both pseudo-symmetry with twinning as well as tNCS. If you want to send me a Phaser log file (off-list), I might be able to make some suggestions about what to consider. Best wishes, Randy Read > On 8 May 2018, at 16:02, 苏纪勇 &l

[ccp4bb] Call for targets (not-yet-released structures) for CASP13 modelling experiment

Posted on behalf of the CASP organizing committee: Request for protein structures to test modeling methods - CASP13 CASP community experiments aim to establish and advance the state of the art in protein structure modeling. To this end, CASP collects information on soon-to-be released

Re: [ccp4bb] According correct space group assignment...

twinning does not turn out to be correct…) Best wishes, Randy Read - Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical ResearchTel: +44 1223 336500 Wellcome Trust/MRC Building Fax: +44 1223 336827 Hills Road

Re: [ccp4bb] Problems with pseudo-symmetry

by symmetry. Best wishes, Randy Read > On 2 Feb 2018, at 15:27, Renuka Kadirvelraj <r...@ccrc.uga.edu> wrote: > > Dear All, > > I am trying to refine a 1.9 A structure that indexed with excellent > statistics (XDS) into a primitive monoclinic cell with cell lengths a=81.

Re: [ccp4bb] coordinate transformation

! Best wishes, Randy Read > On 14 Dec 2017, at 08:39, Kajander, Tommi A <tommi.kajan...@helsinki.fi> > wrote: > > Dear Paul, > > Yes thank you. This was the best answer i think. Someone else already also > suggested that also. Coot is very handy indeed. &

Re: [ccp4bb] P212121 twinning

replacement in P1 first, because if you get a clear solution the symmetry of the solution will tell you what the true space group is. Best wishes, Randy Read - Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical ResearchTel: +44 1223 336500

Re: [ccp4bb] Dubious slide aggregator slideplayer.com

Dear Robbie, Thanks for posting that! When I share my slides, I generally try to do so only as PDF files to make it harder for anyone to reuse them without permission, but I hadn’t realised how much of an issue this is. It seems that I’ve nonetheless let one PowerPoint into the wild (“Using

Re: [ccp4bb] High R/Rfree after MR

ying intensity distribution. The UCLA server actually uses Phaser under the hood — what they add is to turn the anisotropic B-values into suggested resolution limits in the different directions. However, I don’t think they allow you yet to submit intensities, which would be better. Best wishes, R

Re: [ccp4bb] doubt regarding MR search model

iffered only in the coordinate position of ~20 > out of 290 residues (a lid for the enzyme). > > Regards, > > Emily. > > > Best wishes, > > Randy Read > > - > Randy J. Read > Department of Haematology, University of Cambridge > Cambridge Instit

Re: [ccp4bb] doubt regarding MR search model

lower LLG for two copies of a dimer means that the dimer in your structure is slightly different from the dimer in the model. Best wishes, Randy Read - Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical ResearchTel: +44 1223 336500 Wellcome

Re: [ccp4bb] NMR or Homology Model as a MR model

, in the Ensembler program with the "trim=True" flag. For this to work best, it's helpful if you happen to have a number of potential models that are also relatively distantly related to each other, to really highlight what is conserved in the fold. Best wishes, Randy Read > On 29 Aug 2017, at 1

Re: [ccp4bb] ample

Dear Patrick, Apologies for a partly non-CCP4 answer! You can use the HHPRED alignments in some of the software available in Phenix. One option is to provide the .hhr file to MRage, which will fetch the PDB entries, run Sculptor to modify the templates with one or more protocols, based on

Re: [ccp4bb] What are acceptable Rwork/Rfree for publication

Dear Gerard, I was puzzled by the statement that the UCLA anisotropy server characterises anisotropy in terms of a combination of effects restricted to lie along the crystallographic axes. That server is built on the anisotropy correction algorithm in Phaser, and from the beginning Phaser has

Re: [ccp4bb] Se-Met and Se-Cys double labelling

of successes when the highest sequence identity was in the range of 15-25%. Best wishes, Randy Read > On 21 Jun 2017, at 17:08, Mark J van Raaij <mjvanra...@cnb.csic.es> wrote: > > If your data is good enough, your SeMets alone might well be enough. > Soaking native crystals i

Re: [ccp4bb] No improvement in R-factor after Refmac.

that the likelihood score accounting for the effect of tNCS is pretty good at discriminating the two possibilities. Best wishes, Randy Read - Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical ResearchTel: +44 1223 336500 Wellcome Trust/MRC Building

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

your model is incomplete! Best wishes, Randy Read > On 21 Feb 2017, at 21:53, Hunter Moseley <hunter.mose...@gmail.com> wrote: > > Is there a straight-forward way to estimate the amount of missing electron > density that a particular protein structure is missing based on

Re: [ccp4bb] Phaser MR pairwise percent packing criterion

change conformation slightly so you don't want it in the search model, but you want to exclude solutions that would create clashes with that domain. Best wishes, Randy Read > On 17 Feb 2017, at 08:28, Xiao Lei <xiaolei...@gmail.com> wrote: > > Dear CCP4bb members, > > I fo

Re: [ccp4bb] Glass etching of structure

I’ve been very happy with Luminorum too, getting them to make blocks for PhD students when they finish. Patrick Goldsmith there has been incredibly helpful with making sure that all the little things, like the bonds to post-translational modifications that I wanted to be visible, were just

Re: [ccp4bb] phaser

with us! Best wishes, Randy Read > On 6 Jan 2017, at 14:01, Sidhu, Khushwant (Dr.) <k.si...@leicester.ac.uk> > wrote: > > Dear all, > > A user has upgraded to ccp4-7 on her Mac. Previously phaser was running fine. > She is now getting the following error. Could some

Re: [ccp4bb] unusual monoclinic relation?

be some unexpectedly large conformational change, but you probably have a reasonable idea of what kinds of motions occur in your system. Good luck, and have a happy Christmas regardless! Randy Read > On 19 Dec 2016, at 08:43, Andrew Lovering <a.lover...@bham.ac.uk> wrote: > > Dear Al

[ccp4bb] Recent improvements in Phaser for systematically weak data

in hearing from anyone who finds that this makes a difference for other cases. Best wishes, Randy Read -- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: + 44 1223 336500 Wellcome Trust/MRC Building Fax: + 44

Re: [ccp4bb] Phaser: tNCS present but correction not applied

Hi, That message should mean that you didn't ask for a number of molecules divisible by the order of the tNCS. With that vector you need to search for an even number of copies. Let me know if that doesn't explain what you're saying. Best wishes, Randy Read Randy J. Read > On 25

Re: [ccp4bb] MrBump and Balbes Molecular Replacement of multiple copies in ASU Failed even with high homology model

to make an ensemble in which loops that deviate among the different models have been trimmed off. If you need more advice on how to do this, you can get in touch off-line. Best wishes, Randy Read - Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute

Re: [ccp4bb] MR phasing using Negative Stain EM reconstruction

-atomic model by docking them into the shape of the negative stain image. Such a model would add substantial higher-resolution information. Best wishes and good luck, Randy Read > On 25 Oct 2016, at 02:49, Pascal Egea <pas...@msg.ucsf.edu> wrote: > > Dear All, > >

Re: [ccp4bb] Twinning/Spacegroup Woes

considerably better than the current CCP4 version). Also, the tool Zanuda in CCP4 can be very effective for working out the true symmetry. Best wishes, Randy Read > On 4 Oct 2016, at 00:26, Rhys Grinter <rhys.grin...@monash.edu> wrote: > > Dear All, > > As

Re: [ccp4bb] [phenixbb] accept MR solution even if the number of clashes is above the threshold

of spacegroup. Best wishes, Randy Read - Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical ResearchTel: +44 1223 336500 Wellcome Trust/MRC Building Fax: +44 1223 336827 Hills Road

Re: [ccp4bb] reference needed for TRUNCATE NO equation.

Hi Bernhard, Thanks for that, but it reinforces my impression (also reinforced offline by George Sheldrick) that this is something that was floating around at some point, and no-one ever bothered to put it in a proper publication. The background is that we've just submitted a paper on a new

Re: [ccp4bb] SUMMARY: Equation Editor woes with Office 2011 for Mac

in a followup, if other solutions become popular, they'll accommodate them at the IUCr journals. In the meantime, I guess I'll be learning the built-in editor. Randy Read On 18 May 2015, at 09:10, Randy Read rj...@cam.ac.uk wrote: Rather off-topic, but maybe someone on the list has found a way to work

Re: [ccp4bb] Low Phaser RFZ

pseudosymmetry, but as Phil Evans says the space group is a hypothesis, and you always have to be prepared to reconsider the hypothesis later if, say, it turns out to be difficult to refine the structure.) Best wishes, Randy Read On 19 May 2015, at 01:36, Eric Karg 052044071b36-dmarc-requ

[ccp4bb] Equation Editor woes with Office 2011 for Mac

Rather off-topic, but maybe someone on the list has found a way to work around this! There’s a problem with the Equation Editor in Office 2011 for Mac (i.e. the one that is based on a stripped-down version of MathType, which you get with Insert-Object-Microsoft Equation). You can insert an

Re: [ccp4bb] Phaser going into infinite loop in Ample

Hi Dale, It must actually be AMPLE deciding how many copies to search for. Phaser will give you some information about how consistent the specified composition is with the Matthews volume, but it just searches for the number of copies that it's instructed to look for. We haven't put the

Re: [ccp4bb] Sortwater NCS Matrix input

44.51719. Best wishes, Randy Read On 15 Apr 2015, at 17:21, Shane Caldwell shane.caldwel...@gmail.com wrote: good enough to pass the orthonormal test. .. scratch that, it passes sometimes and still fails for other structures/chains. So I'm still in search of a higher-precision

Re: [ccp4bb] adjusting bad Ramachandran angles

applies here (see the Wikipedia page): When a measure becomes a target, it ceases to be a good measure. From memory I believe Randy Read and George Sheldrick have commented that Ramachandran plots are a good measure of structure quality, and therefore should not be used explicitly

Re: [ccp4bb] Poor experimental phases for a largish structure...

in the literature. Best wishes, Randy Read - Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical ResearchTel: +44 1223 336500 Wellcome Trust/MRC Building Fax: +44 1223 336827 Hills Road

Re: [ccp4bb] Absence of contact between layers in a crystal

Actually, if you go back through the archive of CCP4-BB from the first time this came up, I think you'll find that there are real crystals with apparent gaps in the packing. This can arise because of statistical disorder, where there are two or more ways that a statistically-disordered layer

Re: [ccp4bb] Bulk solvent correction in Phaser MR LF

the equation wasn't given in the documentation, so I've just updated that: http://www.phaser.cimr.cam.ac.uk/index.php/Keywords#SOLPARAMETERS Best wishes, Randy Read On 3 Feb 2015, at 13:49, Bernhard Rupp (Hofkristallrat a.D.) hofkristall...@gmail.com wrote: Hi Fellows, I cannot find

Re: [ccp4bb] CCP4 for twinned crystals?

/index.html. Best wishes, Randy Read On 2 Feb 2015, at 16:16, Keller, Jacob kell...@janelia.hhmi.org wrote: Dear Crystallographers, Is there any software in CCP4 which can solve twinned structures? I have several datasets which appear to be tetartohedrally twinned, with possible spacegroup

Re: [ccp4bb] PHASER MR solution

solution, so it was probably at least reasonably clear. We’re stlll working on how to give the clearest possible indication at the end of a run as to whether you should be confident that it is correct. Best wishes, Randy Read - Randy J. Read Department of Haematology, University of Cambridge

Re: [ccp4bb] phase shift vs non-isomorphism

Hi, Bart Hazes' sftools program does map correlation in resolution shells in this way, and may even have been doing it before 1996 if I'm remembering correctly. Randy On 27 Jan 2015, at 21:12, Alexandre OURJOUMTSEV sa...@igbmc.fr wrote: Dear Phil, Gerard Bricogne pointed out a long time

Re: [ccp4bb] PHASER MR solution

orthorhombic space groups is that some of the reflections will become systematically absent so they will be discarded, but Phaser will do that internally when testing all the space groups. Best wishes, Randy Read - Randy J. Read Department of Haematology, University of Cambridge Cambridge

[ccp4bb] Free X-ray diffraction setup

...@cam.ac.uk. Best wishes, Randy Read -- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: + 44 1223 336500 Wellcome Trust/MRC Building Fax: + 44 1223 336827 Hills RoadE

Re: [ccp4bb] CCP4 Scalepack2mtz problem: Anisotropy correction failed

in CCP4. However, I’m not getting the same results, using version 1.15.10 of ctruncate from CCP4-6.4 on a Mac (I haven’t updated yet to 6.5). Which version of ctruncate and which operating system were you using? Best wishes, Randy Read - Randy J. Read Department of Haematology

Re: [ccp4bb] molecular replacement with poor model

Dear Ursula, 18% identity is really in the twilight zone for molecular replacement, where it may work but there are certainly no guarantees. However, there’s a feature in Phaser that is useful for this kind of problem, i.e. the “rotate around” option, where you take advantage of knowing the

Re: [ccp4bb] Challenging Mol.Rep. Problem

, Randy Read - Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical ResearchTel: +44 1223 336500 Wellcome Trust/MRC Building Fax: +44 1223 336827 Hills RoadE-mail: rj

Re: [ccp4bb] Intensities and amplitudes

on F) even though the structure had been refined against intensitites, then everyone was happy. Do I correctly understand that you have developed new (better) maximum likelihood criteria for use with I rather than F? Best wishes, George On 12/02/2014 10:26 PM, Randy Read wrote: Dear

Re: [ccp4bb] Intensities and amplitudes

amplitudes that have been through French Wilson, so that new procedures based on intensities won’t be able to be applied with their full power. Best wishes, Randy Read - Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical ResearchTel: +44 1223

Re: [ccp4bb] Intensities and amplitudes

). Thanks, Pavel On Tue, Dec 2, 2014 at 1:26 PM, Randy Read rj...@cam.ac.uk wrote: Dear Mohamed, At the moment, a lot of programs require amplitudes, but I believe that they should all eventually be updated to use intensities. In fact, we’re in the end stages of a large project to switch

[ccp4bb]

could send me a full logfile offline and I could tell you whether there’s anything you should note in there. Best wishes, Randy Read On 28 Nov 2014, at 13:15, rohit kumar rohit...@gmail.com wrote: Dear all, i am solving a structure of 2.5 A resolution by PHASER but every time i got

Re: [ccp4bb] R free flag missing after ARP/wARP?

the Rfree flag, which makes sense since you need cross-validation data in order for likelihood targets to be calibrated properly. But maybe the developers have some set of test cases that led them to choose the opposite as the default. Best wishes, Randy Read On 20 Oct 2014, at 14:24, luzuok luzuo

Re: [ccp4bb] Molecular Replacement model preparation

strategies. It’s only if this fails that you’ll want to choose the strategy and parameters manually. Best wishes, Randy Read - Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical ResearchTel: +44 1223 336500 Wellcome Trust/MRC Building

Re: [ccp4bb] Phaser question, twinning, DIALS, suggestions welcome

Hi Jurgen, You could send me a logfile off-list, and maybe I would spot something in there. We’ve put some effort into putting more intelligence into the Phaser search, so that it adapts to the initial perceived difficulty of the problem in setting the initial parameters, and then adapts to

Re: [ccp4bb] Phaser question, twinning, DIALS, suggestions welcome

Hi again, I should have mentioned that, if you have a good enough model, it’s often possible to solve the structure in P1. The molecular replacement solution will settle on one of the twin domains (or you may end up with more than one solution, related by the twin law(s)). Then the symmetry

Re: [ccp4bb] Phaser MR problem

(2-fold helps somewhat but is less powerful); otherwise, you’re likely to need some additional phase information. Best wishes, Randy Read - Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical ResearchTel: +44 1223 336500 Wellcome Trust/MRC

Re: [ccp4bb] Multiple pseudotranslations vectors in P1

be a bug and we’d want to see the log file! If you’d like, you could send the logfile off-line and I could tell you how I might approach dealing with tNCS in your case. Best wishes, Randy Read - Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute

Re: [ccp4bb] Problem in molecular replacement

consider is that the space group may not be correct. Good luck! Randy Read On 24 Jul 2014, at 13:06, Antony Oliver antony.oli...@sussex.ac.uk wrote: Try using DNA as a search model - this has worked very successfully in our hands before. Tony. - - - - - - - - - - - - - - - - - - Dr

Re: [ccp4bb] New PDB validation reports

in a similar way. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2631636/) Some indication of completeness probably would be a good thing to include in the validation reports. Best wishes, Randy Read On 10 Jul 2014, at 20:26, Katherine Sippel katherine.sip...@gmail.com wrote: Hi all, I've

Re: [ccp4bb] packing test PHASER

I agree that looking at the packing is a good idea, but I also agree that having the wrong space group is a likely possible explanation. That’s the most common scenario when there are many clashing solutions with high TFZ scores. Randy Read On 17 Jun 2014, at 15:52, Roger Rowlett rrowl

Re: [ccp4bb] CNS MR Help

experimental phasing. Best wishes, Randy Read On 12 Jun 2014, at 20:14, Appu kumar appu.kum...@gmail.com wrote: Hello All, I have tried MR in Phaser, MRage, Molrep , Mrbump but i am not getting the true solution which it supposed to be. Although the resoution of data

Re: [ccp4bb] [ccp4bb] phaser issue MR

and translated. If you look at that file, you’ll see that it doesn’t contain the ENSEMBLE definitions, so those still have to be provided in the script that refers to the .sol file. Best wishes, Randy Read - Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute

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