Re: [ccp4bb] Question about Refmac
I remember we discussed this a lot about a year ago when Ed Berry revived a thread from 2003! https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=ind1905=CCP4BB=D=72099 I think the upshot of it all was that you do not need to use shells even with quite high NCS since Ian Tickle rightly persuaded us that over-fitting is due to measurement errors and there is no reason to expect these to be correlated for NCS-related reflections. However, as you have probably found out by now, you can make an R-free set in shells using the reflection file editor in phenix. From memory you may also need to make sure that you use a CCP4-style R-free flag (i.e. the free-set reflections should be flagged zero) if you are going to use Refmac. There's a screenshot here: http://u.cubeupload.com/jbcooper/202006160114071280x8.png Hope this helps!On Monday, 15 June 2020, 17:42:15 BST, Eleanor Dodson <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote: Hmm - this finally was rather deprecated - there are some less happy consequences to have all reflections in a particular resolution shell excluded. If your NCS means there is pseudo- symmetry in the diffraction and it would be possible to have a cell with higher point symmetry (an example might be be Pmmm or P4mm if a(Pmmm) ~ b(P). ) then you could assign freer flags in the higher symmetry group and extend then to the lower... What is your cell, and do you know the NCS operators?Eleanor On Mon, 15 Jun 2020 at 16:54, wrote: Hello, I'm refining protein structure in Refmac and I have NCS greater than 4 ( I've 8 identical subunits in the asymmetric unit). In the "Refinement parameters" section in Refmac, how can I pick Rfree set based on thin resolution shells rather than in the normal random method? I've read about the program "dataman" from the usf suite which could help with this but found it very complicated. Do you have any advice to solve this? or would you recommend any other program? Thank you in advance To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] Using SFall for map conversion
Ian, I can, as a not very scientific footnote, confirm that Jim Austin still has your Convex on his farm and, it seems, most of the manuals: http://u.cubeupload.com/jbcooper/smallIMGP0087.jpg http://u.cubeupload.com/jbcooper/smallIMGP0086.jpg http://u.cubeupload.com/jbcooper/smallIMGP0078.jpg http://u.cubeupload.com/jbcooper/smallIMGP0077.jpg http://u.cubeupload.com/jbcooper/smallIMGP0089.jpg http://u.cubeupload.com/jbcooper/smallIMGP0084.jpg http://u.cubeupload.com/jbcooper/smallIMGP0103.jpg http://u.cubeupload.com/jbcooper/smallIMGP0110.jpg He also has at least one of the ex-bbk Evans & Sutherland PS300's: http://u.cubeupload.com/jbcooper/smallIMGP0091.jpg http://u.cubeupload.com/jbcooper/smallIMGP0093.jpg A few cobwebs, but pretty good going really for a 'former' pig-shed!! Not sure what happened to the 11/750, though... School of Pharmacy rings a bell?? None of this matters, but I just thought you might like to practice some 'big-iron' byte-swapping again, and if so, York is the place to go, after covid-19, of course ;-0 ;-0On Friday, 15 May 2020, 10:47:40 BST, Ian Tickle wrote: Hi, that would have to be a very old map! I remember implementing the auto-byte swap for VMS (necessary as we had both a Convex C220 running Unix and a VAX 11/750)! In fact the Convex was rescued from scrap by Jim Austin and is still working: http://www.corestore.org/convex.htm Cheers -- Ian Cheers -- Ian On Fri, 15 May 2020 at 09:24, Philippe BENAS <0d88e888355a-dmarc-requ...@jiscmail.ac.uk> wrote: Dear Bernhard, Is it an old map ? Back to the old VAX times I had to dump CCP4 maps to ascii map files, then swap bytes from VAX-DOS to Unix before converting them again to a CCP4 map format (I think I was using mapman from USF) on a Unix workstation and be able to read them in Frodo-Strasbourg or O. At least you could give it a shot and the ascii map file would help you figuring out the issue by a visual inspection of the header and sections. All the best, Philippe Philippe BENAS, Ph.D. ARN UPR 9002 CNRS IBMC Strasbourg 2, Allée Konrad Röntgen F-67084 STRASBOURG cedex +33.3.8841.7109 E-mails: p.be...@ibmc-cnrs.unistra.fr, philippe_be...@yahoo.fr URLs: http://www-ibmc.u-strasbg.fr/ , http://www-ibmc.u-strasbg.fr/spip-arn/ Le jeudi 14 mai 2020 à 22:45:09 UTC+2, Bernhard Rupp a écrit : Hi Fellows, I am failing on conversion of a ccp4 map to mtz using Sfall I provide as a scale reference a mtz with FP SIGFP and R free All cell constants and SG 20 and map headers seem to agree. But I receive following warning: *** WARNING - your map spacegroup is different to the program default one *** and later >> CCP4 library signal library_file:Cannot open file (Warning) raised in tmpfile() failed, opening normal file instead. << INPUT X USED AS X INPUT Y USED AS Z INPUT Z USED AS Y Which then leads to the imho - given above- justified complaint: Check map header agrees with fixed requirements for SFcalc for this spacegroup. Check Nxyz 180 200 120 180 200 120 Check map header agrees with fixed requirements for SFcalc for this spacegroup. Check Iuvw 3 2 1 3 1 2 SFALL: Fatal disagreement between input info and map header How do I fix this ? In principle all the information is there to do the job… Many thx, BR -- Bernhard Rupp Crystallographiae Vindicis Militum Ordo http://www.hofkristallamt.org/ b...@hofkristallamt.org +1 925 209 7429 +43 676 571 0536 -- Many plausible ideas vanish at the presence of thought -- To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] modelling MET (methionine) and SME (met-sulfoxide)
Occupancy. On Sunday, 26 April 2020, 20:41:49 BST, Abhishek Anan wrote: Dear all, Thanks for the suggestions. It is synthetic peptide so the residue identity is unambiguous. I am not clear on how to model both MET and SME in coot, do a real space refinement and then save the file for refinement in phenix. I tried alternate conformation and then mutating one of them but that didn't work as both conformations were mutated. What I also just noticed is that the refinement of structure with just SME results in positive densities around all side chain carbons even with the SME.cif loaded into phenix. What could be wrong here? best wishes, Abhishek On 4/26/20, Paul Emsley wrote: > > On 26/04/2020 16:21, Abhishek Anan wrote: >> Dear all, >> >> I have a peptide crystal structure at 0.97 Å that contains two surface >> exposed Methionine. The CE atoms of both MET have a suspiciously high >> b-factor >40 and a positive density. In addition, the sulfur atom SD >> has a large negative density (b-factor ~23). >> >> I initially suspected that the MET may have oxidized to MET-sulfoxide >> and tried to model only the MET-sulfoxide. This again resulted in >> negative density. >> >> I think that the peptides might be partly oxidized which brings me to >> my question. Is there a way to model both MET and MET-sulfoxide into >> the density much like alternate conformation with options to refine >> their respective occupancies. > > > Yes. This is called micro-heterogeneity > > And is documented here: > > https://www.wwpdb.org/documentation/procedure > > That should "just work" if you then give the model to refmac. > > FWIW, Coot is, AFAIR, not 100% happy with such models. > > Paul. > > > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] Covalent Cysteine Aduct
Sorry, that was the wrong zenodo link! The correct one is: https://doi.org/10.5281/zenodo.220983 On Friday, 27 March 2020, 23:06:01 GMT, Jonathan Cooper <0c2488af9525-dmarc-requ...@jiscmail.ac.uk> wrote: If you can model it as a lysine, it will be the beta-ME adduct. There's a good one in 1b4e (see attached) which Eileen Jaffe pointed out to me and I never got round to sorting out. Now there's another one of 'mine' for which the data have not been deposited, but I did put the images on zenodo 4 years ago (https://doi.org/10.5281/zenodo.51560) if anyone fancies a little lock-down project!! On Friday, 27 March 2020, 22:02:20 GMT, CRAIG A BINGMAN <21371e2fba31-dmarc-requ...@jiscmail.ac.uk> wrote: My guess would be that the chains were prepared under reducing conditions, mixed, and then allowed to oxidize. The surface adduct could easily form during this process. On Mar 27, 2020, at 4:38 PM, Cowan, Richard H. (Dr.) wrote: Hi, The Fab constructs have a c-terminal cysteines on both the heavy and light chains, which should form a disulphide. Adding reducing agent to the purification of the protein would potentially reduce this disulphide, possible causing issues the stability and heterogeneity? At least that's my understanding? Thanks, Dr Richard Cowan Research Associate HWLSB 1/05Department of BiochemistryUniversity of LeicesterLancaster RoadLeicester, LE1 9HN, U.K. Phone +44 (0) 116 229 7077 From: CCP4 bulletin board on behalf of Paul Emsley Sent: 27 March 2020 21:33 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Covalent Cysteine Aduct On 27/03/2020 21:06, Cowan, Richard H. (Dr.) wrote: although [BME] seems unlikely, since the crystallized protein is a Fab. I don't follow. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] Covalent Cysteine Aduct
If you can model it as a lysine, it will be the beta-ME adduct. There's a good one in 1b4e (see attached) which Eileen Jaffe pointed out to me and I never got round to sorting out. Now there's another one of 'mine' for which the data have not been deposited, but I did put the images on zenodo 4 years ago (https://doi.org/10.5281/zenodo.51560) if anyone fancies a little lock-down project!! On Friday, 27 March 2020, 22:02:20 GMT, CRAIG A BINGMAN <21371e2fba31-dmarc-requ...@jiscmail.ac.uk> wrote: My guess would be that the chains were prepared under reducing conditions, mixed, and then allowed to oxidize. The surface adduct could easily form during this process. On Mar 27, 2020, at 4:38 PM, Cowan, Richard H. (Dr.) wrote: Hi, The Fab constructs have a c-terminal cysteines on both the heavy and light chains, which should form a disulphide. Adding reducing agent to the purification of the protein would potentially reduce this disulphide, possible causing issues the stability and heterogeneity? At least that's my understanding? Thanks, Dr Richard Cowan Research Associate HWLSB 1/05Department of BiochemistryUniversity of LeicesterLancaster RoadLeicester, LE1 9HN, U.K. Phone +44 (0) 116 229 7077 From: CCP4 bulletin board on behalf of Paul Emsley Sent: 27 March 2020 21:33 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Covalent Cysteine Aduct On 27/03/2020 21:06, Cowan, Richard H. (Dr.) wrote: although [BME] seems unlikely, since the crystallized protein is a Fab. I don't follow. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] CCP4BB vs COVID19
A bit off-topic, and not wishing to tempt fate, of course, here are the No. cases by date for two typical outer-London boroughs (of absolutely no particular interest to me ;-), one about 4 times bigger than the other: http://u.cubeupload.com/jbcooper/2020032316h22m13s.png Could I be forgiven for seeing a bit of a plateau there? I saw an article yesterday saying you could only make the global numbers slope-off by taking logs on the Y-axis - the age-old adage that logs will flatten everything!! I haven't had to do that in this case. I'll be more crystallographic next time. On Sunday, 22 March 2020, 20:26:51 GMT, Darren Hart wrote: Structure of 2019-nCov RNA polymerase: https://www.biorxiv.org/content/10.1101/2020.03.16.993386v1.full.pdf+html Here we report the cryo-EM structure of 2019-nCoV full-length nsp12 in complex with cofactors nsp7 and nsp8 at a resolution of 2.9-Å...A comparative analysis to show how remdesivir binds to this polymerase is also provided. Darren On 22/03/2020 19:18, Nikolay Dobrev wrote: Dear all, I assume most of you are aware of the EMBL-EBI datahub which was set up in January to provide essential virus research data to all scientists, but in case someone missed it I would like to share the link: https://www.ebi.ac.uk/ena/pathogens/covid-19 You can find all relevant data, from COVID-19 genome sequencing data up to x-ray and cryo-EM structures of relevant proteins. Stay healthy, Nikolay Nikolay Dobrev Scientific Officer, Protein Expression and Purification Core Facility EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany T +49 6221 387 8633 | M +49 173 684 0532 twitter.com/EMBLorg | facebook.com/embl.org | youtube.com/user/emblmedia Visit www.embl.org/events for a complete list of all EMBL events. On Sun, Mar 22, 2020 at 17:26, DUMAS Philippe (IGBMC) wrote: Relevant to the discussion: * Cell, Vol. 110, 551–561, September 6, 2002, Copyright 2002 by Cell Press An RNA Thermosensor Controls Expression of Virulence Genes in Listeria monocytogenes * Bacterial RNA thermometers: molecular zippers and switches Jens Kortmann and Franz Narberhaus NATURE REVIEWS | MICROBIOLOGY VOLUME 10 | APRIL 2012 | 255 *An RNA Thermometer Activity of the West Nile Virus Genomic 30-Terminal Stem-Loop Element Modulates Viral Replication Eciency during Host Switching Viruses 2020, 12, 104; doi:10.3390/v12010104 * Temperature triggers immune evasion by Neisseria meningitidis Edmund Loh1*, Elisabeth Kugelberg2*, Alexander Tracy1, Qian Zhang2, Bridget Gollan2, Helen Ewles2, Ronald Chalmers3, Vladimir Pelicic2 & Christoph M. Tang1,2 Nature (2013) Philippe Dumas De: "James Holton" À: "CCP4BB" Envoyé: Dimanche 22 Mars 2020 16:38:28 Objet: Re: [ccp4bb] CCP4BB vs COVID19 Thank you Patrick, RNA structure is still structural biology, so I think relevant here. It seems to me that RNA as a thermometer would be an easy hypothesis to test? Has anyone measured virulence vs temperature in cell culture? The 3D structure of the genome is no doublt important. I wouldn't want to try crystallizing the whole thing, but I wonder if this might be an excellent target for cryoEM? A challenge for that "we can classify our way out of anything" philosophy? And the result would most certainly be interesting. -James Holton MAD Scientist On 3/21/2020 8:41 AM, Patrick Shaw Stewart wrote: James, this isn't conventional structural biology, but may be of interest, and I haven't been able get any mainstream virologists to think about it. The protein sequences are obviously of interest, but so are the RNA sequences at both ends of the Covid genome, which have conserved secondary structure. A few years ago a paper came out suggesting that wild-type influenza has multiple "RNA thermometers", which may play an important role in the tropism of influenza. Similar mechanisms may exist in other respiratory viruses, including Covid. My take on this, and the relevant papers, are below. Good luck to everyone and stay well, Patrick https://oldwivesandvirologists.blog/Covid-19-and-the-trade-off-model-of-selection/ My paper in Medical Hypotheses http://douglas.co.uk/f_ftp1/ShawStewart_final_1-s2.pdf Narberhaus, Franz, Torsten Waldminghaus, and Saheli Chowdhury. "RNA thermometers." FEMS microbiology reviews 30.1 (2006): 3-16. Chursov, Andrey, et al. "Specific temperature-induced perturbations of secondary mRNA structures are associated with the cold-adapted temperature-sensitive phenotype of influenza A virus." RNA biology 9.10 (2012): 1266-1274. Yang, Dong, and Julian L. Leibowitz. "The structure and functions of coronavirus genomic 3′ and 5′ ends." Virus research 206 (2015): 120-133. On Fri, Mar 20, 2020 at 10:59 PM James Holton wrote: You might think that as a structural biologist you won't be
Re: [ccp4bb] Catalina compatibility
And here: https://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg48104.html Best wishes, Jon Cooper. On Monday, 9 March 2020, 23:13:15 GMT, Jonathan Cooper <0c2488af9525-dmarc-requ...@jiscmail.ac.uk> wrote: I'm probably going to be beaten on this one, as you probably know, it has been discussed here recently: https://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg47716.html https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=CCP4BB;d908309.1911 The thing was to re-install Xquartz. I'm not a mac-person, but I 'helped' someone who is and this was the solution. We also copied .profile to .zprofile so the command line would work, but that may have not been necessary. This was a few months ago, so maybe out-of-date already. I don't know about XDS, sorry!! On Monday, 9 March 2020, 21:43:18 GMT, Oriana Fisher wrote: Dear all, I was wondering if anyone has updates or advice regarding software compatibility issues with the new Mac Catalina operating system. I tried installing several software packages on an iMac running Catalina and have not been able to get some programs (Coot and xdsgui, in particular) to work on it. Has anyone else encountered similar issues, or have workarounds/suggestions you’d be willing to share? I’m looking into buying another computer for my lab (Mac, ideally) and learned that Apple does not re-sell older computers or newer ones that are back-compatible with the older operating systems... Thanks so much in advance, Oriana ---Oriana S. FisherAssistant Professor of ChemistryLehigh University6 E Packer AveBethlehem, PA 18015Email: orf206@lehigh.eduPhone: (610)-758-6259 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] Catalina compatibility
I'm probably going to be beaten on this one, as you probably know, it has been discussed here recently: https://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg47716.html https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=CCP4BB;d908309.1911 The thing was to re-install Xquartz. I'm not a mac-person, but I 'helped' someone who is and this was the solution. We also copied .profile to .zprofile so the command line would work, but that may have not been necessary. This was a few months ago, so maybe out-of-date already. I don't know about XDS, sorry!! On Monday, 9 March 2020, 21:43:18 GMT, Oriana Fisher wrote: Dear all, I was wondering if anyone has updates or advice regarding software compatibility issues with the new Mac Catalina operating system. I tried installing several software packages on an iMac running Catalina and have not been able to get some programs (Coot and xdsgui, in particular) to work on it. Has anyone else encountered similar issues, or have workarounds/suggestions you’d be willing to share? I’m looking into buying another computer for my lab (Mac, ideally) and learned that Apple does not re-sell older computers or newer ones that are back-compatible with the older operating systems... Thanks so much in advance, Oriana ---Oriana S. FisherAssistant Professor of ChemistryLehigh University6 E Packer AveBethlehem, PA 18015Email: orf206@lehigh.eduPhone: (610)-758-6259 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] Protein fold and the moonlighting function
Hello, Re: "I think you’re asking about 2 proteins with a similar fold having similar but not exactly the same functions - yes, that does occur." Indeed, I suspect it is very common, if not the norm. OK, so I now gather/remember moonlighting proteins are ones with more than one function - thank you for the link to the very interesting database. Is perhaps the questioner asking if homologues of a moonlighting protein also have similar moonlighting functions? If so, I'm out of my depth on that one. Best wishes, Jon Cooper.On Sunday, 2 February 2020, 18:22:10 GMT, Jeffery, Constance J wrote: Hi Rajnandani, I’m happy to help you with questions about moonlighting proteins. My lab created the MoonProt Database (moonlightingproteins.org). I think you’re asking about 2 proteins with a similar fold having similar but not exactly the same functions - yes, that does occur. Best regards,Connie Jeffery On Feb 2, 2020, at 4:28 AM, Rajnandani Kashyap wrote: Dear All I am curious to know about the promiscuous activity of a protein based on their fold. Can a protein having same fold also have same function (say not 100% but some activity) as the homologous structure. Please also let me know few relevant PDB structures where such kind of activity is shown promising. Regards Rajnandani Kashyap PhD Student To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] Generating symmetry mates using python
Hello, I am sure that you have found that if you apply the symmetry operations yourself, the resulting molecules can come out miles apart, so you need to find the right unit cell translations that bring them close together again to generate the real crystal packing. Coot does all this very well indeed (happy new year, Paul). In the old ccp4i suite, there is CONTACT and NCONT which you can find in the program list or even more if you are happy to use the command line. I think I would have a look at the documentation, etc, for CONTACT. On Friday, 10 January 2020, 20:41:27 GMT, orly avraham wrote: Hi all, I am a crystallographer currently employing computational methods as well as experimental crystallography.I am trying to generate symmetry mates in python (working with pandas dataframes), in order to analyze inter-sub-unit interactions. To do so I am trying to use the info in "REMARK 290 CRYSTALLOGRAPHIC SYMMETRY" and manually (using numpy) perform a matrix multiplication with the relevant translation (xyz*rotation + translation). For some reason this doesn't work consistently and I feel I need to use the info in CRYST1 to obtain the unit cell and multiplication matrix. Here I ran into trouble with extracting the correct symmetry operations based on each space group. I found spglib but it doesn't quite solve the problem.I also tried opening PyMol through the command and generating symmetry mates this way. It worked on a few files but failed quite quickly (segmentation fault) and was also very slow. Can anyone suggest a useful solution, preferably clear to use and/or well documented? Or even have a python script/code they can share for this? Best regards,Orly -- Orly Avraham, Ph.D.Postdoctoral fellowThe lab of Prof. Oded Livnahand the lab of Prof. Ora Schueler-FurmanThe Hebrew University of JerusalemIsrael To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] Any guesses? - What is this feature modelled (wrongly) as 3 waters
Hello Eleanor If I may ask, are you sure the pucker is correct for the proline on the left? In my humble opinion the proline C-alpha doesn't look very tetrahedral and maybe this residue has some unexplained density at the back. Maybe the peptide with the odd extension wants to go down and to the left a bit. How does the extension behave at higher contour levels and how does the difference map look in that region? It looks quite high resolution data, so in fear of repeating myself today, I am curious if it has been refined with anisotropic B's since this does have a habit of cleaning-up oddities in the maps. Beyond that I can only suggest its a Bernal bug. Best wishes, Jon.C. On Thursday, 7 November 2019, 13:12:45 GMT, Eleanor Dodson <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote: seen in a high resolution map? There is at least one other similar feature??? Eleanor To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] D amino acids in Coot
Hello, you are right but you can get round it by reading in a cif for D-ala first i.e. 'Import cif dictionary' before doing the 'Get Monomer' thing. I got the cif file from the web (its attached). If you do this in the right order you do get a D-ala on the screen! On Wednesday, 30 October 2019, 18:38:56 GMT, Pavel Mader wrote: Hi everyone, if I load D-Ala (Get monomer DAL) in Coot and superpose (LSQ) it with regular L-Ala (ALA), the two amino acids look identical to me (not mirror images of each other), see attached image. I have the same problem with D-His. Is this normal, or am I missing something? Thanks, Pavel To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 Component_data_DAL.cif Description: Binary data
Re: [ccp4bb] Question about losing reflections when refining in PHENIX
Hello, it looks as though the No observations that phenix is reporting is exactly twice the number of unique reflections. Perhaps phenix is reporting the merging statistics for the Friedel pairs (i.e. F(+) and F(-)) within your merged dataset. Hence the stats look much better than those for the raw data fed to Aimless. I think you should be able to make a perfectly respectable Table 1 with the merging stats from Mosflm/Aimless and the refinement stats from phenix but others will know how to do it properly. On Monday, 28 October 2019, 20:05:52 GMT, Nemanja Vuksanovic wrote: Dear All, I need a bit of help with an issue I am encountering with one of my datasets when using phenix.refine. After processing data with Mosflm I get the following parameters: Overall InnerShell OuterShell Low resolution limit 65.69 65.69 2.55High resolution limit 2.45 8.83 2.45Rmerge (within I+/I-) 0.127 0.057 0.817 Rmerge (all I+ and I-)0.130 0.058 0.848Rmeas (within I+/I-)0.140 0.063 0.898Rmeas (all I+ & I-) 0.136 0.061 0.888Rpim (within I+/I-) 0.058 0.027 0.373Rpim (all I+ & I-) 0.040 0.019 0.263Rmerge in top intensity bin 0.062- - Total number of observations 288903 5972 32430Total number unique25576 592 2857Mean((I)/sd(I)) 13.1 23.6 3.5Mn(I) half-set correlation CC(1/2) 0.998 0.998 0.874Completeness 100.0 99.7 100.0Multiplicity 11.3 10.1 11.4Mean(Chi^2) 1.08 0.72 0.96Anomalous completeness 100.0 99.9 100.0 Anomalous multiplicity 5.8 5.6 5.8DelAnom correlation between half-sets -0.270-0.466-0.055Mid-Slope of Anom Normal Probability 0.788 - - After molecular replacement with PHASER and then refinement with Phenix.refine, (defauIt settings in both) I generated a TABLE 1 in PHENIX and noticed that the total number of observations has dropped, significantly lowering multiplicity and R factors. Could you perhaps give me your opinion on what might be causing this discrepancy?I'd be happy to provide the mtz file and any other information if needed. Table 1. Data collection and refinement statistics. Wavelength Resolution range 56.89 - 2.451 (2.539 - 2.451) Space group I 2 3 Unit cell 160.9 160.9 160.9 90 90 90 Total reflections 51076 (5030) Unique reflections 25538 (2515) Multiplicity 2.0 (2.0) Completeness (%) 99.96 (100.00) Mean I/sigma(I) 13.37 (3.56) Wilson B-factor 41.08 R-merge 0.0263 (0.1879) R-meas 0.03719 (0.2657) R-pim 0.0263 (0.1879) CC1/2 0.999 (0.895) CC* 1 (0.972) Reflections used in refinement 25532 (2515) Reflections used for R-free 1300 (121) R-work 0.2698 (0.3589) R-free 0.3115 (0.3897) CC(work) 0.908 (0.679) CC(free) 0.885 (0.444) Number of non-hydrogen atoms 2310 macromolecules 2310 Protein residues 286 RMS(bonds) 0.010 RMS(angles) 1.01 Ramachandran favored (%) 96.40 Ramachandran allowed (%) 2.52 Ramachandran outliers (%) 1.08 Rotamer outliers (%) 0.00 Clashscore 8.47 Average B-factor 43.55 Best Regards,Nemanja Vuksanovic -- Graduate StudentDepartment of Chemistry and BiochemistryUniversity of Wisconsin-Milwaukee To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] Diffractometer archeology
Its more history than science, but for posterity I have started putting together some images and other memorabilia of the Hilger and Watts diffractometer, which some may remember! In case anyone is interested, the link is here: hilgerwatts.blogspot.com Feel free to drop me a line if you have anything that could be added! To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] Prepare files with anisotropic B-values for deposition in i2.
In i2 if you try the 'Prepare files for deposition' to make the cif's, it seems to do a round of refinement, presumably to get the final stats, etc, but the anisotropic B-factors seem to be ignored and are lost from the output file, as far as I can tell. Hence, the R and R-free rise quite a bit. I can get round it with pdb_extract on the deposition web site, but was wondering if I am missing something in the i2 approach. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] Figure of merit in refinement
This is a very good place to start: https://www-structmed.cimr.cam.ac.uk/Course/Statistics/statistics.html Also recommend this one: https://doi.org/10.1107/S0108767386099622 and Main, P. (1979) Acta Cryst. A35, 779-85 - the maths in this one are a bit easier! On Wednesday, 2 October 2019, 22:47:56 BST, Andre LB Ambrosio wrote: Dear all, How is the phase error estimated for any given reflection, specifically in the context of model refinement? In terms of math I mean. How useful is FOM in assessing the phase quality, when not for initial experimental phases? Many thank in advance, Andre. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] Optimisation of 2D very thin plates to thick pl
Adding chymotrypsin to your crystallisations in about 1:100 mass ratio with
your protein can help. You can quite easily find some papers on this method.
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Re: [ccp4bb] Calculating RMSD of a loop
Sorry, I was wrong about using STDEV in Excel. Instead you would need to put
in a formula to calculate the root mean square of your distances. On
Tuesday, 17 September 2019, 15:14:02 BST, Jonathan Cooper
wrote:
I think LSQKAB can output a list of CA distances of two structures. Might be
easier to fit them first in Coot since LSQKAB can be a pig to run and you may
have to use the command line. You could then select the region(s) you are
interested in and use a spreadsheet or a script to calculate the RMSD. I think
it will only be meaningful if the loops being compared are the same length in
both structures? If it is only one loop you could measure the CA-distances in
Coot and plug them into Excel for a quick STDEV.
Sent from Yahoo Mail on Android
On Tue, 17 Sep 2019 at 14:42, Kyle
Gregory<3632e92fcc15-dmarc-requ...@jiscmail.ac.uk> wrote:#yiv2001353542
P {margin-top:0;margin-bottom:0;}Hi all,
What is the best/easiest way to calculate RMSD of a loop for 2 c-alpha aligned
structures?
Thought I could do this in Coot but I only see this if I align the specific
loops, which I don't want to do.
Thanks,
Kyle
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Re: [ccp4bb] Calculating RMSD of a loop
I think LSQKAB can output a list of CA distances of two structures. Might be
easier to fit them first in Coot since LSQKAB can be a pig to run and you may
have to use the command line. You could then select the region(s) you are
interested in and use a spreadsheet or a script to calculate the RMSD. I think
it will only be meaningful if the loops being compared are the same length in
both structures? If it is only one loop you could measure the CA-distances in
Coot and plug them into Excel for a quick STDEV.
Sent from Yahoo Mail on Android
On Tue, 17 Sep 2019 at 14:42, Kyle
Gregory<3632e92fcc15-dmarc-requ...@jiscmail.ac.uk> wrote:#yiv2516608606
P {margin-top:0;margin-bottom:0;}Hi all,
What is the best/easiest way to calculate RMSD of a loop for 2 c-alpha aligned
structures?
Thought I could do this in Coot but I only see this if I align the specific
loops, which I don't want to do.
Thanks,
Kyle
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Re: [ccp4bb] Rfree from another mtz file
You should be able to get an idea of whether it has worked or not with viewHKL in the old GUI e.g. find a few reflections with R-free flag zero in your old dataset and note the indices. Then you can search the new dataset for these reflections and see if they are still flagged zero. You may need to export the MTZ's from the new GUI first. On Monday, 16 September 2019, 23:39:28 BST, Mariana Ajalla wrote: Dear all, We tried to use the Rfree set from a lower resolution data with a higher resolution from the same Crystal. To do so We used aimless at ccp4i with the option use free flag from another mtz file and extend the data. I think it worked, but now we don't know how to be sure we have the same Rfree set. Does anyone have a way to prove it? Thank you in advance, Best, Mariana To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] One protein, two data sets
I take it that the datasets are from different crystals. Are the crystallisation conditions the same? I can't spot any signs of a difference in indexing (but I may be wrong) so they look like different crystal forms. Are the processing statistics good for both? Is this a case for molecular replacement or experimental phasing? You could work with best diffracting one and solve that one first and then use it to solve the other by molecular replacement. Hope some of this helps. Sent from Yahoo Mail on Android On Sun, 8 Sep 2019 at 12:16, Prerana G. wrote: Dear all, We have two data sets of a protein with the following parameters:1. Space group P212121 a=61.0, b=100.34, c=133.23 No. of molecules in ASU - 2 2. Space group P212121 a=58.33, b=62.86, c=109.45 No. of molecules in ASU - 1 Can we use them as two different structures? Regards,Prerana To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] Another difficult MR case
Sorry forgot to mention, if you go down the impurities route, there is SAUC to
check for similar unit cells in the PDB
http://iterate.sourceforge.net/sauc/
And there used to be Nearest Cell but my phone can't find that one anymore ;-
Sent from Yahoo Mail on Android
On Thu, 29 Aug 2019 at 18:41, Jonathan Cooper wrote:
It would be useful to know the number of molecules per asymmetric unit and the
sequence similarity of the search model and target. There is always Molrep to
try which is good at NCS ;-
Sent from Yahoo Mail on Android
On Thu, 29 Aug 2019 at 18:30, David Briggs wrote:
#yiv8743831735 #yiv8743831735 -- .yiv8743831735EmailQuote
{margin-left:1pt;padding-left:4pt;border-left:#80 2px solid;}#yiv8743831735
Following on from Ivan's suggestion, SIMBAD might he worth a shot.
https://journals.iucr.org/d/issues/2018/07/00/rr5159/
The other thing you might try is handing the MR phases to the density modifying
and autobuilding program of your choice, increasing the number of cycles by
$arbitarylargenumber and then leaving it to run for a few hours/over night.
This has worked for me in the past when resolution was decent, phaser had found
an obviously correct MR solution, but the domain placed was only ~30-40% of the
total scattering mass of the ASU, and more conventional refinement was not
yielding decent maps outside the aforementioned domain.
Good luck!
Dave
--
Dr David C. Briggs
Senior Laboratory Research Scientist
Signalling and Structural Biology Lab
The Francis Crick Institute
London, UK
==
about.me/david_briggs
From: CCP4 bulletin board on behalf of Phil Jeffrey
Sent: Thursday, August 29, 2019 5:24:48 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Another difficult MR case Are you *sure* there's no
translational NCS ?
For example your first molecular replacement solution out of Phenix shows
EULER 293.6 27.7 288.7
FRAC -0.02 0.02 0.02
(that's "first molecule at origin in P1")
and
EULER 294.0 27.9 288.8
FRAC -0.37 0.02 0.02
which is essentially the same orientation, and a translation down one
crystallographic axis (a*)
And this suggests to me that either Xtriage or Phaser is missing
something here. Does Phaser find translational NCS in its initial data
analysis ? Unmodeled translational NCS could cause significant problems
with the molecular replacement search.
Phil Jeffrey
Princeton
On 8/29/19 11:28 AM, Napoleão wrote:
> Deal all,
> Sorry for the long post.
> I have a data set obtained from a crystal produced after incubating a
> protease with a protein which is mostly composed by an antiparallel beta
> sheet. I have tried numerous approaches to solve it, and failed.
> Molecular replacement using Phaser, and the protease or the protein as a
> template yields no solution. However, molecular replacement using only
> part of the beta sheet yields LLG=320 TFZ==28.0 (see below).
>
> The apparently good data extends to 1.9 A, as processed by XDS, and the
> space group is P1 (pointless agree). XDS info below:
>
> SPACE_GROUP_NUMBER= 1
> UNIT_CELL_CONSTANTS= 44.43 72.29 77.30 97.802 89.939 101.576
>
> a b ISa
> 9.647E-01 3.176E-03 18.07
>
> RESOLUTION NUMBER OF REFLECTIONS COMPLETENESS R-FACTOR
> R-FACTOR COMPARED I/SIGMA R-meas CC(1/2) Anomal SigAno Nano
> LIMIT OBSERVED UNIQUE POSSIBLE OF DATA observed
> expected Corr
> 1.90 24890 19149 23814 80.4% 58.1%
> 63.7% 11482 0.77 82.2% 63.8* 3 0.694 492
> total 163756 125884 146938 85.7% 10.6%
> 10.8% 75744 3.78 15.0% 99.0* -3 0.761 5834
>
>
> Xtriage in Phenix 1.16-3549 gives me all green lights (print below),
> suggesting the data presents no twinning, no translational NCS, no ice
> rings and is not anisotropic.
> https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Ffullonline.org%2Fscience%2Fphenix_xtriage_green.pngdata=02%7C01%7C%7Cde40f97d75824ea6519308d72c9d6fe0%7C4eed7807ebad415aa7a99170947f4eae%7C0%7C0%7C637026927009132543sdata=RMV8abo87ybMyxaqD%2FHgOakRhGvzGgsQXzkuzC4c8HI%3Dreserved=0
>
> Molecular replacement in Phaser yields single solutions like:
>
> Solution annotation (history):
> SOLU SET RFZ=3.0 TFZ=* PAK=0 LLG=29 RFZ=2.8 TFZ=8.8 PAK=1 LLG=310
> TFZ==27.6
> LLG=320 TFZ==28.0
> SOLU SPAC P 1
> SOLU 6DIM ENSE ensemble1 EULER 293.6 27.7 288.7 FRAC -0.02
> 0.02 0.02 BFAC
> -6.03
> SOLU 6DIM ENSE ensemble1 EULER 294.0 27.9 288.8 FRAC -0.37
> 0.02 0.02 BFAC
> -6.52
> SOLU ENSEMBLE ensemble1 VRMS DELTA -0.1983 RMSD 0.49 #VRMS 0.21
>
> or partial solutions like:
>
> Partial Solution #1 annotation (history):
>
Re: [ccp4bb] Another difficult MR case
It would be useful to know the number of molecules per asymmetric unit and the
sequence similarity of the search model and target. There is always Molrep to
try which is good at NCS ;-
Sent from Yahoo Mail on Android
On Thu, 29 Aug 2019 at 18:30, David Briggs wrote:
#yiv8743831735 #yiv8743831735 -- .yiv8743831735EmailQuote
{margin-left:1pt;padding-left:4pt;border-left:#80 2px solid;}#yiv8743831735
Following on from Ivan's suggestion, SIMBAD might he worth a shot.
https://journals.iucr.org/d/issues/2018/07/00/rr5159/
The other thing you might try is handing the MR phases to the density modifying
and autobuilding program of your choice, increasing the number of cycles by
$arbitarylargenumber and then leaving it to run for a few hours/over night.
This has worked for me in the past when resolution was decent, phaser had found
an obviously correct MR solution, but the domain placed was only ~30-40% of the
total scattering mass of the ASU, and more conventional refinement was not
yielding decent maps outside the aforementioned domain.
Good luck!
Dave
--
Dr David C. Briggs
Senior Laboratory Research Scientist
Signalling and Structural Biology Lab
The Francis Crick Institute
London, UK
==
about.me/david_briggs
From: CCP4 bulletin board on behalf of Phil Jeffrey
Sent: Thursday, August 29, 2019 5:24:48 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Another difficult MR case Are you *sure* there's no
translational NCS ?
For example your first molecular replacement solution out of Phenix shows
EULER 293.6 27.7 288.7
FRAC -0.02 0.02 0.02
(that's "first molecule at origin in P1")
and
EULER 294.0 27.9 288.8
FRAC -0.37 0.02 0.02
which is essentially the same orientation, and a translation down one
crystallographic axis (a*)
And this suggests to me that either Xtriage or Phaser is missing
something here. Does Phaser find translational NCS in its initial data
analysis ? Unmodeled translational NCS could cause significant problems
with the molecular replacement search.
Phil Jeffrey
Princeton
On 8/29/19 11:28 AM, Napoleão wrote:
> Deal all,
> Sorry for the long post.
> I have a data set obtained from a crystal produced after incubating a
> protease with a protein which is mostly composed by an antiparallel beta
> sheet. I have tried numerous approaches to solve it, and failed.
> Molecular replacement using Phaser, and the protease or the protein as a
> template yields no solution. However, molecular replacement using only
> part of the beta sheet yields LLG=320 TFZ==28.0 (see below).
>
> The apparently good data extends to 1.9 A, as processed by XDS, and the
> space group is P1 (pointless agree). XDS info below:
>
> SPACE_GROUP_NUMBER= 1
> UNIT_CELL_CONSTANTS= 44.43 72.29 77.30 97.802 89.939 101.576
>
> a b ISa
> 9.647E-01 3.176E-03 18.07
>
> RESOLUTION NUMBER OF REFLECTIONS COMPLETENESS R-FACTOR
> R-FACTOR COMPARED I/SIGMA R-meas CC(1/2) Anomal SigAno Nano
> LIMIT OBSERVED UNIQUE POSSIBLE OF DATA observed
> expected Corr
> 1.90 24890 19149 23814 80.4% 58.1%
> 63.7% 11482 0.77 82.2% 63.8* 3 0.694 492
> total 163756 125884 146938 85.7% 10.6%
> 10.8% 75744 3.78 15.0% 99.0* -3 0.761 5834
>
>
> Xtriage in Phenix 1.16-3549 gives me all green lights (print below),
> suggesting the data presents no twinning, no translational NCS, no ice
> rings and is not anisotropic.
> https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Ffullonline.org%2Fscience%2Fphenix_xtriage_green.pngdata=02%7C01%7C%7Cde40f97d75824ea6519308d72c9d6fe0%7C4eed7807ebad415aa7a99170947f4eae%7C0%7C0%7C637026927009132543sdata=RMV8abo87ybMyxaqD%2FHgOakRhGvzGgsQXzkuzC4c8HI%3Dreserved=0
>
> Molecular replacement in Phaser yields single solutions like:
>
> Solution annotation (history):
> SOLU SET RFZ=3.0 TFZ=* PAK=0 LLG=29 RFZ=2.8 TFZ=8.8 PAK=1 LLG=310
> TFZ==27.6
> LLG=320 TFZ==28.0
> SOLU SPAC P 1
> SOLU 6DIM ENSE ensemble1 EULER 293.6 27.7 288.7 FRAC -0.02
> 0.02 0.02 BFAC
> -6.03
> SOLU 6DIM ENSE ensemble1 EULER 294.0 27.9 288.8 FRAC -0.37
> 0.02 0.02 BFAC
> -6.52
> SOLU ENSEMBLE ensemble1 VRMS DELTA -0.1983 RMSD 0.49 #VRMS 0.21
>
> or partial solutions like:
>
> Partial Solution #1 annotation (history):
> SOLU SET RFZ=3.7 TFZ=* PAK=0 LLG=32 RFZ=2.8 TFZ=13.0 PAK=0 LLG=317
> TFZ==30.2
> LLG=331 TFZ==30.5 RFZ=2.4 TFZ=7.2 PAK=0 LLG=464 TFZ==18.5 RFZ=2.7
> TFZ=5.7 PAK=1
> LLG=501 TFZ==6.8 LLG=509 TFZ==6.6
> SOLU SPAC P 1
> SOLU 6DIM ENSE ensemble1 EULER 85.4 153.0 138.5 FRAC -0.01 -0.00
> -0.00 BFAC
> -12.30
> SOLU 6DIM ENSE ensemble1 EULER 86.2 153.2 139.5 FRAC -0.36 -0.01
> -0.01 BFAC
> -9.16
> SOLU 6DIM ENSE ensemble1 EULER 83.8 152.3
Re: [ccp4bb] Fo-Fc map in WinCoot
When you open the map, in the window which comes up there is a little box to tick which says "Is difference map?" in the lower left hand corner from memory. Then it will display the -ve contours. Sent from Yahoo Mail on Android On Mon, 26 Aug 2019 at 15:34, Raymond Brown wrote: Hi folks, I notice that WinCoot does not appear to display the negative peaks in Fo-Fc difference maps. Is there a fix for this? Best Ray Brown To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] Problem in .mtz creation
Sorry, it's mapmask, not extend anymore. Sent from Yahoo Mail on Android On Tue, 20 Aug 2019 at 15:28, Jonathan Cooper<0c2488af9525-dmarc-requ...@jiscmail.ac.uk> wrote: You should be able to make a map with FFT by assigning F1 to your Fcalc and PHI to your Phicalc, if not with the gui, then certainly with the command line. You will need to make it cover your coordinates by ticking a gui option or running extend in the command line. Sent from Yahoo Mail on Android On Tue, 20 Aug 2019 at 15:02, Vijayakumar Rajendran wrote: Dear All,I have a problem in viewing electron density map by opening .mtz file in coot. Actually I have a PDB cordinates of water molecules of my protein using Hollow program. I generated the .mtz file using SFall program in CCP4i by providing the cryst card. The generated mtz file contains FCalc and PhiCalc. When I open this mtz file in coot along with the hollow pdb file, I am not getting the electron density. I tried running FFT, but it failed as it doesn't have SIGFP and FOM column since its a non experimental co-ordinates.Please help me where is the issue. Thanks in advance. ---Dr. R. Vijayakumar, Research Associate, Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] Problem in .mtz creation
You should be able to make a map with FFT by assigning F1 to your Fcalc and PHI to your Phicalc, if not with the gui, then certainly with the command line. You will need to make it cover your coordinates by ticking a gui option or running extend in the command line. Sent from Yahoo Mail on Android On Tue, 20 Aug 2019 at 15:02, Vijayakumar Rajendran wrote: Dear All,I have a problem in viewing electron density map by opening .mtz file in coot. Actually I have a PDB cordinates of water molecules of my protein using Hollow program. I generated the .mtz file using SFall program in CCP4i by providing the cryst card. The generated mtz file contains FCalc and PhiCalc. When I open this mtz file in coot along with the hollow pdb file, I am not getting the electron density. I tried running FFT, but it failed as it doesn't have SIGFP and FOM column since its a non experimental co-ordinates.Please help me where is the issue. Thanks in advance. ---Dr. R. Vijayakumar, Research Associate, Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] Recommendations for a Desktop Computer for Crystallography Programs
A 10 year old laptop (64 bit) with Linux on it will be absolutely fine ;-) Sent from Yahoo Mail on Android On Wed, 14 Aug 2019 at 6:22, Matthew Bratkowski wrote: Hi, Can anyone recommend a good desktop computer for running crystallography programs? I am looking for a Mac or Linux computer that is relatively fast and moderately priced. I am not interested in building my own system; I want a computer that ready to use right out of the box. Any suggestions would be appreciated. Thanks, Matt To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] Improve your previously released coordinates with OneDep
Thank you for that. Good idea to look at the policy. I think it would be classed as a minor change after release: https://www.wwpdb.org/documentation/policy#toc_changes "Update or change on structure factor or constraint file due to format corrections or addition of data set while coordinates remain unchanged." On Friday, 2 August 2019, 21:28:50 BST, Robbie Joosten wrote: Hi Jonathan, It would be great if you deposit missing reflection data. It is very commendable. I don't know what the policy is, but I have seen quite a few legacy entries for which the data were deposited (or corrected) much later than the model. Sometimes more than 20 years. These kept the original PDBid. Cheers,Robbie On 2 Aug 2019 21:18, Jonathan Cooper <0c2488af9525-dmarc-requ...@jiscmail.ac.uk> wrote: Hello David I note that no changes will be allowed to the experimental data, but if there are no experimental data, will the depositor be allowed to upload it/them, without starting a new deposition? I'm finding a few reflection files that ought to be deposited so that the corresponding structures can benefit from re_do's, etc, but I would like to preserve the original PDB-IDs, as published, and I don't want to spend too long on it! Thank you, Jon.C.On Thursday, 1 August 2019, 09:34:40 BST, David Armstrong wrote: Dear CCP4BB, The wwPDB are pleased to announce the availability of PDB versioning, allowing depositors to update their entries while retaining the same PDB accession code. Depositors can now submit new coordinates for existing entries. Initially, this is limited to PDB entries that were submitted via the OneDep system, which was introduced in 2014. The wwPDB plans to extend this functionality to entries deposited in the legacy systems (ADIT and Autodep) in future, and will announce a timeline for this in due course. Requests should be initiated using the OneDep communication panel within the deposition session for the entry in question. Once submitted, the revised model will be processed by wwPDB biocurators and a new version released. Versioning of PDB entries will be limited to changes in the coordinate files, with no changes permitted to the deposited experimental data. PDB versioning will be limited to one replacement per PDB entry per year, and three entries per Principal Investigator per year. For more, please visit the wwPDB news pages. -- David Armstrong Outreach and Training Coordinator PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK Tel: +44 1223 492544 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] Improve your previously released coordinates with OneDep
Hello David I note that no changes will be allowed to the experimental data, but if there are no experimental data, will the depositor be allowed to upload it/them, without starting a new deposition? I'm finding a few reflection files that ought to be deposited so that the corresponding structures can benefit from re_do's, etc, but I would like to preserve the original PDB-IDs, as published, and I don't want to spend too long on it! Thank you, Jon.C.On Thursday, 1 August 2019, 09:34:40 BST, David Armstrong wrote: Dear CCP4BB, The wwPDB are pleased to announce the availability of PDB versioning, allowing depositors to update their entries while retaining the same PDB accession code. Depositors can now submit new coordinates for existing entries. Initially, this is limited to PDB entries that were submitted via the OneDep system, which was introduced in 2014. The wwPDB plans to extend this functionality to entries deposited in the legacy systems (ADIT and Autodep) in future, and will announce a timeline for this in due course. Requests should be initiated using the OneDep communication panel within the deposition session for the entry in question. Once submitted, the revised model will be processed by wwPDB biocurators and a new version released. Versioning of PDB entries will be limited to changes in the coordinate files, with no changes permitted to the deposited experimental data. PDB versioning will be limited to one replacement per PDB entry per year, and three entries per Principal Investigator per year. For more, please visit the wwPDB news pages. -- David Armstrong Outreach and Training Coordinator PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK Tel: +44 1223 492544 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] Phosphorylated arginine in COOT
Hello, can you get a good idea of the distance between the arginine sidechain nitrogen and the phosphorus? It should be less than 2 A for a covalent bond. A non-covalent complex will have an oxygen-nitrogen distance of about 2.8 A. If the Arg is phosphorylated, then this residue is already one of the RCSB standard ligands: https://www.rcsb.org/ligand/RPI So adding it should not be too hard in Coot and the other PDB entries with this residue (see link) should give you an idea of how the final PDB file should look. Apols for poetic spelling and hope some of this helps. Sent from Yahoo Mail on Android On Sat, 27 Jul 2019 at 4:48, Anirudha Dutta wrote: Hello everyoneFrom electron density, It looks like one of the arginines in my protein is post-translationally modified as phospho-arginine. How to make sure it's a real phospho-arginine, not an arginine interacting with phosphate or acetate ion? The resolution of the structure is 2.3 A. Can anybody helps me with step by step procedure to incorporate a phospho-arginine in my structure using COOT and if anything special need to be done during refinement in Phenix. Thanks and regardsSincerelyAnirudha Dutta To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] More LCF archaeology (unit cell parameters this time).
I am trying to use a hex editor to read the unit cell parameters from the headers of 80's VAX LCF files and I can definitely find them in front of the column labels as six regularly spaced 32-bit floats. However, they seem to be multiplied by a factor of 4 and the final corrected values of a, b, c, alpha, beta and gamma are a bit more approximate than I would expect. I can't work out what's going on from the fortran yet so any clues would be much appreciated. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] Fo-Fc density close to cysteine residue
Refining B-aniso's will clean up a difference map at that resolution.
Sent from Yahoo Mail on Android
On Tue, 9 Jul 2019 at 16:57, Bonsor, Daniel wrote:
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Have you mass-speced the protein before crystallization to make sure it wasn’t
derivatized during expression and/or purification, or compared the mass spec of
the crystals verses purified protein? Any fancy reagents or other reductants
used during purification?
What about S-Acetyl-cysteine (3-letter code: SCY).
Best,
Dan
Daniel A Bonsor PhD.
Sundberg Lab
Institute of Human Virology
University of Maryland, Baltimore
725 W Lombard Street N370
Baltimore
Maryland
MD 21201
Tel: (410) 706-7457
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK]On Behalf Of Lumbini
Yadav
Sent: Tuesday, July 09, 2019 5:22 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Fo-Fc density close to cysteine residue
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 crystallization
condition, we have PEG 3350, Potassium phosphate monobasic, glycerol and
protein was in Tris and NaCl. Before freezing the crystals were soaked in
mother liquor containing sodium dithionite.
I have tried different modified cysteine (CSX, CSO, OCS, CME, CSS, SNC, CSD,
CXM, SCH, CSU) from the library and also SO3, SO2 and peroxide. But in all the
screenings we do see some part of Fo-Fc density unaddressed at 3 sigma.
Does anyone have an idea about what this density could be? Covalent
modification?
Thanks.
Kind regards,
Lumbini
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[ccp4bb] Reading LCF files.
For those who suffer from 80's nostalgia, I have worked-out a simple-man's way of recovering the reflection data from this, now obsolete, format. Its here: https://readingccp4lcffiles.blogspot.com and it works for most of my VAX lcf files. Just thought this might be of interest as the question has popped-up once or twice over the years! To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] inter- and atomic interactions comparison
For dynamics, you have probably already found VMD which is fairly easy to get started with. Sent from Yahoo Mail on Android On Mon, 1 Jul 2019 at 16:17, Mirella Vivoli Vega wrote: Dear CCP Fo(r)lks, I wonder if someone could help me about prediction servers or programs or molecular dynamics I could use/run to compare the wild type protein structure and a mutant (I do not have the structure for the mutant), with/without substrate. The mutation (Asparagine to Aspartate) enhanced the hydrolysis of cellulosic substrates, increased the protein thermal stability, without affecting the protein fold. It would be interesting if there is a way to see the structural differences in the atomic and interatomic interactions determining the increased activity we have observed. I really appreciate your comments, help and opinions. Cheers, Mirella -- Mirella Vivoli Vega, PhD Senior Postdoctoral Fellow Department of Experimental and Clinical Biomedical Sciences, University of Florence,Viale Morgagni 50, 50134, Florence, Italy email: mirella.viv...@unifi.it "I do not want to believe, I want to know"[c. Sagan] To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] [phenixbb] Copying mtz file
It sounds like you have swapped the R-free set from being in phenix/xplor-style to ccp4-style. Sent from Yahoo Mail on Android On Tue, 25 Jun 2019 at 8:08, Tim Grüne wrote: Dear Mirek, it is a stubborn myth the Free-R flags need to be conserved. You can simply regenerate a new set of flags. This does not compromise the free F-value. This is based on what I would call Tickle's conjecture, even though with one of his latest emails on the ccp4bb, where he explained this in an extremely beautiful manner, it is not a conjecture anymore, rather a corollary. It is sad that even some well established crystallographers stick to said myth. Best regards, Tim cc ccp4bb for information Am 25.06.2019 04:09, schrieb Cygler, Miroslaw: > Hi Phenixers, > I have copied mtz file to a new file with a lower resolution limit > using the "Reflection file editor” tool. I copied all arrays to the > output file. When I attempted to continue refinement with the new mtz > file, a message appears saying that there are no R-free flags in the > mtz file. Yet, the new file contains the R-free-flags column but the > values are inverted, 1 is changed to 0 and 0 is changed to 1. In the > output option dialog the box “Preserve original flag values” was > checked. > How to fix this? > Thanks, > > Mirek > ___ > phenixbb mailing list > pheni...@phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > Unsubscribe: phenixbb-le...@phenix-online.org -- -- Tim Gruene Head of the Centre for X-ray Structure Analysis Faculty of Chemistry University of Vienna Phone: +43-1-4277-70202 GPG Key ID = A46BEE1A To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] Phenix / Coot neutron queries.
I am trying to refine a neutron structure for someone and I have come across a couple of things which I need help with. I am struggling to get the occupancy refinement of the hydrogens/deuteriums on the N-terminal nitrogens to behave right. Some of them get deleted by readyset but the trick seems to be to call them hydrogen in the atom name field yet say they are D in the element symbol field. Is that the best way? Also, readyset seems to delete the D's in D2O? I would appreciate any tips on what is the best 'strategy' for refining with neutron data i.e. reciprocal- versus real-space or both, etc, because my R-free just seems to go up. Also, if I do a real-space refine on a D2O molecule (DOD) in Coot it stretches the O-D bond length from around 1 to 1.3 Angstrom and the bond angle from ~110 to about 120 degrees so it seems to be picking-up wrong geometry info from somewhere. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] Does ncs bias R-free? And if so, can it be avoided by special selection of the free set?
s don't have to be correlated, just the modelling errors. > >> > >> Best wishes, > >> > >> Randy > >> > >> On 5 Jun 2019, at 13:58, Ian Tickle wrote: > >> > >> > >> Hi Jon > >> > >> Sorry I didn't intend for my response to be interpreted as saying that > >> anyone has suggested directly that the measurement errors of NCS-related > >> reflection amplitudes are correlated. In fact the opposite is almost > >> certainly true since the only obvious way in practice that errors in Fobs > >> could be correlated is via errors in the batch scale factors which would > >> introduce correlations between errors in Fobs for reflections in the same > >> or adjacent images, but that has nothing to do with NCS. That's the > >> 'elephant in the room': no-one has suggested that reflections on the same > >> or adjacent images should not be split between the working and test sets, > >> yet that's easily the biggest contributor to CV bias with or without NCS! > >> I think taking that effect into account would be much more productive than > >> worrying about NCS, but performing the test-set sampling in shells can't > >> possibly address that, since the images obviously cut across all shells. > >> > >> The point I was making was that correlation of errors in NCS-related Fobs > >> would appear to be the inevitable _implication_ of what certainly has been > >> claimed, namely that NCS can introduce bias into CV statistics if the > >> test-set sampling is not done correctly, i.e. by splitting NCS-related Fobs > >> between the working and test sets. Unless there's something I've missed > >> that's > >> the only possible explanation for that claim. This is because overfitting > >> results from fitting the model to the errors in Fobs, and the CV bias > >> arises from correlation of those errors if the NCS-related Fobs are split > >> up, thus causing the degree of overfitting to be underestimated and giving > >> a too-rosy picture of the structure quality. Indeed you seem to be saying > >> that because the NCS-related Fobs are correlated (a patently true > >> statement), then it follows that the errors in those Fobs are also > >> correlated, or at least no more correlated than for non-NCS-related Fobs, > >> but I just don't see how that can be true. > >> > >> Rfree is not unbiased: as a measure of the agreement it is biased upwards > >> by overfitting (otherwise how could it be used to detect overfitting?), by > >> failing to fit with the uncorrelated errors in the test-set Fobs, just as > >> Rwork is biased downwards by fitting to the errors in the working-set > >> Fobs. Overfitting becomes immediately apparent whenever you perform any > >> refinement, so the only point at which there is no overfitting is for the > >> initial model when Rwork and Rfree are equal, apart from a small > >> difference arising from random sampling of the test-set (that sampling > >> error could be reduced by performing refinements with all 20 working/test > >> sets combinations and averaging the R values). From there on the 'gap' > >> between Rwork and Rfree is a measure of the degree of overfitting, so we > >> should really be taking some average of Rwork and Rfree as the true measure > >> of agreement (though the biases are not exactly equal and opposite so it's > >> not a simple arithmetic mean). The goal of choosing the appropriate > >> refinement parameters, restraints and weights is to _minimise_ overfitting, > >> not eliminate it. It is not possible to eliminate it completely: if it > >> were then Rwork and Rfree would become equal (apart from that small effect > >> from random sampling). > >> > >> I don't follow your argument about correlation of Fobs from NCS. > >> Overfitting, and therefore CV bias, arises from the _errors_ in the Fobs > >> not from the Fobs themselves, and there's no reason to believe that the > >> Fobs should be correlated with their errors. You say "any correlation > >> between the test-set and the working-set F's due to NCS would be expected > >> to reduce R-free". If the working and test sets are correlated by NCS that > >> would mean that Rwork is correlated with Rfree so they would be reduced > >> equally! There are two components of the Fobs - Fcalc difference: Fcalc - > >> Ftrue (the model error) and Fobs - Ftrue (the data error). The former is > >> completely correlated between the workin
[ccp4bb] Some Phenix R-free set queries
In the Phenix reflection file editor, where you pick the R-free set, there are two boxes where you can enter the fraction of reflections to go into the test set (see below), but they don't seem to talk to each other. Change the one in the "More options" sub-menu and the other stays the same with apparently no effect on the calculations. https://www.ucl.ac.uk/~rmhajc0/phenixrfree.jpg Also, even if you tick the "Adjust test set size to specified fraction" option, it won't allow you to have more than 2000 reflections in your test set (2020 tops) i.e. there seems to be no way of overriding the "max_free = 2000" command with the gui. Probably this is very sensible and I assume it is intended? To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] Refmac per-cycle and all-cycle statistics.
I was wondering why everything appears twice in the report, as below ;-? https://www.ucl.ac.uk/~rmhajc0/percycle.jpg To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] Does ncs bias R-free? And if so, can it be avoided by special selection of the free set?
Thanks Ian, I think I understood you correctly and have worked out the change in R-free for each refinement. The results are here: https://www.ucl.ac.uk/~rmhajc0/rfreechange.pdf I don't think it shows any sign of the bias we discussed. On Friday, 7 June 2019, 14:37:03 BST, Ian Tickle wrote: Hi Jon It's not valid to use model-selection metrics such as R factors to compare different datasets: they are just not designed for that purpose. Model-selection metrics are designed to select the best model from a set of possible models all obtained using the _same_ data (or sample of data for CV), but with different model parameters and restraints. The reason is very simple: R factors will vary purely according to the data sample used (the 'sampling error') and this variation can easily wipe out any variation due to NCS bias. This is particularly true of CV metrics like Rfree because they use a relatively small sample, so if that sample is 5% then the size of test set will be 1/19th of the working set and the sampling error will be at least sqrt(19) times as big. Also the 20 working sets generated by e.g. FREERFLAG have ~ 95% reflections in common which reduces the variation, whereas the 20 test sets have none in common. You can see that the Rfree values vary much more than the Rwork values for this reason. Having said that there is one possible way around it. The sampling error obviously doesn't change _during_ a single refinement run since it's the same data, i.e. we could assume that the effect of the sampling error is the same at the beginning and at the end of the run. Clearly if the Rfree for one data sample at the beginning of a run is higher than the Rfree at the beginning of a run for a different data sample then it's hardly fair to compare the Rfree values at the end of the two runs. It's like giving some runners a 1 hour start in the marathon and deciding who is the winner according to who crosses the finishing line first! So assuming that every run starts with the same model but different sample of data, you may be able reduce the effect of sampling errors by comparing the _changes_ in the R factors from the beginning to the end of a refinement run. It's like every marathon runner using their own timer so each measures their finishing time _relative_ to their starting time, rather than using the same timer for everyone. Cheers -- Ian On Fri, 24 May 2019 at 23:27, Jonathan Cooper <0c2488af9525-dmarc-requ...@jiscmail.ac.uk> wrote: Having been fond of the idea discussed above i.e. that when NCS is present, one should have the R-free set chosen in shells, I did some simple tests. Many others must have done the same, but here's how it went: 1) Choose a few familiar structures, both with and without NCS and get the data. 2) Since there was some difficulty in remembering if the original R-free sets were in shells or not, I ditched any existing test set (shock, but see 3 below) and generated new ones, both at random and in shells (using SFTOOLS and I repeated some with an old copy of SHELXPRO). Some of the reflection files lacked original R-free sets since they weredeposited before the R-free was invented. 3) Reduce the bias of each model to the reflections that are now in the new test setsand tease out over-fitting by rattling the structures a bit, i.e. add a random +/-0.1 Angstroms to x, y and z of each atom (0.17 Angstroms net shift) and reset all the B-factors to 30 A^2. 4) Refine the rattled structures with the new R-free sets, i.e. random and in shells (no NCS restraints). 5) If anyone is really interested, the results are here: https://www.ucl.ac.uk/~rmhajc0/rfreetests.pdf but to summarise, assuming the programs have picked the test sets in shells or otherwise correctly (!), there seems to be no significant difference between the R-free in shells and the normal one, whether NCS is present or not. If anything, the R-free in shells tends to be a tiny bit lower than the normal R-free when NCS is present, although this is probably by chance due to the small number of tests done! I am sure this is a well known fact, but haven't had the chance to test it till now!On Sunday, 19 May 2019, 13:22:00 BST, Ian Tickle wrote: Hi Ed Yes, Rfree: my favourite topic, I'll take this one on! First off, we all need to be ultra-careful and precise about the terminology here, for fear of creating even more confusion. For example what on earth is meant by "reflections ... are uncorrelated"? A reflection can be regarded as a object that possesses a set of attributes (indices, d spacing, setting angles, position on detector, LP correction, intensity, amplitude, phase, errors in those, etc. etc.). An object as such is not associated with any kind of value (it is rather an instance of a class of objects possessing the same set of attributes but with different values for those attributes), so it's totally meaningle
[ccp4bb] Coot in i2
For the past few weeks I have noticed that when you start Coot from the i2 gui it works fine for up to an hour or so but then its hangs completely and any unsaved changes go missing. It seems more stable if I start it outside the i2 gui. Is this just me or my linux box? To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] Does ncs bias R-free? And if so, can it be avoided by special selection of the free set?
Ian, statistics is not my forte, but I don't think anyone is suggesting that the measurement errors of NCS-related reflection amplitudes are correlated. In simple terms, since NCS-related F's should be correlated, the working-set reflection amplitudes could be correlated with those in the test-set, if the latter is chosen randomly, rather than in shells. Am I right in saying that R-free not just indicates over-fitting but, also, acts as an unbiased measure of the agreement between Fo and Fc? During a well-behaved refinement run, in the cycles before any over-fitting becomes apparent, the decrease in R-free value will indicate that the changes being made to the model are making it more consistent with Fo's. In these stages, any correlation between the test-set and the working-set F's due to NCS would be expected to affect the R-free (cross-validation bias), making it lower than it would be if the test set had been chosen in resolution shells? However, you are always right and, as you know, I failed to detect any such effect in my limited tests. Thanks to you and others for replying. On Tuesday, 4 June 2019, 02:07:10 BST, Edward A. Berry wrote: On 05/19/2019 08:21 AM, Ian Tickle wrote: ~~~ >> So there you have it: what matters is that the _errors_ in the NCS-related >> amplitudes are uncorrelated, or at least no more correlated than the errors >> in the non-NCS-related amplitudes, NOT the amplitudes themselves. Thanks, Ian! I would like to think that it is the errors in Fobs that matter (as may be the case), because then: 1. ncs would not bias R-free even if you _do_ use ncs constraints/restraints. (changes in Fcalc due to a step of refinement would be positively correlated between sym-mates, but if the sign of (Fo-Fc) is opposite at the sym-mate, what impoves the working reflection would worsen the free) 2. There would be no need to use the same free set when you refine the structure against a new dataset (as for ligand studies) since the random errors of measurement in Fobs in the two sets would be unrelated. However when I suggested that in a previous post, I was reminded that errors in Fobs account for only a small part of the difference (Fo-Fc). The remainder must be due to inability of our simple atomic models to represent the actual electron density, or its diffraction; and for a symmetric structure and a symmetric model, that difference is likely to be symmetric. Whether that difference represents "noise" that we want to avoid fitting is another question, but it is likely that (Fo-Fc) will be correlated with sym-mates. So I settled for convincing myself that the changes in Fc brought about by refinement would be uncorrelated, and thus the _changes_ in (Fo-Fc) at each step would be uncorrelated. Below are some of the ideas I come up with in trying to think about this, and about bias in general. (Not very well organized and not the best of prose, but if one is a glutton for punishment, or just wants to see how the mind of a madman works . . .) Warning- some of this is contrary to current consensus opinion and the conclusions may be, in the words of a popular autobuilding program, partly WRONG! In particular, the idea that coupling by the G-function does not bias R-free, but rather is the only reason that R-free works at all! - - - - - - - - - - The differences (Fo-Fc) can be divided between (1) errors in measurement of reflection intensities and (2)failure of the model to represent the true structure. The first can be considered "noise" and we would expect it to be random, with no correlation between symm mates. However most of the difference between Fc and Fobs is not due to random noise in the data, but to failures of our model to accurately represent the real thing. These differences are likely to be ncs-symmetric. Leaving aside the question of whether or not we want to fit this kind of "noise" (bringing the model closer to the real structure?), we conclude that (Fo-Fc) is likely to be correlated between ncs-mates. But for refinement against the working set to bias the contribution of sym-related free-set reflections to R-free would require that _changes_ in |Fo-Fc| from a step of refinement would be ncs-correlated. If on the contrary they are not correlated, i.e. if a change that decreases |Fo-Fc| for a working reflection is equally likely to decrease or increase |Fo-Fc| for its sym mate (which may be) in the free set, then it is hard to see how refinement against the working reflection would bias R-free. Under what conditins would |Fo-Fc| for symmetry related reflections be correlated? This would be the case if change in Fc correlates AND the sign of (Fo-Fc) correlates. Again, if the difference were only due to random error in Fobs, then the sign of Fo-Fc of a symmetry related reflection would be as likely to be the opposite as the same (as the original reflection) so even if changes in Fc are correlated, what improves the fit to the
Re: [ccp4bb] Does ncs bias R-free? And if so, can it be avoided by special selection of the free set?
t positions of intermediate bonding and non-bonding partners and propagate through crystallographic terms to all atoms. To overcome this problem we replaced the calculation of phase error estimates, which is based on the TEST subset of structure factors, by calculation of phase error estimates which is using WORK subset or all data and Fmodel structure factors calculated from kicked model generated by randomly displacing atomic positions. In the Figures 6 and 7 there is a poor or non-existing correlation between R-free gaps and phase errors. For details please read ( Praznikar, J. & Turk, D. (2014) Free kick instead of cross-validation in maximum-likelihood refinement of macromolecular crystal structures. Acta Cryst. D70, 3124-3134. http://journals.iucr.org/d/issues/2014/12/00/lv5072/lv5072.pd) We concluded “Since the ML FK approach allows the use of all data in refinement with a gain in structure accuracy and thereby delivers lower model bias, this work encourages the use of all data in the refinement of macromolecular structures.” Just to add, it appears that the R-free discussions keep resurfacing, because the use of the R-free concept in refinement and structure validation persistently raises doubts about its validity. The discussions that follow try to strengthen the beliefs. In my opinion, however, »the persistent use of R-free as an indicator of structure correctness is a result of the desire to simplify the reality by wishful thinking.” (Turk (2017), Boxes of Model Building and Visualization, Protein Crystallography, Methods in MolecularBiology 1607, Springer protocols). I hope this helps to clarify a few issues. dusan turk > On 25 May 2019, at 01:00, CCP4BB automatic digest system > wrote: > > Date: Fri, 24 May 2019 22:27:28 + > From: Jonathan Cooper > Subject: Re: Does ncs bias R-free? And if so, can it be avoided by special > selection of the free set? > > Having been fond of the idea discussed above i.e. that when NCS is present, > one should have the R-free set chosen in shells, I did some simple tests. > Many others must have done the same, but here's how it went: > 1) Choose a few familiar structures, both with and without NCS and get the > data. > 2) Since there was some difficulty in remembering if the original R-free sets > were in shells or not, I ditched any existing test set (shock, but see 3 > below) and generated new ones, both at random and in shells (using SFTOOLS > and I repeated some with an old copy of SHELXPRO). Some of the reflection > files lacked original R-free sets since they weredeposited before the R-free > was invented. > 3) Reduce the bias of each model to the reflections that are now in the new > test setsand tease out over-fitting by rattling the structures a bit, i.e. > add a random +/-0.1 Angstroms to x, y and z of each atom (0.17 Angstroms net > shift) and reset all the B-factors to 30 A^2. > 4) Refine the rattled structures with the new R-free sets, i.e. random and in > shells (no NCS restraints). > 5) If anyone is really interested, the results are here: > https://www.ucl.ac.uk/~rmhajc0/rfreetests.pdf > but to summarise, assuming the programs have picked the test sets in shells > or otherwise correctly (!), there seems to be no significant difference > between the R-free in shells and the normal one, whether NCS is present or > not. If anything, the R-free in shells tends to be a tiny bit lower than the > normal R-free when NCS is present, although this is probably by chance due to > the small number of tests done! > I am sure this is a well known fact, but haven't had the chance to test it > till now! On Sunday, 19 May 2019, 13:22:00 BST, Ian Tickle > wrote: > > > Hi Ed > Yes, Rfree: my favourite topic, I'll take this one on! First off, we all > need to be ultra-careful and precise about the terminology here, for fear of > creating even more confusion. For example what on earth is meant by > "reflections ... are uncorrelated"? A reflection can be regarded as a object > that possesses a set of attributes (indices, d spacing, setting angles, > position on detector, LP correction, intensity, amplitude, phase, errors in > those, etc. etc.). An object as such is not associated with any kind of > value (it is rather an instance of a class of objects possessing the same set > of attributes but with different values for those attributes), so it's > totally meaningless to talk about the correlation, or lack thereof, of two > sets of objects (what's the correlation of a bag of apples and a bag of > oranges?). You can only talk about the correlation of the values of the > objects' attributes (e.g. the apples' and oranges' size or weight). Perhaps > you'll say that it was clear from the context that you meant the
Re: [ccp4bb] tNCS incompatible with cell dimensions
Does the SAXS model contain more than one subunit? If so, I would be tempted to
go back to the model and try each one separately. This may not apply, but if
there are monomers in the SAXS model that are related by space group symmetry
in the crystal, I think the MR would never work. Good luck with it! Bests, Jon.
Cooper
Sent from Yahoo Mail on Android
On Sat, 1 Jun 2019 at 9:45, Jrh Gmail wrote: Dear
KevinYou could try reindexing into P1, then run Phaser and with its solution as
input to Zanuda determine the space group. Best wishes,John
Emeritus Professor of Chemistry John R Helliwell DSc_Physics
On 31 May 2019, at 21:09, Kevin Jude wrote:
Hello community, I wonder if I could solicit advice about a problematic
dataset. I plan to solve the structure by molecular replacement and expect that
the protein is relatively compact, ie not elongated. SAXS data supports this
expectation.
The crystals diffract to 2.6 Å resolution and appear to be in P 21 21 2 with a
= 49, b = 67, c = 94, which should fit <=2 molecules in the ASU with 40%
solvent. The native Patterson shows a large peak (12 sigma) suggesting a tNCS
vector of {0.5, 0.5, 0}.
If you're sharper than me, you may have already spotted the problem - c is the
long axis of the unit cell, but tNCS constrains the proteins to a plane
parallel to the a,b plane. Indeed, molecular replacement attempts using Phaser
will not give a solution in any orthorhombic space group unless I turn off
packing, and then I get large overlaps in the a,b plane and huge gaps along c.
Since I believe that my model is good (or at least the correct shape, based on
SAXS), I wonder if I'm misinterpreting my crystallographic data. Any insights
into how to approach this problem would be much appreciated.
--
Kevin Jude, PhDStructural Biology Research Specialist, Garcia LabHoward Hughes
Medical InstituteStanford University School of MedicineBeckman B177, 279 Campus
Drive, Stanford CA 94305Phone: (650) 723-6431
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Re: [ccp4bb] A Question about crystal packing
Hello, can you use the pisa server or similar to compare the extent of domain-domain and domain-DNA contacts versus crystal contacts in your structures? It might help to show which is the dominant factor affecting domain orientation. Sent from Yahoo Mail on Android On Tue, 28 May 2019 at 14:45, Zizi Tian<18311218...@163.com> wrote: Hi All,I has recently solved my X-ray structures of the ZnF domains of Bo and its complex with dsDNA. A structural comparison of holo-Bo and the Bo-DNA binary complex reveals that the relative orientation of domains ZnF3 undergoes a rotation of 50.5 degrees Does anyone know how to show there are no effects of the crystal packing . Please help me in this regard. Best regards At 2019-05-28 20:55:07, "Anamika Singh" wrote: Hi All, Does anyone know what is the actual difference between CIP and EDTA method for exchanging the GppNHp (non-hydrolysable GTP) or GDP with the purified RAS protein? I have a protocol according to which I need to incubate the purified RAS with GppNHp having 20U of alkaline phosphatase, 10uM of Zinc Chloride and 200mM ammonium sulfate for 2 hr at room temperature. In this protocol, they have mentioned that ammonium sulfate needs to be added in the last. I am quite confused, according to them do I need to add it after 2 hrs incubation or I have to add this at last to the mixture of (purified RAS+GppNHp+Zinc chloride and alkaline phosphatase)? Since this protein and its mechanism is new to me so not sure what to do. After reading some papers also I am not able to understand which method is good for exchange and how these reactions behave? Please help me in this regard. -- Anamika Singh Post-Doctoral FellowSilberman Institute of Life Sciences Hebrew University of Jerusalem, IsraelNo: 054-294-8036 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] Question on author provided HELIX/SHEET records and assignment of a continuous helix that changes its helix class.
Re: question 2, for simplicity, I would call it all one helix and regard the 3-10 part as a distortion. Just my opinion. Sent from Yahoo Mail on Android On Tue, 28 May 2019 at 13:48, Paul Emsley wrote: On 28/05/2019 11:51, Stephan Grunwald wrote: > > I [have] recently solved [my] first X-ray structure and I would like to have > an opinion on > two questions, both dealing with secondary structure assignments. > > First of all, the wwPDBs says ”We encourage authors to use the calculated > helix (or sheet) records and not > provide their own remarks.” (https://www.wwpdb.org/documentation/procedure). > It says in the same > documentation, that the Promotif software will automatically assign SSE upon > deposition (does Promotif use > the DSSP algorithm?). 1) Your are encouraged, not mandated. ProMOTIF/dssp is one of a number of ways to generate secondary structure annotations. You seem to have a good reason to use "your own" assignment. Go ahead and do so, don't give it a second thought. I don't have an opinion about question 2. Paul. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] Disulphide occupancies.
When you refine structures with disulphide bridges you often get negative difference density for the sulphurs, presumably due to the well-known radiation damage effects. The negative difference density often won't disappear with usual B-factor refinement. However, it seems to go away if you refine the occupancy of the affected sulphur atoms e.g. to 0.9 or thereabouts. Would it be acceptable to publish/deposit structures where the sulphur occupancy is less than one, given a suitable REMARK in the pdb file? Thank you. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb]
I am interested in why you want to join 16 mtz files sideways. That is a lot of derivatives. On Saturday, 11 May 2019, 20:10:16 BST, CCP4BB <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote: That'll teach me to reply straight off a flight from SFO... Harry--Dr Harry Powell On 11 May 2019, at 18:17, Phil Evans wrote: Pointless won’t do this with merged files - CAD is the thing On 11 May 2019, at 15:24, CCP4BB <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote: Or use Pointless to merge them together... Harry -- Dr Harry Powell On 11 May 2019, at 06:48, graeme.win...@diamond.ac.uk wrote: Hi Scott, You can run CAD two or more times - merge the columns incrementally (i.e. 1..9 then (1..9)+10..16) Best wishes Graeme On 10 May 2019, at 23:57, Scott Horowitz mailto:horow...@umich.edu>> wrote: Hi all, I’m trying to combine 16 datasets together using Cad, and it’s failing with the following in the log file: Key_Word Error, For LABIN FILE_NUMBER line:- File_Number Given = 10 Is invalid only files 1 to 9 Allowed, Ignoring this line - It does that for all the datasets starting with number 10, which makes it seem like it can only combine 9 datasets at a time. I was just wondering if that’s something others have run into and dealt with before? The whole of the log file is below, if you want to peruse it. Thanks, Scott #CCP4I VERSION CCP4Interface 7.0.045 #CCP4I SCRIPT LOG cad #CCP4I DATE 10 May 2019 14:54:40 #CCP4I USER 'UNKNOWN' #CCP4I PROJECT Serena #CCP4I JOB_ID 7 #CCP4I SCRATCH C:/ccp4temp #CCP4I HOSTNAME DU-1KDZDH2 #CCP4I PID 17552 ### ### ### ### CCP4 7.0.045: CAD version 7.0.045 : ## ### User: Scott.Horowitz Run date: 10/ 5/2019 Run time: 14:54:41 Please reference: Collaborative Computational Project, Number 4. 2011. "Overview of the CCP4 suite and current developments". Acta Cryst. D67, 235-242. as well as any specific reference in the program write-up. Data line--- title [No title given] Data line--- monitor FULL Data line--- labin file 1 E1 = R-free-flags(+) E2 = R-free-flags(-) Data line--- labout file 1 E1 = R-free-flags(+) E2 = R-free-flags(-) Data line--- ctypin file 1 E1 = I E2 = I Data line--- labin file 2 E1 = F E2 = SIGF E3 = DANO E4 = SIGDANO E5 = F(+) E6 = SIGF(+) E7 = F(-) E8 = SIGF(-) E9 = ISYM E10 = IMEAN E11 = SIGIMEAN E12 = I(+) E13 = SIGI(+) E14 = I(-) E15 = SIGI(-) Data line--- labout file 2 E1 = F E2 = SIGF E3 = DANO E4 = SIGDANO E5 = F(+) E6 = SIGF(+) E7 = F(-) E8 = SIGF(-) E9 = ISYM E10 = IMEAN E11 = SIGIMEAN E12 = I(+) E13 = SIGI(+) E14 = I(-) E15 = SIGI(-) Data line--- ctypin file 2 E1 = F E2 = Q E3 = D E4 = Q E5 = G E6 = L E7 = G E8 = L E9 = Y E10 = J E11 = Q E12 = K E13 = M E14 = K E15 = M Data line--- labin file 3 E1 = R-free-flags Data line--- labout file 3 E1 = R-free-flags_4p5 Data line--- ctypin file 3 E1 = I Data line--- labin file 4 E1 = F E2 = SIGF E3 = DANO E4 = SIGDANO E5 = F(+) E6 = SIGF(+) E7 = F(-) E8 = SIGF(-) E9 = ISYM E10 = IMEAN E11 = SIGIMEAN E12 = I(+) E13 = SIGI(+) E14 = I(-) E15 = SIGI(-) Data line--- labout file 4 E1 = F_4p5 E2 = SIGF_4p5 E3 = DANO_4p5 E4 = SIGDANO_4p5 E5 = F(+)_4p5 E6 = SIGF(+)_4p5 E7 = F(-)_4p5 E8 = SIGF(-)_4p5 E9 = ISYM_4p5 E10 = IMEAN_4p5 E11 = SIGIMEAN_4p5 E12 = I(+)_4p5 E13 = SIGI(+)_4p5 E14 = I(-)_4p5 E15 = SIGI(-)_4p5 Data line--- ctypin file 4 E1 = F E2 = Q E3 = D E4 = Q E5 = G E6 = L E7 = G E8 = L E9 = Y E10 = J E11 = Q E12 = K E13 = M E14 = K E15 = M Data line--- labin file 5 E1 = R-free-flags Data line--- labout file 5 E1 = R-free-flags_2p87 Data line--- ctypin file 5 E1 = I Data line--- labin file 6 E1 = F E2 = SIGF E3 = DANO E4 = SIGDANO E5 = F(+) E6 = SIGF(+) E7 = F(-) E8 = SIGF(-) E9 = ISYM E10 = IMEAN E11 = SIGIMEAN E12 = I(+) E13 = SIGI(+) E14 = I(-) E15 = SIGI(-) Data line--- labout file 6 E1 = F_2p87 E2 = SIGF_2p87 E3 = DANO_2p87 E4 = SIGDANO_2p87 E5 = F(+)_2p87 E6 = SIGF(+)_2p87 E7 = F(-)_2p87 E8 =
Re: [ccp4bb] Refmac in i2
The numbers do make sense now: AaA, AbA, etc, correspond to different HETATM groups and (what was confusing me a lot) the No. atoms includes riding hydrogens. On Thursday, 2 May 2019, 23:27:49 BST, Jonathan Cooper wrote: In the output statistics part of the GUI there is table of mean B-factors, e.g. Chain mean B (No. atoms) AAA 23.6( 2596 )AaA 35.4( 29 )AbA 35.2( 10 )AcA 18.9( 10 )AdA 58.5( 10 )AeA 39.5( 119 )BBB 25.5( 2545 )BaB 42.0( 10 )BbB 46.9( 5 )BcB 37.3( 92 ) There is an A- and a B-chain in the structure, each with their own waters, but can someone explain the AaA, AbA,...AeA, BaB...BcB notation please, since it is not obvious how this relates to the contents of the PDB file. Thank you. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] Refmac in i2
In the output statistics part of the GUI there is table of mean B-factors, e.g. Chain mean B (No. atoms) AAA 23.6( 2596 )AaA 35.4( 29 )AbA 35.2( 10 )AcA 18.9( 10 )AdA 58.5( 10 )AeA 39.5( 119 )BBB 25.5( 2545 )BaB 42.0( 10 )BbB 46.9( 5 )BcB 37.3( 92 ) There is an A- and a B-chain in the structure, each with their own waters, but can someone explain the AaA, AbA,...AeA, BaB...BcB notation please, since it is not obvious how this relates to the contents of the PDB file. Thank you. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] Coot and symmetry-related waters.
Many thanks to all who replied. The best scheme seems to be to add the new waters into the main molecule and then make use of the options to renumber them and change the chain ID later on. This has the added advantage of avoiding the situation where, if you are not careful with the 'Place atom at pointer' options, some of the new waters go into Pointer-Atoms and some go into the main molecule. On Tuesday, 30 April 2019, 21:23:55 BST, Eleanor Dodson wrote: Not a solution to your problem - just a way to avoid it.. I always put the waters into the original file - you can always delete them or change the occupancy if there is a clash..Eleanor On Tue, 30 Apr 2019 at 21:21, Jonathan Cooper <0c2488af9525-dmarc-requ...@jiscmail.ac.uk> wrote: One thing I have wondered about Coot is when you add new waters into the structure and these go into a molecule called 'Pointer Atoms...', I have never worked out how to get the symmetry mates of these newly inserted waters to appear unless I eventually merge them into the same pdb file as the protein. As an example, here is a newly inserted water molecule (A6) in Pointer-Atoms close to a 2-fold: http://www.ucl.ac.uk/~rmhajc0/watersym.jpg Is there a trick to get its symmetry mate to appear without merging the pdb's? I am trying to avoid the situation where you accidentally build two or more waters into the same density because the symmetry mates are not showing and have to go through all the waters again afterwards to sort it out. I have checked the 'Show Symmetry' box for that molecule and I have tried changing the radius, etc. Any clues much appreciated. Jon.C. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] weak anomalous phasing (magic triangle I3C)
Hello Tiantian since there don't seem to be any replies to your message, I can suggest looking at the following points: 1) What is the unit cell and space group? Is there any scope for misindexing or twinning problems? 2) You have several heavy atom datasets, so why do you want to solve it with SAD? There may be isomorphous signal there which should be stronger. 3) Do you have the figures of merit and phasing power for the individual derivatives? Also, do the sites have good occupancies after refinement? 4) Are the derivatives all indexed consistently and are the sites of the different derivatives all on a common hand and origin? This is handled correctly by solve/resolve on the phenix side of things, and I guess the Crank pipeline, but we used to do it by cross-phased Fouriers. That's all that springs to mind for now. Hope some of it helps. Jon.C. On Thursday, 25 April 2019, 16:05:23 BST, ChenTiantian wrote: Dear all, I'm working on a 18kD protein, the secondary structure prediction says most of the structure is beta sheets, trying to solve the structure with SAD.Heavy atom soaking gives several datasets with I, W, Au, range from 2.7~3.7A, however, the anomalous signal is pretty weak, I couldn't find a reasonable solution.We got a co-crystal dataset with the magic triangle I3C, extends to around 2.5A, this is the best data we got so far.shelxc gives me the following result: Resl. Inf. 12.59 7.75 5.84 4.77 4.08 3.59 3.22 2.94 2.70 2.51 2.35 N(data) 79 257 429 635 811 1010 1235 1384 1698 1555 1954 Chi-sq 0.69 0.63 0.60 0.67 0.61 0.88 1.05 1.02 0.80 0.55 0.42 79.4 34.1 30.3 32.2 31.8 26.6 21.1 14.6 8.3 3.9 2.4 %Complete 94.0 98.1 97.5 99.5 99.4 99.0 99.7 100.0 99.9 85.4 96.1 Multipl. 4.0 4.5 3.9 4.5 4.7 4.2 4.4 4.8 5.0 4.3 4.4 R(pim)% 2.27 1.72 2.29 2.05 2.02 2.62 3.51 4.84 7.90 14.43 22.78 Ranom% 6.49 3.68 5.19 4.29 4.27 6.35 9.50 12.97 20.90 33.58 52.21 0.73 0.80 1.08 0.85 0.95 1.03 1.00 0.91 0.85 0.78 0.70 CC(1/2) 5.1 41.7 68.8 38.1 42.7 49.9 49.9 25.5 24.9 13.3 -4.7 then I tried shelxd with different heavy atom sites number and resolution cut, the best CC I got is CC/CCweak: 24.75/7.69, and I can identify a triangle, (length: 6.5/6.5/5.0A), however, both shelxe and autosol didn't end up with a promising result. It would be great if anyone can give me some suggestions. Thank you in advance!-- Tiantian To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] Some ccp4i2 menu options seem missing.
[SOLVED] Sorry folks, that was an easy one, "Clone Job" sorted it. Thanks for the tip Huw. Sent from Yahoo Mail on Android On Wed, 24 Apr 2019 at 23:14, Huw Jenkins<288da93ae744-dmarc-requ...@jiscmail.ac.uk> wrote: Hi, > On 24 Apr 2019, at 22:42, Jonathan Cooper > <0c2488af9525-dmarc-requ...@jiscmail.ac.uk> wrote: > > Any clues much appreciated, otherwise I'm back to the old gui. The linux one looks like a job that has been run. If you got to the task menu and click on Refinement - REFMAC5 does the new job open up with those fields un-editable? If so which version of CCP4 is this? Best wishes, Huw To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] Some ccp4i2 menu options seem missing.
Hello, on linux (Lubuntu) my install of the latest ccp4i2 does not allow me to change certain options, e.g. from isotropic to anisotropic refinement: www.ucl.ac.uk/~rmhajc0/jbc.jpg whereas my spy with a Mac gets: www.ucl.ac.uk/~rmhajc0/jg.jpg and the desired options are there and working. Any clues much appreciated, otherwise I'm back to the old gui. Best wishes Jon Cooper To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] BCA Winter Meeting, 4 days left to register.
Biological Structures Group Winter Meeting 2016: "Seeing the Wood for the Trees in Structural Biology." The meeting will be held on Monday 19th Dec 2016 at Birkbeck College, London at 11.00 am. The aim of the meeting is to glimpse at some of the contemporary approaches for assembling individual molecular structures into a bigger picture of biological systems, be they structural, metabolic, functional, disease-related or such-like. The meeting doubles as a career celebration event for the many ex-students, colleagues and collaborators of Prof Steve Wood whose research in Sussex, Birkbeck, Southampton and more recently UCL spans at least some 5 decades. Speakers include: Prof Tom Blundell FRS, Department of Biochemistry, University of Cambridge. "Increasing complexity to obtain selectivity in cell regulation: structural studies of multiprotein signalling systems."Prof Liz Carpenter, Structural Genomics Consortium, University of Oxford. "Structures of human ion channels, TREKs and TRPs, by X-ray, xFEL and cryoEM."Prof Jonas Emsley, School of Pharmacy, University of Nottingham. "Investigation of the contact system assembly and activation."Dr Simon Kolstoe, School of Biological Sciences, University of Portsmouth. "Determining the molecular interactions of serum amyloid P component."Prof Neil McDonald, The Francis Crick Institute and Birkbeck College, London. "Dissecting and exploiting RET receptor tyrosine kinase signalling."Prof Laurence Pearl FRS, School of Life Sciences, University of Sussex. "Phosphorylation dependent assembly of the DNA Damage Response."Prof Helen Saibil FRS, Department of Biological Sciences, Birkbeck. "Protein aggregation, chaperones and disaggregation."Patrick Shaw-Stewart, Douglas Instruments Ltd. "Microseed matrix-screening (rMMS): introduction, theory, practice and a new technique for membrane protein crystallization in LCP."Prof Garry Taylor, School of Biology, University of St Andrews. "An engineered multivalent sialic acid binding biologic as a preventative of influenza."Dr Marcus Winter. "Rigaku Oxford Diffraction: Advances in Crystallography. As usual, the registration fee will include one year's membership of the BCA. The closing date for registration is Friday 9th December 2016. For more information and to register for the meeting, please visit the meeting website: Biological Structures Group Winter Meeting 2016 | | | Biological Structures Group Winter Meeting 2016 | | | _ P.S. Could anyone coming please bring a poster? There is a poster prize, but so far only one entry! _
[ccp4bb] BCA Winter Meeting 2016 (1st reminder).
BCA Biological Structures Group Winter Meeting 2016: "Seeing the Wood for the Trees in Structural Biology." The meeting will be held on Monday 19th December 2016 at Birkbeck College, London starting at 11.00 am. The aim of the meeting is to glimpse at some of the contemporary approaches for assembling individual molecular structures into a bigger picture of biological systems, be they structural, metabolic, functional, disease-related or such-like. The meeting doubles as a career celebration event for the many ex-students, colleagues and collaborators of Prof Steve Wood whose research in Sussex, Birkbeck, Southampton and more recently UCL spans at least some 5 decades. Speakers include: Prof Tom Blundell FRS, Department of Biochemistry, University of Cambridge. "Increasing complexity to obtain selectivity in cell regulation: structural studies of multiprotein signalling systems." Prof Liz Carpenter, Structural Genomics Consortium, University of Oxford. Prof Jonas Emsley, School of Pharmacy, University of Nottingham. "Investigation of the contact system assembly and activation." Dr Simon Kolstoe, School of Biological Sciences, University of Portsmouth. "Determining the molecular interactions of serum amyloid P component." Prof Laurence Pearl FRS, School of Life Sciences, University of Sussex. "Phosphorylation dependent assembly of the DNA Damage Response." Prof Helen Saibil FRS, Department of Biological Sciences, Birkbeck. Patrick Shaw-Stewart, Douglas Instruments Ltd. "Microseed matrix-screening (rMMS): introduction, theory, practice and a new technique for membrane protein crystallization in LCP." Prof Garry Taylor, School of Biology, University of St Andrews. "An engineered multivalent sialic acid binding biologic as a preventative of influenza." Prof Martin Warren, School of Biosciences, University of Kent. Dr Marcus Winter. "Rigaku Oxford Diffraction: Advances in Crystallography." The closing date for registration is Friday 9th December 2016. As usual, the registration fee will include one year's membership of the BCA. For more information and to register, please visit the meeting website: http://bsg.crystallography.org.uk/wint16.html
[ccp4bb] BCA Biological Structures Group Winter Meeting: "Seeing the Wood for the Trees in Structural Biology".
Registration is now live for the British Crystallographic Association, Biological Structures Group Winter Meeting 2016. "Seeing the Wood for the Trees in Structural Biology." The meeting will be held on Monday December 19th 2016 at Birkbeck College London starting at 11.00 am. The aim of the meeting is to glimpse at some of the contemporary approaches for assembling individual molecular structures into a bigger picture of biological systems, be they structural, metabolic, functional, disease-related or such-like. The meeting doubles as a career celebration event for the many ex-students, colleagues and collaborators of Prof Steve Wood whose research in Sussex, Birkbeck, Southampton and more recently UCL spans at least some 5 decades. Speakers include: Prof Tom Blundell FRS, Department of Biochemistry, University of Cambridge. "Increasing complexity to obtain selectivity in cell regulation: structural studies of multiprotein signalling systems." Prof Liz Carpenter, Structural Genomics Consortium, University of Oxford. Prof Jonas Emsley, School of Pharmacy, University of Nottingham. "A PhD student's quest for the crystalline entity, touch wood." Dr Simon Kolstoe, School of Biological Sciences, University of Portsmouth. "Determining the molecular interactions of serum amyloid P component." Prof Laurence Pearl FRS, School of Life Sciences, University of Sussex. Prof Helen Saibil FRS, Department of Biological Sciences, Birkbeck. Prof Garry Taylor, School of Biology, University of St Andrews. Prof Martin Warren, School of Biosciences, University of Kent The closing date for registration is Friday 9th December 2016. As usual, the registration fee will include one year's membership of the BCA. For more information please visit the meeting website: http://bsg.crystallography.org.uk/wint16.html Please spread the word and hope to see you there! Jon Cooper
[ccp4bb] reference needed for TRUNCATE NO equation.
Dear all I have been asked by Randy for a reference for the following equation which appears in Sherwood Cooper: http://www.ucl.ac.uk/~rmhajc0/truncate_no.jpg ... or in text form: sigma(F) = sqrt(I + sigma(I)) - sqrt(I) It is the equation which TRUNCATE uses to calculate sigma(|F|) if the user switches off the French-Wilson treatment, although that is never usually done! Can anyone shed any light on who derived it and where/whether it has been published, etc? Cheers for now. Jon Cooper
[ccp4bb] Errata for Dennis Sherwood's book, revised paperback.
Dear All For info, a few errata for my latest attempt to update Dennis Sherwood's book 'Crystals, X-rays and Proteins' (which is now firmly out in revised paperback form ;-) can be found here... http://www.ucl.ac.uk/~rmhajc0 Please let me know if anything else shows up. Best wishes for now. Jon Cooper (UCL).
[ccp4bb] BCA Biological Structures Group (BSG) Winter Meeting, 15-17Dec 2014.
Dear All Please support the BCA winter meeting this year which, in a break from convention, is being held at ESRF/ILL, Grenoble, France - as you know, a major centre for structural biology research and infra-structure. This is an experiment for the BSG committee, really, being in the spirit of the International Year of Crystallography, etc, and is perhaps a one-off event. However, registrations from the UK are low so please register, publicise the meeting and encourage your group members to attend, if at all possible. There is some urgency in this and I can't put it better than one of the local organisers: ...it needs to be done soon and it needs to have as many people as possible trying to get it going. We are trying hard to mobilise people at this end... The BSG is extremely appreciative of the hard-working organisers in Grenoble who have put together an excellent programme covering: Research Infrastructures: State-of-the-Art and Impact for Structural Biology, Future Opportunities for UK Structural Biology in Grenoble, Combining X-rays Neutrons in Structural Biology, Structural Biology on the EPN Campus, Emerging Techniques in Structural Biology. Registration and all other details are available at this link: http://bsg.crystallography.org.uk/index.html We look forward to seeing you there. Best wishesJon Cooper
[ccp4bb] Book refinement
Evening all. It seems that the publisher of my efforts to update the 'Crystals, X-rays and Proteins' book by Dennis Sherwood would like to print a revised version, so I was wondering if anyone has noted any typos, glitches, misprints, etc, perhaps they could possibly let me know, in return for an acknowledgement!! I have a set of corrections and reviewer comments at the erratum site (http://www.ucl.ac.uk/~rmhajc0/) but any more would be very much appreciated. Best wishes for now. Jon Cooper P.S. The best e-mail for this would be: jon.coo...@ucl.ac.uk
[ccp4bb] Abstract Submission for BCA Spring Meeting 2014
Dear BCA members, The 2014 Spring BCA meeting is not far away now and the abstract submission deadline is fast approaching – 1 week remains! Abstracts can be submitted at: http://www.hg3.co.uk/bca/ The deadline for submissions is 9 am on Monday January 20th. This deadline applies to both oral and poster presentations and to both contributed and invited abstracts. The deadline cannot be extended. The theme of the meeting is Crystallography@100: Looking to the Future, Learning from the Past, and reflects the period of centenary celebration of the field of crystallography, marked by 2014 being designated the International year of Crystallography (IYCr) by UNESCO. The main meeting will be held at The University of Loughborough on April 8-10th, 2014, and features 13 symposia, the Bragg and Lonsdale lectures, 4 additional plenary lectures and 4 prize lectures for early career researchers. The meeting is preceded as usual, by the one-day Young Scientists Satellite Meeting (April 7-8th). Details of the meeting programme, as well as registration details, can be found on the BCA website at: http://crystallography.org.uk/bca-spring-meeting-7th-10th-april-2014/ I hope to see many of you at the meeting this year and look forward to seeing the abstracts flowing in. Best wishes Lee Brammer BCA 2014 Programme Chair Professor of Chemistry University of Sheffield
[ccp4bb] BCA Winter Meeting Monday 16th
places still available register on the day BCA Winter Meeting 2013 Title: New X-ray Developments and Macromolecular Structures in the Bragg Centenary Year. Venue: King’s College London (New Hunt's House, Guy's Campus, London Bridge, SE1 1UL). Date: 16th December 2013. Organisers: The Randall Division of Cell Molecular Biophysics, KCL. - - - - - - - Invited speakers include: Bonnie Wallace, Birkbeck College London. Voltage-gated Sodium Channels: Complementary Insights into Structure and Function and Disease using Crystallography and Spectroscopy David Stuart, University of Oxford. In silico drug design - perhaps it really works James Naismith, St. Andrew’s University. The UK plans for XFEL: what it can do for crystallography Ivan Laponogov, King’s College London. Structure of an ‘open’ clamp type II topoisomerase-DNA complex provides a mechanism for DNA capture and transport David Leys, University of Manchester. Structural studies on poly-ADP-ribose glycohydrolases Stefano Pernigo, King’s College London. Structural basis of kinesin-1:cargo interaction Liz Carpenter, SGC Oxford. A novel structure for a nuclear membrane zinc metalloprotease involved in premature ageing diseases - - - - - - - - For details please visit the meeting website: http://crystallography.org.uk/bsg-winter-meeting-2013/ - - - - - - - - Contacts: Dr Mark Sanderson (mark.sander...@kcl.ac.uk) and Dr Yu Wai Chen (yu-wai.c...@kcl.ac.uk)
[ccp4bb] BCA Winter Meeting, 16th Dec, Kings College London
Title: New X-ray Developments and Macromolecular Structures in the Bragg Centenary Year. Venue: King’s College London. Date: 16th December 2013. Organisers: Dr Yu-Wai Chen and Prof Mark Sanderson. - - - - - - - Invited speakers include: Bonnie Wallace, Birkbeck College London. “Voltage-gated Sodium Channels: Complementary Insights into Structure and Function and Disease using Crystallography and Spectroscopy” David Stuart, University of Oxford. Title to be announced James Naismith, St. Andrew’s University. “The UK plans for XFEL: what it can do for crystallography” Ivan Laponogov, King’s College London. “Structure of an ‘open’ clamp type II topoisomerase-DNA complex provides a mechanism for DNA capture and transport” David Leys, University of Manchester. “Structural studies on poly-ADP-ribose glycohydrolases” Stefano Pernigo, King’s College London. “Structural basis of kinesin-1:cargo interaction” Liz Carpenter, SGC Oxford. “A novel structure for a nuclear membrane zinc metalloprotease involved in premature ageing diseases” - - - - - - - - For details and registration, please visit the meeting website: http://crystallography.org.uk/bsg-winter-meeting-2013/ Registration deadline: Wednesday 11 November 2013.
Re: [ccp4bb] Curious electron density associated with Asp sidechain
Hello Tony is that Asp-Gly? If so, it could be prone to succinimide formation. Check out this paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2323960/ and references therein! Good luck Jon.Cooper --- On Thu, 25/4/13, Antony Oliver antony.oli...@sussex.ac.uk wrote: From: Antony Oliver antony.oli...@sussex.ac.uk Subject: [ccp4bb] Curious electron density associated with Asp sidechain To: CCP4BB@JISCMAIL.AC.UK Date: Thursday, 25 April, 2013, 17:10 Dear CCP4 colleagues. I'm just finishing up a refinement, but am left with one little curio that I just can't seem to solve. One aspartic acid residue is associated with some extra, unexplained electron density. -- please see: http://i.imgur.com/vCYOqam.png Where, the Fo-Fc map is contoured at 3.78 rsmd in Coot. I have tried a number of different modelling scenarios, but as yet can't reach a wholly satisfactory conclusion; waters, alternate conformers, really don't seem to cut it. I though about some radiation-induced phenomena, but this data set was collected on a home-source, so I guess this is unlikely. So, I would really appreciate some ideas and suggestions. Hopefully it is blindingly obvious to someone. Random Thought: could it be PEGylation of the side-chain? Some other hopefully useful background information: * I'm sure it is/was an ASP, because the same protein (made from the same construct) has been used in previous crystallisations, and the resultant structures have clear, unambiguous electron density for the side chain. * the crystallization condition is PEG 200, with some Na/K phosphate at pH 5.8, and NaCl. The protein itself contains HEPES buffer. With many thanks, Tony. --- Dr Antony W Oliver Senior Research Fellow CR-UK DNA Repair Enzymes Group Genome Damage and Stability Centre Science Park Road University of Sussex Falmer, Brighton, BN1 9RQ email: antony.oli...@sussex.ac.uk tel (office): +44 (0)1273 678349 tel (lab): +44 (0)1273 677512
