Re: [ccp4bb] AI and cis-peptides
Yes - our CASP15 target H1157 contained intramolecular and inter-molecular SS bonds - the former were well predicted but the latter were not: https://predictioncenter.org/casp15/multimer_results.cgi?target=H1157 The article discussing this aspect (as well a few other CASP15 targets) is at the proofs stage in Proteins. Ciao Pietro On 13-07-2023 18:07, Guillaume Gaullier wrote: Interesting. Has someone similarly looked at whether AlphaFold predicts disulfide bridges? Guillaume On 13 Jul 2023, at 15:12, Randy John Read wrote: I’m not sure about other methods, but AlphaFold does predict peptides in both cis and trans configurations. In a recent paper, Osnat Herzberg and John Moult show that it was pretty successful in predicting proline cis-peptides, among the novel structures in the CASP15 set of targets (https://www.pnas.org/doi/10.1073/pnas.2221745120). For non-proline cis-peptides, I’m not aware of published work but Tristan Croll has shown me examples of correctly-predicted non-proline cis-peptides, including cases where some of the related structures in the PDB have an incorrect trans configuration. This implies that AlphaFold is not slavishly reproducing what it has seen during training. Best wishes, Randy Read On 13 Jul 2023, at 13:56, Oliviero Carugo wrote: Does anybody know if cis-peptides are predicted by the AI tools (AlphaFold2, ColabFold, or ESM-2)? To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of http://www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by http://www.jiscmail.ac.uk/, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ - Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: +44 1223 336500 The Keith Peters Building Hills Road E-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk [1] To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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/ VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen avsändaren och vet att innehållet är säkert. CAUTION: Do not click on links or open attachments unless you recognise the sender and know the content is safe. Page Title När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy - To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 Links: -- [1] http://www-structmed.cimr.cam.ac.uk -- Dr. Pietro Roversi, PhD Italian National Research Council (CNR) Institute of agricultural biology and biotechnology (IBBA-CNR) Via Edoardo Bassini 15, 20133 Milano, Italy Tel. +39 02 23699428 Mobile +39 351 6800096 Fax: +39 02 23699411 https://ibba.cnr.it/en/staff/pietro-roversi/ Adjunct Lecturer in Mathematical Modeling for Biology Master in Quantitative Biology, Department of Biosciences, University of Milano, Italy Email: pietro.rove...@unimi.it URL: https://www.unimi.it/en/ugov/person/pietro-roversi Honorary Lecturer at LISCB - Department of Molecular and Cell Biology Leicester University, Lancaster Rd. Leicester LE1 7HB, England, UK Tel. +44 7927 952047 Email: pr...@leicester.ac.uk URL: https://le.ac.uk/liscb/research-groups/honorary-members/pietro-roversi To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] About the A in AI
Whata shame this journal does not reveal the identity of their reviewers, I think I recognise the writing style of my competitor, Dr. Ångstrom Imbecile. On 12-05-2023 17:15, Bernhard Rupp wrote: For those who concern themselves with such matters, here the responses from Bing and ChatGPT to the prompt: "Please write a critical review report rejecting a scientific paper reporting that the 1.0 angstrom crystal structure shows that psiX is a trimethylating enzyme" Enjoy the frightening reading and then we can chat (LOL) about the creepy feeling of déjà-vu you might experience…. https://www.dropbox.com/s/2fo9u3d11dk8n0o/Bing.docx?dl=0 https://www.dropbox.com/s/9gr34grpcrf7yk7/ChatGPT.docx?dl=0 Cheers, BR - Bernhard Rupp k.k. Hofkristallamt 001 (925) 209-7429 +43 (676) 571-0536 b...@ruppweb.org hofkristall...@gmail.com http://www.hofkristallamt.org/ [1] - Hope is not a strategy - hope is a mistake. - - To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 Links: -- [1] http://www.hofkristallamt.org/ -- Dr. Pietro Roversi, PhD Italian National Research Council (CNR) Institute of agricultural biology and biotechnology (IBBA-CNR) Via Edoardo Bassini 15, 20133 Milano, Italy Tel. +39 02 23699428 Mobile +39 351 6800096 Fax: +39 02 23699411 https://ibba.cnr.it/en/staff/pietro-roversi/ Adjunct Lecturer in Mathematical Modeling for Biology Master in Quantitative Biology, Department of Biosciences, University of Milano, Italy Email: pietro.rove...@unimi.it URL: https://www.unimi.it/en/ugov/person/pietro-roversi Honorary Lecturer at LISCB - Department of Molecular and Cell Biology Leicester University, Lancaster Rd. Leicester LE1 7HB, England, UK Tel. +44 7927 952047 Email: pr...@leicester.ac.uk URL: https://le.ac.uk/liscb/research-groups/honorary-members/pietro-roversi To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] To Trim or Not to To Trim
07750321-dmarc-requ...@jiscmail.ac.uk>> wrote: Hi Rhys, I am also all for leaving side chains and letting the B-factors deal with the weak/absent density. I don’t think there is a consensus, but I kind of remember that somebody did a poll a few years ago and if I remember correctly the main approaches were the one described above, or trimming the side-chains. Bernhard *Bernhard C. Lechtenberg* PhD NHMRC Emerging Leadership Fellow Laboratory Head Ubiquitin Signalling Division E lechtenber...@wehi.edu.au <mailto:lechtenber...@wehi.edu.au> T +61 3 9345 2217 *From: *CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> on behalf of Rhys Grinter <22087c81e8c6-dmarc-requ...@jiscmail.ac.uk <mailto:22087c81e8c6-dmarc-requ...@jiscmail.ac.uk>> *Date: *Friday, 10 March 2023 at 12:26 pm *To: *CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK> mailto:CCP4BB@JISCMAIL.AC.UK>> *Subject: *[ccp4bb] To Trim or Not to To Trim Hi All, I'm trying to crowdsource an opinion on how people deal with modelling side chains with poorly resolved electron or cryoEM density. My preference is to model the sidechain and allow the B-factors to go high in refinement to represent that the side chain is flexible. However, I'm aware that some people truncate sidechains if density is not present to justify modelling. I've also seen models where the sidechain is modelled but with zero occupancy if density isn't present. Is there a consensus and justifying arguments for why one approach is better? Cheers, Rhys To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> -- --- LinkedIn: www.linkedin.com/in/debanudas <http://www.linkedin.com/in/debanudas> Cal Alumni: cal.berkeley.edu/debanudas <http://cal.berkeley.edu/debanudas> To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> VARNING:Klicka inte på länkar och öppna inte bilagor om du inte känner igen avsändaren och vet att innehållet är säkert. CAUTION:Do not click on links or open attachments unless you recognise the sender and know the content is safe. Page Title När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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/ -- Dr. Pietro Roversi, PhD Italian National Researc
Re: [ccp4bb] Tools for structure-based multiple sequence alignment
Dear Manoj, I usually utilize SALIGN to produce structure-based sequence alignments: https://modbase.compbio.ucsf.edu/salign/ Ciao Pietro On 02-03-2023 08:45, Manoj N wrote: Dear all, We want to generate a structure-based multiple sequence alignment for a large number of homologous structures (>100). What are the available programs (stand-alone or webserver) to do this? Thank you, Best wishes, Manoj - To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 -- Dr. Pietro Roversi, PhD Italian National Research Council (CNR) Institute of agricultural biology and biotechnology (IBBA-CNR) Via Edoardo Bassini 15, 20133 Milano, Italy Tel. +39 02 23699428 Mobile +39 351 6800096 Fax: +39 02 23699411 https://ibba.cnr.it/en/staff/pietro-roversi/ Adjunct Lecturer in Mathematical Modeling for Biology Master in Quantitative Biology, Department of Biosciences, University of Milano, Italy Email: pietro.rove...@unimi.it URL: https://www.unimi.it/en/ugov/person/pietro-roversi Honorary Lecturer at LISCB - Department of Molecular and Cell Biology Leicester University, Lancaster Rd. Leicester LE1 7HB, England, UK Tel. +44 7927 952047 Email: pr...@leicester.ac.uk URL: https://le.ac.uk/liscb/research-groups/honorary-members/pietro-roversi To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] Map superposition!
Thank you Pavel, very useful. I imagine I have to invert the hand *beforehand* if it is not the correct one :-) Just saying - checking hand and picking the better one would be a nice feature to implement in this tool. P On 25-01-2023 17:06, Pavel Afonine wrote: Hi Rams, phenix.match_maps will superpose maps and models. Totally general: target/moving boxes (unit cells) and symmetry can be different, gridding can be different too. I can help off list should you need any assistance! Pavel On Wed, Jan 25, 2023 at 6:30 AM Subramanian, Ramaswamy wrote: Hi All, I have two maps - both cryo-EM. One with and one without ligand. I am trying to superpose them and I cannot seem to get ChimeraX to work. I then tried VESPER and that also does not work. The built models superpose very well. What is the best way to superpose maps. Thank you. Rams subra...@purdue.edu - To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 - To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 -- Dr. Pietro Roversi, PhD Italian National Research Council (CNR) Institute of agricultural biology and biotechnology (IBBA-CNR) Via Edoardo Bassini 15, 20133 Milano, Italy Tel. +39 02 23699428 Mobile +39 351 6800096 Fax: +39 02 23699411 https://ibba.cnr.it/en/staff/pietro-roversi/ Adjunct Lecturer in Mathematical Modeling for Biology Master in Quantitative Biology, Department of Biosciences, University of Milano, Italy Email: pietro.rove...@unimi.it URL: https://www.unimi.it/en/ugov/person/pietro-roversi Honorary Lecturer at LISCB - Department of Molecular and Cell Biology Leicester University, Lancaster Rd. Leicester LE1 7HB, England, UK Tel. +44 7927 952047 Email: pr...@leicester.ac.uk URL: https://le.ac.uk/liscb/research-groups/honorary-members/pietro-roversi To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] Regarding Patents
Dear all, one of the most interesting documents in recent times on the matter of translational research and IP comes from the Wellcome Trust: https://wellcome.ac.uk/sites/default/files/transforming-uk-translation-20170725.pdf In particular, under committments 4-8, they spell out - although implicitly - the push for a change in which IP is handled in Universities. Let's see which way it goes but I remain hopeful with best wishes Pietro = Dr. Pietro Roversi As of July 2018 I shall take up a two-year LISCB and Leicester-Wellcome Trust ISSF Fellowship at Leicester University: http://www2.le.ac.uk/institutes/liscb Until June 2018: Oxford Glycobiology Institute Department of Biochemistry University of Oxford South Parks Road Oxford OX1 3QU England - UK Tel. 0044 1865 275339 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Alun R Coker [alun.co...@ucl.ac.uk] Sent: 05 November 2017 20:35 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Regarding Patents In the UK many Universities policies lay claim to IPR as belonging to the university, rather than the academic (this is based on UK IPR law which says that IP belongs to the employer rather than the employee). So giving up IPR can be problematical and could leave an academic in breach of contract though I don't suppose that most universities would pursue this. Recently, at UCL we were presented with new IPR policy which says that all patentable IP created during the course of our duties is owned the university. We are challenging this through our academic board (senate) and have managed to get a Academic Board members to sit on a committee to redraft it. It would be interesting to hear what the IPR policies of other universities are like. I have heard that in Aberdeen academics on their senate have managed to get their IPR policy rewritten by invoking the 1926 Slavery Convention, which states that slavery is defined as "the status or condition of a person over whom any or all of the powers attaching to the right of ownership are exercised". Their augment was that by seeking ownership over an academic's intellectual property was tantamount to seeking ownership over the academic. All the best, Alun On 04/11/17 23:44, Patrick Shaw Stewart wrote: There are some interesting anti-patent initiatives https://en.wikipedia.org/wiki/Patent#Anti-patent_initiatives including prizes as an alternative to patents https://en.wikipedia.org/wiki/Prizes_as_an_alternative_to_patents#Other_areas_for_prize_models_over_patents On 4 November 2017 at 15:08, Bernhard Rupp mailto:hofkristall...@gmail.com>> wrote: > to publish it so the world can benefit from it. Isn’t that exactly the idea of a patent? Instead of keeping the invention a trade secret (occasionally a viable alternative) you publish the invention, and the inventor (and in general, the supporting institutions) can get rewarded if someone plans to use the idea commercially. Someone (in academia often the tax payer) did pay for the work after all, and having an option to recover the money (or god forbid, make a profit…) seems a reasonable proposition…. Best, BR From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>] On Behalf Of Abhishek Anan Sent: Saturday, November 4, 2017 05:31 To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> Subject: Re: [ccp4bb] Regarding Patents I second Gert's thoughts Best, Abhishek On Sat, Nov 4, 2017 at 10:21 AM, Gert Vriend mailto:gerrit.vri...@radboudumc.nl>> wrote: A related question. If you have a crystal structure and found a novel ligand binding site that can be used to regulate protein activity, could you patent such "binding site"? If not, how to make the best use of such findings? I would say that the best one can do with important novel data/information/knowledge/insights is to publish it so the world can benefit from it. Gert -- patr...@douglas.co.uk<mailto:patr...@douglas.co.uk>Douglas Instruments Ltd. Douglas House, East Garston, Hungerford, Berkshire, RG17 7HD, UK Directors: Peter Baldock, Patrick Shaw Stewart http://www.douglas.co.uk Tel: 44 (0) 148-864-9090US toll-free 1-877-225-2034 Regd. England 2177994, VAT Reg. GB 480 7371 36 -- Dr Alun R. Coker Senior Lecturer Wolfson Institute for Biomedical Research University College London The Cruciform Building London WC1E 6BT Tel: 020 7679 6703 Ext 46703 Web: www.ucl.ac.uk/pxmed<http://www.ucl.ac.uk/pxmed>
Re: [ccp4bb] Incorrect Structure in the PDB
On the subject of withdrawal of entries from the PDB, I just flag up another interesting aspect. Four years ago I was Visiting Fellow in a colleague's lab, and in the course of the year I determined, refined and deposited 4 good structures, authored by me and my colleagues who were part of the research. Due to a scientific disagreement on the manuscript describing the structures, my colleague wrote to the PDB and unilaterally withdrew the 4 entries, without letting me know in advance nor consulting me and against my will. When I wrote to the PDB to complain (i was the depositor) they answered: "Thank you for your email. According to the wwPDB policy, if there is a case of conflict between authors, the PI of the project makes the final decision. Since Dr. is the PI for this project, we have to take his word as final. Please see below the extract of the policy (http://www.wwpdb.org/policy.html). Please note, PDB cannot resolve any conflict between authors. This has to be resolved by the authors." My colleague has since re-determined, re-refined and re-deposited the structures against the data taken from the crystals I grew (with his name as the only author of all 4 entries0 and they have published the work without granting me co-authorship on the paper. I wrote immediately to the journal and they suggested that the Institute where I carried out the research carry out an internal investigation. Which is ongoing. It's all very well that all is done in good faith but sometimes on-trust policy + absence of a "court" to appeal to in case of misconduct are a rather insufficient combination when it comes to PDB depositions/withdrawals. with best wishes, Pietro best regards, Sanchayita Sen PDBe Depositions Sent from my Desktop Dr. Pietro Roversi Oxford University Biochemistry Department - Glycobiology Division South Parks Road Oxford OX1 3QU England - UK Tel. 0044 1865 275339 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Trevor Sewell [trevor.sew...@uct.ac.za] Sent: 27 June 2017 07:34 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Incorrect Structure in the PDB I have come across a key paper in my field that describes an enzyme mechanism. Their work is based on a deposited structure – by other authors - that is incorrectly interpreted. Is there a process for removing a demonstrably wrong structure (deposited by others) from the PDB and replacing it with a correctly interpreted structure based on the original data? Or is there an alternative, and generally recognized, way of getting the correct structure in the public domain? Many thanks for your advice on this matter. Trevor Sewell Disclaimer - University of Cape Town This e-mail is subject to UCT policies and e-mail disclaimer published on our website at http://www.uct.ac.za/about/policies/emaildisclaimer/ or obtainable from +27 21 650 9111. If this e-mail is not related to the business of UCT, it is sent by the sender in an individual capacity. Please report security incidents or abuse via cs...@uct.ac.za
[ccp4bb] I am struggling to compile fasta36
Dear all, I apologise for the dullness of the question, but I am struggling to compile the fasta36 binary that I need to run MrBump: emmaWT:/software/fasta-36.3.7/src> sudo make -f ../make/Makefile.linux64_sse2 all gcc -g -O -msse2 -o ../bin/fasta36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_fa.o drop_nfa.o wm_align.o calcons_fa.o scale_se.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o url_subs.o mrandom.o -lm -lz -lpthread /usr/bin/ld: cannot find -lz collect2: error: ld returned 1 exit status make: *** [fasta36] Error 1 Googling for this -lz ld flag does not seem to hit anything immediately relevant in the top pages. Please help! Pietro Sent from my Desktop Dr. Pietro Roversi Oxford University Biochemistry Department - Glycobiology Division South Parks Road Oxford OX1 3QU England - UK Tel. 0044 1865 275339
Re: [ccp4bb] Selenomethionine crystals
Can I remind everyone that animals scattering is in reality *anisotropic* and therefore in some crystals, depending on the distribution of the anomalous scatterers in the protein and the symmetry of the space group, there may be relative orientations of beam and crystal in which one has lots of anomalous signal and others in which there is little. See the Templetons' work and also: Bricogne, G., Capelli, S.C., Evans, G., Mitschler, A., Pattison, P., Roversi, P., Schiltz, M. X-ray absorption, refraction and resonant scattering tensors in selenated protein crystals: implications for data collection strategies in macromolecular crystallography J. Appl. Cryst., 38, 168-182, 2005 I suspect there have been times in which lack of signal or lots of signal have been attributed to oxidation/reduction of Se atoms, when in fact it may have been the luck of the draw of how the crystal went up into the beam. Ciao Pietro Sent from my Desktop Dr. Pietro Roversi Oxford University Biochemistry Department - Glycobiology Division South Parks Road Oxford OX1 3QU England - UK Tel. 0044 1865 275339 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of James Holton [jmhol...@lbl.gov] Sent: 07 July 2014 00:59 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Selenomethionine crystals I general I agree with Tim, but provided it doesn't kill your protein, oxidation of selenomethionine can actually enhance your anomalous signal considerably (http://dx.doi.org/10.1107/S0907444901008666). The reason for this is because the "white line" peak in the SeMet x-ray absorption spectrum is actually a pre-edge feature. Although the "edge" itself represents the point when the incoming photon has just enough energy to completely eject a core electron from the Se atom, it is also possible for the electron to be not exactly "ejected" but merely promoted to an empty orbital with energy a few eV below that of a free electron in a vacuum. It is because of these extra landing sites that the near-edge structure of the x-ray absorption specturm (XANES or NEXAFS) can be influenced by chemistry. Specifically, the "peak" of the normal SeMet spectrum is a 1s-4p transition (http://dx.doi.org/10.1021/es9a043 http://dx.doi.org/10.1107/S0909049506048898), and the more oxidized the Se atom is, the less occupied the 4p level becomes and the bigger the while line gets. And, of course, the bigger the while line the more f" phasing signal you get. Unfortunately, the extra oxygens stuck on the Se can sterically disrupt the local environment of the SeMet, and fear of this is probably why so many people have not tried it. However, if you're desperate for that extra little "boost" of phasing signal, it might be a refreshing change to do the opposite of trying to keep your protein from oxidizing all the time. Perhaps even adding a dash of H2O2. The worst your crystals can do is not diffract. -James Holton MAD Scientist On 7/1/2014 8:54 AM, Tim Gruene wrote: > Dear Maher, > > as far as I understand, the anomalous scattering comes from inner shell > electrons, not the valence electrons. So while you might notice a slight shift > in the peak wavelength, the strength of the signal will only reduce if you > crystal order suffered over time, but not from any oxidation of the Se. > > Best, > Tim > > On Tue, Jul 01, 2014 at 10:51:20AM -0500, Maher Alayyoubi wrote: >> Hi everyone, >> >> Would anyone know for how long Selenomethionine derivative crystals are >> good if kept in plate at RT. In other words, would SE loose its scattering >> properties due to oxidation over time? I have SElmet crystals that have >> been lying in a plate for 2 months by now so I was wondering if they are >> still worthwhile the effort of collecting new data from them. >> >> Thank you very much, >> >> >> Maher
Re: [ccp4bb] Phasing with Many Monomers/AU
Dear James and all,
just to throw into the pot an idea I never came across anywhere,
and I could never test because I never had such data/problem:
1. many NCS copies in the asymmetric unit;
2. either isomorphous differences and/or anomalous differences from heavy atoms
3. more than one heavy atom bound per molecule;
4. clear self rotation function indicating the directions of the NCS axes and
the point group of the NCS
I always thought in this case one should try and average
under the NCS point symmetry the isomorphous and difference Pattersons around
the origin
to boost the intramolecular heavy-atom Patterson vectors.
Has anyone ever had such data and tried that strategy?
Is it implemented in any of the currently available difference
Patterson-solvers/heavy atom finders?
Ciao!
Pietro
Sent from my Desktop
Dr. Pietro Roversi
Oxford University Biochemistry Department - Glycobiology Division
South Parks Road
Oxford OX1 3QU England - UK
Tel. 0044 1865 275339
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of James Holton
[jmhol...@lbl.gov]
Sent: 22 January 2014 02:24
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Phasing with Many Monomers/AU
The problem of many monomers in the "ASU" is not restricted to
macromolecules. An interesting recent small molecule example is the
structure of L-tryptophan (http://dx.doi.org/10.1107/S0108768112033484)
which, amazingly, was not published until 2012. This is perhaps in part
due to difficulty in accepting 16 monomers in the ASU (they call this
Z=16), which was unprecedented.
As a beamline scientist, I have seen "high Z" macromolecular crystals on
many occasions, but they almost never get solved. Yes, they don't
diffract well, but neither does anything else in the early stages of a
project. The reason for not solving them seems more psychological than
anything else. The prospect of amplifying the building and refinement
headache by a factor of "Z" when Z > 10 is perhaps too much for an early
term graduate student to bear.
On the other hand, automated building and refinement has come a long
way, and 24-fold NCS is a great restraint if you can get it! In fact,
for virus structures, it has been shown that you can phase the structure
starting with nothing but a crude spherical envelope and lots of density
modification (http://dx.doi.org/10.1107/S0108767391013211).
but your initial problems are going to be phasing. Ideally what you'd
want is a way of folding back NCS information into the heavy atom
finding and phase refinement process, but I know of no programs that
actually do that. In fact, both molecular replacement and heavy-atom
finding are hindered by this "pseodo-translation" rather than helped by
it. Personally, I blame the fact that methods developers seldom get
their hands on "interesting" datasets like yours. And if you look in
the PDB there are very few examples of "high Z'" structures. Ahem.
Best advice I can give is to try the "usual" approach, but look very
seriously for NCS as early as you can. Then apply building/phasing
packages like shelx{cde}, phenix.autobuild, or the newly-released Crank2.
-James Holton
MAD Scientist
On 1/18/2014 11:18 PM, Felix Frolow wrote:
> Francis, It can happened
> We have (not yet published) P1 with 24 molecules. When we cut His-tag we get
> P1 with 32 molecules.
> In our case we believe it is dictated by very strong interaction between two
> monomers, and strong interaction between dimers with build a flattish
> tetramer. Probably such formations
> is more difficult to oaks than globular oligomers.
> In this moment I do not recall what we see in solution, I have to check.
> Relating to structure solution, P1 is very convenient space group.
> I would go for determination this structure by SAD (SHELXC/D/E pipe, PHENIX
> or SHARP). For the native - molecular replacement.
> In our time after tremendous developments in Refmac and Phenix and
> development o DM refinement is 3-3.4 Ang. Is not very difficult.
> I would use in addition to NCS restraints in refinement also multi crystal
> averaging. Roumors say it is the most strongest phasing method (attributed to
> Eleanor Dodson, myself never used it).
>
>
> FF
>
> Dr Felix Frolow
> Professor of Structural Biology and Biotechnology, Department of Molecular
> Microbiology and Biotechnology
> Tel Aviv University 69978, Israel
>
> Acta Crystallographica F, co-editor
>
> e-mail: mbfro...@post.tau.ac.il
> Tel: ++972-3640-8723
> Fax: ++972-3640-9407
> Cellular: 0547 459 608
>
> On Jan 19, 2014, at 08:48 , Francis Reyes wrote:
>
>> You sure about this space group? 24 monomers in P1 is unusual (at least to
>> me)
>>
>> F
>>
>>> On Jan 18, 2014, at 9:14 AM, Chris Fage wrote
[ccp4bb] in summary
Yes, thank you Bob! and therefore, as first pointed out in this thread by Loes Kroon-Batenburg, and as explainedin (among other places) the Ladd and Palmer book that Dom Bellini pointed me to, the indices 001, 010 etc. for example, will index first order diffraction maxima, while 002, 020 etc. will be the indices for the second order diffraction maxima from the same sets of lattice planes. I feel now reconciled with Bragg's law (although for obvious reasons I like Ewald's constructions much better) and this is happening just in time for next year's 2014 IUCr celebrations :-) Thank you all contributors to the thread! Regards Pietro Sent from my Desktop Dr. Pietro Roversi Oxford University Biochemistry Department - Glycobiology Division South Parks Road Oxford OX1 3QU England - UK Tel. 0044 1865 275339 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Robert Blessing [bless...@hwi.buffalo.edu] Sent: 23 August 2013 15:52 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] sin(theta_hkl)=n*lambda/(2*d_hkl) A point to bear in mind is that only planes with co-prime h k l indices are "lattice planes" that pass through lattice points. Planes with indices that are composite numbers nh nk nl are "virtual lattice planes" that do not pass through lattice points. Bob Robert H. Blessing, Ph.D. Hauptman-Woodward Medical Research Institute, Inc. and State University of New York at Buffalo Hauptman-Woodward Institute 700 Ellicott Street Buffalo, New York 14203, USA Phone716-898-8613 Fax 716-898-8660 eMail bless...@hwi.buffalo.edu<mailto:bless...@hwi.buffalo.edu> Internet http://www.hwi.buffalo.edu<http://www.hwi.buffalo.edu/>
[ccp4bb] Dependency of theta on n/d in Bragg's law
Dear all, I am shocked by my own ignorance, and you feel free to do the same, but do you agree with me that according to Bragg's Law a diffraction maximum at an angle theta has contributions to its intensity from planes at a spacing d for order 1, planes of spacing 2*d for order n=2, etc. etc.? In other words as the diffraction angle is a function of n/d: theta=arcsin(lambda/2 * n/d) several indices are associated with diffraction at the same angle? (I guess one could also prove the same result by a number of Ewald constructions using Ewald spheres of radius (1/n*lambda with n=1,2,3 ...) All textbooks I know on the argument neglect to mention this and in fact only n=1 is ever considered. Does anybody know a book where this trivial issue is discussed? Thanks! Ciao Pietro Sent from my Desktop Dr. Pietro Roversi Oxford University Biochemistry Department - Glycobiology Division South Parks Road Oxford OX1 3QU England - UK Tel. 0044 1865 275339
Re: [ccp4bb] Rmerge of the last shell is zero
HKL2000 sets to 0 the Rmerge in any shell where it is higher than 100% OUCH Sent from my Desktop Dr. Pietro Roversi Oxford University Biochemistry Department - Glycobiology Division South Parks Road Oxford OX1 3QU England - UK Tel. 0044 1865 275339 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Yafang Chen [yafangche...@gmail.com] Sent: 14 August 2013 16:32 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Rmerge of the last shell is zero Dear All, Here are some more details about the question I asked earlier about "Rmerge is 0 in the last shell". I processed the data using HKL2000. The space group is I213. Redundancy is 10.2 (10.3). I/sigma is 34.8 (2.3). Rmerge is 6.5 (0.0). Since I/sigmaI is more than 2 in the last shell, I preferred not to cut back the resolution any more. But I don't know how to explain Rmerge in the last shell being 0. Besides, I am wondering if this data is publishable (with Rmerge being 0 in the last shell). Thank you so much for your help! Best, Yafang On Wed, Aug 14, 2013 at 10:59 AM, Yafang Chen mailto:yafangche...@gmail.com>> wrote: Dear All, I recently processed a dataset, in which I/sigmaI of the last shell is 2.3, while Rmerge of the last shell is 0. Does anyone know why the Rmerge is 0? The completeness is 100 (100). Thank you so much for your help in advance! Best, Yafang -- Yafang Chen Graduate Research Assistant Mesecar Lab Department of Biological Sciences Purdue University Hockmeyer Hall of Structural Biology 240 S. Martin Jischke Drive West Lafayette, IN 47907 -- Yafang Chen Graduate Research Assistant Mesecar Lab Department of Biological Sciences Purdue University Hockmeyer Hall of Structural Biology 240 S. Martin Jischke Drive West Lafayette, IN 47907
[ccp4bb] X-rays gas scattering picture needed
Dear all, together with two fellow crystallographers, I am writing a pamphlet to introduce schoolchildren to X-ray crystallography. For the introductory chapter, we would need a picture of X-rays scattered by air. Or by any gas for that matter. I have tried Google images without much luck. Can anyone either kindly donate, or point me to, an image of X-rays scattered by a gas? Thanks! Pietro PS of course a picture of X-ray scattering by a liquid would also be very welcome
[ccp4bb] 2D-bar code scanner to read Hampton pins barcodes
Dear all, I am looking into a 2D-bar code scanner to read Hampton pins barcodes. Something we can plug directly to any computer running Windows, Mac or Linux, via a supplied USB cable, and feed the barcodes into Excel. Does anybody know a cheaper alternative to the FOCUS MS-1690-38? Grazie, ciao! Pietro
Re: [ccp4bb] Babinet solvent correction [WAS: R-free flag problem]
Dear all, just to add that Clemens Vonrhein already a few years ago has implemented a procedure similar to the one Simon describes, to automatically fill the cavities in the macromolecule before computing the mask for the solvent, thus avoiding placing solvent where the core of the protein is, in the refinement suite autoBUSTER. It works! Incidentally, plotting the correlation coefficients between the Fobs and the F computed from the model alone (i.e. without babinet solvent correction) and the one bewteen Fobs and the full Fcalc (also a plot acessible during autoBUSTER refinement), one can easily see differences all the way up to 5 A. Regards Pietro From: CCP4 bulletin board [ccp...@jiscmail.ac.uk] On Behalf Of Simon Phillips [s.e.v.phill...@leeds.ac.uk] Sent: 25 October 2010 09:09 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] FW: [ccp4bb] Babinet solvent correction [WAS: R-free flag problem] Dear Tim, Interesting discussion, and I agree with your last description of the issues. When I started playing with this for oxymyoglobin [J. Mol. Biol. 142, 531-544 (1980)] it seemed immediately apparent (i.e. by thinking about it before starting to write programs) that the simple Babinet approach was deficient since the solvent was not just the inverse of the protein. This is Tim's point about not using Fc in the Babinet method because protein density is not flat (but you could use a flat protein model Fm). As pointed out in this discussion, there is not much difference between the two at 20A resolution anyway, but what did become apparent when I started doing actual calculations was that the solvent effect was noticeable even at moderate resolutions. It seemed to me then that the obvious was to go was a flat solvent to generate Fs. The issues then were where to put the protein-solvent boundary, and how sharp to make it (i.e. a B factor). I also noticed that when the mask was made, small cavities in the protein would generate bits of "solvent" in the interior of the protein that should not be there (another issue alluded to in the discussion). In those days I was looking at maps/masks plotted on paper rather than graphics, and I solved the cavity problem manually by adding atoms in the cavities in the pdb file I used to make the mask until I couldn't see any more cavities left in a plot. This is not, of course, an automatic procedure, and that would need a bit of thought. The determination of the border width between protein and solvent, and the B factor, were just optimised by trial and error, running several values, plotting R factors and fitting a function to them (parabola I think) to help find a minimum. Again the issue for automating this requires finding suitable parameters with derivatives. Having done all this in a simple-minded way, I was very impressed by the effect on the refinement, and on of the figures in the JMB paper shows how dramatic it was and how far up the resolution range the effect was felt. At this stage I should have programmed it properly, but the oxymyglobin structure was done, I had to move jobs and projects and good intentions fell by the wayside (mea culpa). Luckily more public spirited people picked up some of the ideas and improved them, but the protein cavity issue is still there it seems. Obviously I would like to add my vote for a proper flat (or nearly?) solvent mask model as being the right apporach. Simon --- | Simon E.V. Phillips | --- | Director, Research Complex at Harwell (RCaH)| | Rutherford Appleton Laboratory | | Harwell Science and Innovation Campus | | Didcot | | Oxon OX11 0FA | | United Kingdom | | Email: simon.phill...@rc-harwell.ac.uk | | Tel: +44 (0)1235 567701 | |+44 (0)1235 567700 (sec) | |+44 (0)7884 436011 (mobile) | | www.rc-harwell.ac.uk| --- | Astbury Centre for Structural Molecular Biology | | Institute of Molecular and Cellular Biology | | University of LEEDS | | LEEDS LS2 9JT | | United Kingdom
[ccp4bb] How do I set up a Refmac5 dictionary to constrain octahedrally coordinated Ca++
Dear all, How do I set up a Refmac dictionary to constrain octahedrally coordinated Ca++? Refmac5 seems to detect the potential bond between the Ca++ and the ligands: INFO: link is found (not be used) dist= 2.229 ideal_dist= 2.320 ch:AA res: 263 GLU at:O .->ch:Ag res: 600 CA at:CA . but it does not enforce them, and I cannot figure out what the CCP4 convention for a O-Ca++ bond is. Thanks for any suggestions! Pietro
[ccp4bb] Molecular replacement with merohedarlly twinned data
Dear all, when searching in Molecular Replacement against say perfectly merohedrally twinned data (i.e. an alpha=0.5 twin) do I understand it right that I should expect two sets of solutions that are equivalent under the twin operator (bar xtal symmetry and/or origin shifts)? Thanks! Ciao Pietro -- Pietro Roversi EP Abraham Fellow in Biochemistry - Lincoln College - Oxford Sir William Dunn School of Pathology, Oxford University South Parks Road, Oxford OX1 3RE, England UK Tel. 0044-1865-275385
Re: [ccp4bb] DM and MR
Dear James and Andy, my twopenny worth. I am using dm and dmmulti to solvent flatten after molecular replacement phases when no shred of experimental phases is available. If the model is severely incomplete (say at least 25% missing or more) I use phases from Buster-TNT refinement with missing atoms modelling switched on (this reduces the model bias imp[roves the scaling and helps bringing up weaker features from the yet unmodelled bits). I also blur the phase distribution either by multiplying the FOMs by a number less than one (say 0.6-0.8) or by doing the same to the Hendrickson-Lattmann coefficients (the idea is driectly inspired from this paper: Perrakis, A., Harkiolaki, M., Wilson, K. S. & Lamzin, V. S. (2001). Acta Crystallogr D Biol Crystallogr 57, 1445-1450. I tend to try a few values of the multiplicative factor and choose the one that gives the maps that I like the best. Ah: it may be trivial again, but for the project I am working on at the moment even a 6.7 A dataset in a different crystal form has made a big difference! the dmmulti fourfold averaging across 2 crystal forms being much better than the twofold averaging in dm in the high-resolution form. Admittedly this extra crystal form has 90% solvent! So if possible at all use dmmulti and multi-crystal averaging. I hope this helps! Pietro -- Pietro Roversi EP Abraham Fellow in Biochemistry - Lincoln College - Oxford Sir William Dunn School of Pathology, Oxford University South Parks Road, Oxford OX1 3RE, England UK Tel. 0044-1865-275385
Re: [ccp4bb] Se oxidation
Dear all, one comment on the subject of white lines and anomalous phasing power - one has to be extremely careful to jump to conclusions about the effect that a chemical treatment of the heavy atom (say oxydation/reduction of Se) has on the shape of the edge and the associated anomalous signal: there are crystals where the intrinsic anisotropy of the dispersive and anomalous scattering combines with the geometry of the heavy-atom arrangement and the symmetry of the lattice to give a very strong dependency of the edge (and therefore the signal) on the orientation of the sample in the polarized beam. In other words you may observe a wonderful white line but to check if this improved edge comes from oxydising/reducing the sample that went into the crystal you would need to check it by reorienting the crystal in a number of orientations. And of course one would want to do the same on a crystal comign from the protein before the treatment. And I would not be surprised if in some cases the phenomenon would make the difference between succeeding in determining the structure or not - even when non chemical treatment is involved - just a series of crystals of the same kind but mounted and measured in crucially different orientations. See Exploiting the anisotropy of anomalous scattering boosts the phasing power of SAD and MAD experiments. Schiltz M, Bricogne G. Acta Crystallogr D Biol Crystallogr. 2008 Jul;D64(Pt 7):711-29. Epub 2008 Jun 18. and references cited therein. Regards Pietro -- Pietro Roversi EP Abraham Fellow in Biochemistry - Lincoln College - Oxford Sir William Dunn School of Pathology, Oxford University South Parks Road, Oxford OX1 3RE, England UK Tel. 0044-1865-275385
[ccp4bb] http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html
Dear Fred, try the EBI PISA server: http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html Ciao Pietro On Thu, 2008-11-20 at 11:20 +0100, Vellieux Frederic wrote: > Dear Colleagues, > > I am looking for a program (if there is one...) that would allow to list > all interactions at a dimer interface (polar, ie hydrogen bonds and salt > bridges, and non polar). > > Thanks in advance for your replies. > > Best regards, > > Fred. -- Pietro Roversi EP Abraham Fellow in Biochemistry - Lincoln College - Oxford Sir William Dunn School of Pathology, Oxford University South Parks Road, Oxford OX1 3RE, England UK Tel. 0044-1865-275385
Re: [ccp4bb] phased MR
Dear Ed, in the past we have successfully searched in an electron density map (computed in the whole cell) with Molrep. If you have a second crystal form and you can cut the density of the monomer off, Phaser also gives very good results when searching with that electron density - after that your maps can be improved with dmmulti cross-crystal averaging. Good luck! Pietro -- Pietro Roversi EP Abraham Fellow in Biochemistry - Lincoln College - Oxford Sir William Dunn School of Pathology, Oxford University South Parks Road, Oxford OX1 3RE, England UK Tel. 0044-1865-275385
[ccp4bb] CCP4-ecalc crashes
Dear everyone,
is anyone else experiencing problems with
CCP4-ecalc? No matter how many reflexions I declare per resolution shell
(keyword SHELL), nor what mtz file I use, it seems to be crashing always
with the following message:
###
###
###
### CCP4 6.0: ECALC version 6.0 : 06/09/05##
###
ECALC: ERROR - Empty shell - increase NSHELL.
ECALC: ERROR - Empty shell - increase NSHELL.
Times: User: 0.5s System:0.0s Elapsed: 0:00
BTW if I follow this error message's suggestion and I use NSHELL instead
of SHELL (as per ecalc manual) I get a crash too ("ERROR(S) IN INPUT")
I think the keyword is correct in the manual and wrong in the error
message.
Thanks
Pietro
--
Pietro Roversi
Sir William Dunn School of Pathology, Oxford University
South Parks Road, Oxford OX1 3RE, England UK
Tel. 0044-1865-275385
Re: [ccp4bb] is it Ok to freeze
Well everyone, talking of early applications of cryocooling to X-ray crystallography, what about Sten Samson's marvellous helium cryostat which was operational at Caltech since the end of the 1970s and used to reach temperatures around 20 K routinely , see for example: Proc Natl Acad Sci U S A. 1982 Jul;79(13):4040-4. Structure of a B-DNA dodecamer at 16 K. Drew HR, Samson S, Dickerson RE. That instrument (and its twin) are now both with Riccardo Destro in Milano. Ciao! Pietro -- Pietro Roversi Sir William Dunn School of Pathology, Oxford University South Parks Road, Oxford OX1 3RE, England UK Tel. 0044-1865-275385
Re: [ccp4bb] Crystals grown directly on loop?
Dear Jacob and Mathew, one night at the pub a few months ago a colleague and I had been thinking along similar lines but we were rather envisaging microcapillaries feeding the mother liquor components into the loop at controlled rates from the stem ... expensive hi-tech loops to be sure but maybe not so in a few years should technology stay with us for longer. Time will tell. Good luck with your efforts! Pietro > Dear Jacob, > > We have been working on this for an year or so. We have a paper partially in > the review process. Unfortunately, the referees were not very excited about > the idea. However, we are developing some automation to speed up the time > consuming process of placing the drops on the loops. > > This method seems to have some advantges and some issues in using the known > crystallization conditions. This could also give trouble with solutions > containing volatile compounds. > > Kind regards, > Mathews > > > -Original Message- > From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Jacob Keller > Sent: Tuesday, June 03, 2008 1:14 PM > To: CCP4BB@JISCMAIL.AC.UK > Subject: [ccp4bb] Crystals grown directly on loop? > > Dear crystallographers, > > Has anyone ever tried to grow crystals directly on some kind of mountable > support, such as some kind of loop or film, which could be frozen directly? > I understand that there are some microfluidic plates through which the > crystals can be diffraction-screened, but what about for more conventional, > known crystallization conditions? It seems that this would be a spectacular > way to decrease damages/stresses caused by handling... > > Jacob Keller > > *** > Jacob Pearson Keller > Northwestern University > Medical Scientist Training Program > Dallos Laboratory > F. Searle 1-240 > 2240 Campus Drive > Evanston IL 60208 > lab: 847.491.2438 > cel: 773.608.9185 > email: [EMAIL PROTECTED] > *** -- Pietro Roversi Sir William Dunn School of Pathology, Oxford University South Parks Road, Oxford OX1 3RE, England UK Tel. 0044-1865-275385
[ccp4bb] sfall in "MODE ATMMAP RESMOD" mode misreads PDB coordinates
Dear everyone, I am using sfall in "MODE ATMMAP RESMOD" to compute a tagged map with which to score a model against a map. The input PDB is OK and regularly read by all programs - but sfall seems to interpret the coordinates wrongly (see the list of the first 10 atoms coordinates that the program outputs, both in orthogonal and fractional): First 10 atoms of atsort - orthog coordinates 1NCYS 140283.0180251.2380115.7960 1.00 500.003 fractional coordinates 1.57127 1.39484 0.64288 First 10 atoms of atsort - orthog coordinates 2CA CYS 140281.9190250.4390115.2740 1.00 500.002 fractional coordinates 1.56517 1.39040 0.63998 3CCYS 140280.7020251.2870114.8740 1.00 500.002 fractional coordinates 1.55842 1.39511 0.63776 4OCYS 140279.7890250.8050114.1860 1.00 500.004 fractional coordinates 1.55335 1.39243 0.63394 5CB CYS 140281.5250249.4400116.3580 1.00 500.002 fractional coordinates 1.56299 1.38485 0.64600 6SG CYS 140280.3360248.2280115.8470 1.00 500.005 fractional coordinates 1.55638 1.37813 0.64317 7NSER 141280.6900252.5440115.3270 1.00 500.003 fractional coordinates 1.55835 1.40209 0.64028 8CA SER 141279.5620253.4720115.1380 1.00 500.002 fractional coordinates 1.55209 1.40724 0.63923 9CB SER 141279.7800254.7110116.0260 1.00 500.002 fractional coordinates 1.55330 1.41412 0.64416 10OG SER 141280.9710255.4130115.6440 1.00 500.004 fractional coordinates 1.55991 1.41802 0.64204 11CSER 141279.3470253.9090113.6680 1.00 500.002 fractional coordinates 1.55089 1.40967 0.63107 First 10 atoms of sorted file in asym unit - 10.55639 0.64317 0.37813699.89 1.00 5 102SG CYS 10.56299 0.64600 0.38485599.89 1.00 2 102CB CYS 10.56517 0.63998 0.39040299.89 1.00 2 102CA CYS 10.55335 0.63394 0.39243499.89 1.00 4 102O CYS 10.57127 0.64288 0.39484199.89 1.00 3 102N CYS 10.55842 0.63776 0.39511399.89 1.00 2 102C CYS 10.55835 0.64028 0.40209799.89 1.00 3 103N SER 10.55209 0.63923 0.40724899.89 1.00 2 103CA SER 10.55330 0.64416 0.41412999.89 1.00 2 103CB SER 10.55991 0.64204 0.41802 1099.89 1.00 4 103OG SER As a result of course the tagged map is completely screwed. Has anyone encountered this problem and if so how did they solve it? I would rather avoid digging into the code if I can! Best regards Pietro -- Pietro Roversi Sir William Dunn School of Pathology, Oxford University South Parks Road, Oxford OX1 3ER, England UK Tel. 0044-1865-275385
Re: [ccp4bb] DM - NCS averaging after phaser molecular replacement run-confused about coefficients
Dear Hari, you also might want to specify, on the dm input LABOUT card, the FCDM=FCDM and PHICDM=PHICDM coefficients, that output Fourier coefficients avoiding the recombination with the initial phases, and will allow you to inspect the truly-solvent-flattened, truly-averaged dm map. Good luck! Ciao Pietro
Re: [ccp4bb] Placing an EM map in a large P1 box
Hi Larry, here is how I'd do it: mapmask MAPIN MAPOUT << EOF SYMMETRY 1 XYZLIM CELL PAD 0.0 END EOF Good luck with it! Ciao Pietro -- Pietro Roversi Sir William Dunn School of Pathology, Oxford University South Parks Road, Oxford OX1 3ER, England UK Tel. 0044-1865-275385
[ccp4bb] MTZ cell troubles after sortmtz reindexing from P321 to C2
Dear all, after much sweat and grief I managed to index my data in P321 but looking at the symmetry I think they might be C2: reindexing from P321 to C2 with the 2h+k, k, l operator in sortmtz produces the right cell (and yes I did tick the "Reduce reflexions to the asymmetric unit" button so that noreduce is not among the sortmtz keywords): P321 209.3168 209.3168 40.6822 90. 90. 120. C2 362.5473 209.3168 40.6822 90. 90. 90. But: scala then decides that the asymmetric unit is not the right one and it mysteriously changes cell parameters (which I think points to a bug in the sortmtz process of reindexing): Reciprocal space symmetry: Space group: "C 1 2 1" Point group: "PG2" Laue group: "2/m" Reference asymmetric unit: "k>=0 and (l>0 or (l=0 and h>=0))" (change of basis may be applied) and I end up with this C2 cell in the mtz output from scala: 285.9320 285.9320 40.6824 90. 90. 90. I have tried OUTPUT ORIGINAL ans some such in scala but to no avail. Now please don't all tell me to go back and reindex-reintegrate these images - although I might have to do it to get the best out of these data once I am convinced they are monoclinic. Rather, I would appreciate suggestions on what program to feed the multirecord mtz to sort its asymmetric unit in C2 so that scala does not play tricks on me; or what keyword to feed scala to keep reflexions in the current asymmetric unit (and use cad or sftools afterwards on the scaled/merged file) Thanks Pietro -- Pietro Roversi Sir William Dunn School of Pathology, Oxford University South Parks Road, Oxford OX1 3ER, England UK Tel. 0044-1865-275385
Re: [ccp4bb] Question about strange MR solution
Dear Michele, I think your MR solution is on a different allowed origin - that's all Ciao Pietro -- Pietro Roversi Sir William Dunn School of Pathology, Oxford University South Parks Road, Oxford OX1 3ER, England UK Tel. 0044-1865-275385
Re: [ccp4bb] How to refine a structure with ATP and AMP and pyrophosphate sharing the same density in CCP4i?
Hello Sun, Roman Hillig and I refined a mixture of ADP+PO4 and ATP in the active site of ARL2 - it is enough to exclude all contacts of the superposing ligands and let the occupancies refine. The protocol we followed is described in: Hanzal-Bayer M, Renault L, Roversi P, Wittinghofer A, Hillig RC. Free in PMC The complex of Arl2-GTP and PDE delta: from structure to function. EMBO J. 2002 May 1;21(9):2095-106. Best of luck! Pietro <[EMAIL PROTECTED]> writes: > Hello everyone, > > I have a structure of intermediate state in which about half amount of ATP > decomposed to AMP and pyrophosphate. The ATP and AMP + pyrophosphate have > little difference in conformation, sharing the same electron density. > > I just gave them different residue ID and did the TLS and restrained > refinement in CCP4i. It is hard to tell from the R-factor because they are > only a very small part of the whole structure. Can anyone tell whether it is > the correct way to do? > > Any suggestions are greatly appreciated. > > Thank you very much! > > Sincerely, > > Sun Tang > > > - > Never miss a thing. Make Yahoo your homepage.
[ccp4bb] How to override the use of NCS in Molrep?
Dear all, I am working on a multidomain structure in P31 with two copies in the asymmetric unit and pseudo-P3121 symmetry - the NCS is a twofold relating most of copy A to copy B but one domain violates the higher symmetry. I have placed all the NCS-obeying domains of A and B, plus copy A of the NCS-violating domain, and am looking for the second copy of the latter using molecular replacement. I am using all the programs I know of including Molrep. Now, the Molrep binary I downloaded from http://www.ysbl.york.ac.uk/YSBLPrograms/index.jsp is far too clever: it autodetects the NCS-twofold in the self rotation function and switches the NCS on - which is not what I want: INFO:Relations between peaks see in molrep.doc NCS_model (from Model Self rotation Function): 1 Program will use NCS =: 1 Does anyone know how to turn this off? Thanks! Pietro -- Pietro Roversi Sir William Dunn School of Pathology, Oxford University South Parks Road, Oxford OX1 3ER, England UK Tel. 0044-1865-275385
[ccp4bb] Rotation search using the Patterson in a non-spherical neighbourhood of the origin
Dear everyone, is any of the currently available molecular replacement programs capable of accepting a description of an ellipsoid (rather than the radius of a sphere) to define the portion of the Patterson around the origin to be used in a Molecular Replacement rotation search? Our search model is an elongated object and we are searching in a cell with a=205 b=100 c=21 Angstrom ... ;-) Ciao Pietro -- Pietro Roversi Sir William Dunn School of Pathology, Oxford University South Parks Road, Oxford OX1 3ER, England UK Tel. 0044-1865-275385
