[ccp4bb] refmac output query
Dear All, A quick question about Refmac on ccp4i. When refining an RNA oligonucleotide structure using the findwaters option, the pdb output labels all the atoms as HETATM (inluding the original RNA atoms which were not so labelled in the input pdb). It is of course trivial to correct this, but I was wondering if there is a hidden problem somewhere, that might influence more crucial things. Many thanks, Emmanuel -- Dr. Emmanuel Saridakis Institute of Nanoscience and Nanotechnology National Centre for Scientific Research "DEMOKRITOS" 15310 Athens GREECE 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] AlphaFold: more thinking and less pipetting (?)
Dear John, Your article touches all the important points about this breakthrough and its caveats. I would just like to add that the ligand problem is of a different order: it is fundamentally not about whether, where and how a ligand is predicted to bind, but rather about whether it indeed binds where and in the way it is predicted to. So I daresay that it is an irreducibly experimental problem. Best, Emmanuel Dr Emmanuel Saridakis National Centre for Scientific Research DEMOKRITOS Athens, Greece - Original Message - From: John R Helliwell To: CCP4BB@JISCMAIL.AC.UK Sent: Tue, 08 Dec 2020 15:15:14 +0200 (EET) Subject: Re: [ccp4bb] AlphaFold: more thinking and less pipetting (?) Dear Isabel, My article in the IUCr Newsletter on DeepMind and CASP14 is released today and can be found here:- https://www.iucr.org/news/newsletter/volume-28/number-4/deepmind-and-casp14 Best wishes, John Emeritus Professor John R Helliwell DSc > On 3 Dec 2020, at 11:17, Isabel Garcia-Saez wrote: > > > Dear all, > > Just commenting that after the stunning performance of AlphaFold that uses AI > from Google maybe some of us we could dedicate ourselves to the noble art of > gardening, baking, doing Chinese Calligraphy, enjoying the clouds pass or > everything together (just in case I have already prepared my subscription to > Netflix). > > https://www.nature.com/articles/d41586-020-03348-4 > > Well, I suppose that we still have the structures of complexes (at the > moment). I am wondering how the labs will have access to this technology in > the future (would it be for free coming from the company DeepMind - Google?). > It seems that they have already published some code. Well, exciting times. > > Cheers, > > Isabel > > > Isabel Garcia-SaezPhD > Institut de Biologie Structurale > Viral Infection and Cancer Group (VIC)-Cell Division Team > 71, Avenue des Martyrs > CS 10090 > 38044 Grenoble Cedex 9 > France > Tel.: 00 33 (0) 457 42 86 15 > e-mail: isabel.gar...@ibs.fr > FAX: 00 33 (0) 476 50 18 90 > http://www.ibs.fr/ > > > 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 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. Emmanuel Saridakis Principal Researcher Institute of Nanoscience and Nanotechnology National Centre for Scientific Research "DEMOKRITOS" 15310 Athens GREECE tel: +30-2106503793 email: e.sarida...@inn.demokritos.gr 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] Macromolecular Crystallography workshop in South America 2020
And Eleanor Dodson, of course!!! E. From: "ΕΜΜΑΝΟΥΗΛ ΣΑΡΕΙΔΑΚΗΣ" To: "CCP4BB" Sent: Thursday, 6 February, 2020 12:15:07 Subject: Re: [ccp4bb] Macromolecular Crystallography workshop in South America 2020 Dear All, To strike a more positive note, crystallography (esp. macromolecular) has always had a very high representation of women at top levels: Kathleen Lonsdale, Dorothy Crowfoot Hodgkin, Rosalind Franklin and Ada Yonath are the most famous names that immediately come to mind, but there are many more highly distinguished ones like Elena Conti, Naomi Chayen, Elspeth Garman, Petra Fromme and scores more. There seems to be no "glass ceiling" for women in crystallography so I believe it is one of very few scientific fields where gender balance discussions and constraints are irrelevant. This might be due to Bragg son, who apparently was a champion of women in Science. If this is indeed the case, that would provide strong support to the argument that underrepresenation of women in Science (and elsewhere) is due to historical reasons that can be easily overturned, rather than to any biological predetermination. Crystallography after all is a field which is heavy on maths, space visualisation and high-tech instrumentation, which people would traditionally more readily associate with males. Let me finish with a famous quote by author William Golding: " I think women are foolish to pretend they are equal to men. They are far superior and always have been." Emmanuel - Dr. Emmanuel Saridakis Principal Researcher Institute of Nanoscience and Nanotechnology National Centre for Scientific Research "DEMOKRITOS" 15310 Athens GREECE email: e.sarida...@inn.demokritos.gr From: "Bärbel Blaum" To: "CCP4BB" Sent: Thursday, 6 February, 2020 11:30:36 Subject: Re: [ccp4bb] Macromolecular Crystallography workshop in South America 2020 Dear all, yes, there are more male computational crystallographers than females – the question we can ask ourselves here is: Do we think there is some biological reason for this? Obviously there isn’t. So things are wrong as they stand. Are we, nevertheless, ok with this current state of affairs? We are not talking some minor issue here – if half of the population is under-represented, that is a giant intellectual loss (actually for * all * professions that lack diversity, childcare included, and of course the loss is not just on the intellectual level). If you think you have been lucky to work in a place where there is no bias against women it just means you are lucky in not being one. If you care to know, simply try and put the other side’s shoes on. Start asking your female colleagues, friends, partners, students about their experience, moments they witnessed were they felt overlooked or deliberately excluded, treated in sexist ways, you name it. You will be surprised. Then think about the moments, institutions, relationships that have been instrumental in your own careers. University meetings and important talks routinely held and given in the evenings. Conferences with no childcare. Many male researchers only being able to work as much as they do because some female is looking after the house and the kids. Babies being colored-coded by gender, mummys at home and daddys at work. Girls being told it’s ok to be bad at math. You must be joking if you wonder where all the female scientists are! We all grow up and are educated in a world that is heavily biased in terms of which roles which gender adopts - how are we supposed to not think that this reflects some form of “natural” order? There are plenty of other groups that grow up systematically underestimating their potentials, just compare students from academic homes with those from working class backgrounds. And there is plenty of research on the subject. The question is if you care to notice this bias, discrimination, lack of equal opportunities, and if you care to do something about it - of course we all have other things to attend to. But if teaching is part of our job description then we have to think about how to be good teachers, and that does not stop at how to explain Fourier transforms or python. The reason I suggested a meeting by a female group of scientists as only organizers and speakers is because as long as we have these male-dominated environments at workshops and meetings the respective younger generation will be presented with this order as being the natural way things work * because we taught them so *. If we want these younger guys to get things right in ways we did not we have to create alternative perspectives and come up with new forms of community work. Bärbel -- Bärbel Blaum, PhD Inthera Bioscience AG Einsiedlerstrasse 34 CH-8820 Waedenswil Switzerland E-Mail: baerbel.bl...@intherabio.com Phone: +41 43 477 94 72--
Re: [ccp4bb] Macromolecular Crystallography workshop in South America 2020
Dear All, To strike a more positive note, crystallography (esp. macromolecular) has always had a very high representation of women at top levels: Kathleen Lonsdale, Dorothy Crowfoot Hodgkin, Rosalind Franklin and Ada Yonath are the most famous names that immediately come to mind, but there are many more highly distinguished ones like Elena Conti, Naomi Chayen, Elspeth Garman, Petra Fromme and scores more. There seems to be no "glass ceiling" for women in crystallography so I believe it is one of very few scientific fields where gender balance discussions and constraints are irrelevant. This might be due to Bragg son, who apparently was a champion of women in Science. If this is indeed the case, that would provide strong support to the argument that underrepresenation of women in Science (and elsewhere) is due to historical reasons that can be easily overturned, rather than to any biological predetermination. Crystallography after all is a field which is heavy on maths, space visualisation and high-tech instrumentation, which people would traditionally more readily associate with males. Let me finish with a famous quote by author William Golding: " I think women are foolish to pretend they are equal to men. They are far superior and always have been." Emmanuel - Dr. Emmanuel Saridakis Principal Researcher Institute of Nanoscience and Nanotechnology National Centre for Scientific Research "DEMOKRITOS" 15310 Athens GREECE email: e.sarida...@inn.demokritos.gr From: "Bärbel Blaum" To: "CCP4BB" Sent: Thursday, 6 February, 2020 11:30:36 Subject: Re: [ccp4bb] Macromolecular Crystallography workshop in South America 2020 Dear all, yes, there are more male computational crystallographers than females – the question we can ask ourselves here is: Do we think there is some biological reason for this? Obviously there isn’t. So things are wrong as they stand. Are we, nevertheless, ok with this current state of affairs? We are not talking some minor issue here – if half of the population is under-represented, that is a giant intellectual loss (actually for * all * professions that lack diversity, childcare included, and of course the loss is not just on the intellectual level). If you think you have been lucky to work in a place where there is no bias against women it just means you are lucky in not being one. If you care to know, simply try and put the other side’s shoes on. Start asking your female colleagues, friends, partners, students about their experience, moments they witnessed were they felt overlooked or deliberately excluded, treated in sexist ways, you name it. You will be surprised. Then think about the moments, institutions, relationships that have been instrumental in your own careers. University meetings and important talks routinely held and given in the evenings. Conferences with no childcare. Many male researchers only being able to work as much as they do because some female is looking after the house and the kids. Babies being colored-coded by gender, mummys at home and daddys at work. Girls being told it’s ok to be bad at math. You must be joking if you wonder where all the female scientists are! We all grow up and are educated in a world that is heavily biased in terms of which roles which gender adopts - how are we supposed to not think that this reflects some form of “natural” order? There are plenty of other groups that grow up systematically underestimating their potentials, just compare students from academic homes with those from working class backgrounds. And there is plenty of research on the subject. The question is if you care to notice this bias, discrimination, lack of equal opportunities, and if you care to do something about it - of course we all have other things to attend to. But if teaching is part of our job description then we have to think about how to be good teachers, and that does not stop at how to explain Fourier transforms or python. The reason I suggested a meeting by a female group of scientists as only organizers and speakers is because as long as we have these male-dominated environments at workshops and meetings the respective younger generation will be presented with this order as being the natural way things work * because we taught them so *. If we want these younger guys to get things right in ways we did not we have to create alternative perspectives and come up with new forms of community work. Bärbel -- Bärbel Blaum, PhD Inthera Bioscience AG Einsiedlerstrasse 34 CH-8820 Waedenswil Switzerland E-Mail: baerbel.bl...@intherabio.com Phone: +41 43 477 94 72-- Von: CCP4 bulletin board im Auftrag von Susan Lea Antworten an: Susan Lea Datum: Donnerstag, 6. Februar 2020 um 02:21 An: Betreff: Re: [ccp4bb] Macromolecular Crystallography workshop in South America 2020 Perhaps so
Re: [ccp4bb] Protein fold and the moonlighting function
I believe this is more than a fluke. It looks to me like a very powerful evolutionary tool which may have rendered the early stages in the evolution of life less improbable. Best wishes, Emmanuel Saridakis - Original Message - From: "Peter Stogios" To: "CCP4BB" Sent: Monday, 3 February, 2020 02:18:45 Subject: Re: [ccp4bb] Protein fold and the moonlighting function I think you’re asking if two proteins with the same fold can have different activities. As was previously mentioned, this is quite common. The best characterized example is the TIM barrel fold - such proteins can be isomerases, transferases, hydrolases, lyases, or oxidoreductases, to name a few... To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
Re: [ccp4bb] crystallization optimization
Dear All, Fine-tuning protein and precipitant concentration is of course the first line of approach, followed by both rMMS and streak-seeding. I would like to remind you of a far less popular but often successful in my hands, optimisation technique: It consists in incubating the trial at the condition that gives the ugly crystals for some time (shorter than the time it takes for the ugly crystals to appear), and then changing the condition to one of lower supersaturation for the growth to proceed. That can be done either by diluting the reservoir with water (vapour diffusion) or diluting the drop with buffer (microbatch), or by just transferring your plate to a different (usually higher) temperature. Described in more (but perhaps unecessary for most practical purposes) detail in: E. Saridakis , P.D. Shaw Stewart, L.F. Lloyd and D.M. Blow. Acta Crystallogr. (1994) D 50 , 293. E E . Saridakis and N.E. Chayen. Protein Science (2000) 9 , 755. Best, Emmanuel De: "Alun R Coker" À: "CCP4BB" Envoyé: Mercredi 12 Juillet 2017 15:40:10 Objet: Re: [ccp4bb] crystallization optimization Hi Everyone, Franks point is really interesting. We routinely reduce the protein concentration when we see too many precipitated wells, but we never dilute the screen. Has anyone tried this? All the best, Alun On 12/07/17 08:48, Frank von Delft wrote: The point I was failing to make: reducing either protein or precipitant concentration will indeed reduce nucleation, but often won't get you bigger or more single crystals: it will just make the appearance of crystals less reliable. The way to get big single reliable crystals is to increase protein and greatly reduce precipitant. (Even better: do seeding. Like Vicky said. Incredible how often people don't bother to do seeding, yet it solves so many problems.) phx On 12/07/2017 07:50, Vicky Tsirkone wrote: BQ_BEGIN Dear Frank, I may see in the attached pic several nucleation points and a considerable amount of microcrystals. Based to my knowledge decreasing the concentration of the precipitant and/or the protein concentration would be a reasonable approach to refine the initial hits. By checking the diagram as you correctly mentioned you may see that the fine tuning of protein and precipitant concetration may lead to the desirable result without reaching the precipitation zone. Patrick just check your screens. Just a rule of thumb, if you see precipitation in the ~60% of your drops then you should definitely reduce the protein concentration. ps dont forget to try the streak seeding , as well. Have a nice day and again good luck. Vicky On Wed, Jul 12, 2017 at 8:50 AM, Frank von Delft < [ mailto:frank.vonde...@sgc.ox.ac.uk | frank.vonde...@sgc.ox.ac.uk ] > wrote: BQ_BEGIN Actually, you should try increasing the protein concentration - a lot. But be prepared to drop the precipitant concentration to almost nothing (1 or 2% isn't "low"). To understand why, look at the phase diagram and what we assume about vapour diffusion. (Which I'm assuming is what you're doing.) On 12/07/2017 06:28, Vicky Tsirkone wrote: BQ_BEGIN Dear Patrick, You may reduce the protein concentation, as well. Another option could be the streak seeding by exploiting the drop of your initial condition. Good luck, V.T. On Mon, Jul 10, 2017 at 7:17 PM, Patrick Shaw Stewart < [ mailto:patr...@douglas.co.uk | patr...@douglas.co.uk ] > wrote: BQ_BEGIN Microseed them into two or three random screens. Search for MMS and rMMS online. Good luck Patrick On 10 July 2017 at 15:47, Liuqing Chen < [ mailto:519198...@163.com | 519198...@163.com ] > wrote: BQ_BEGIN hello everyone! I get a condition (10% w/v PEG 6000, 100mm HEPES PH7.0) in which my protein grow small needle like crystals, how can i optimize it to get bigger crystals? the attach is the crystals figure. thanks in advance sincerely Liuqing Chen -- [ mailto:patr...@douglas.co.uk | 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/ | http://www.douglas.co.uk ] Tel: 44 (0) 148-864-9090 US toll-free [ tel:%28877%29%20225-2034 | 1-877-225-2034 ] Regd. England 2177994, VAT Reg. GB 480 7371 36 BQ_END BQ_END BQ_END BQ_END BQ_END -- 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: [ http://www.ucl.ac.uk/pxmed | www.ucl.ac.uk/pxmed ]
Re: [ccp4bb] Alexander Rich
Dear Colleagues, I do not think it is "highly inappropriate" that a crucial episode in the history of crystallography is described/commmented on in this thread, and I am not sure by whom its removal will be "highly appreciated", other than by Prof. Berger. I do not know any of the protagonists of this episode, except by reputation, and the only thing I would be ready to concede is that maybe the subject was brought up a bit too close to the sad death of Prof. Rich. But if someone is that distinguished, his/her life story will be discussed, for better (mostly) or worse (occasionally). Emmanuel Dr. Emmanuel Saridakis PhD Biophysics, MSc History and Philsophy of Science Institute of Nanscience and Nanotechnology N.C.S.R. "Demokritos" Athens 15310 Greece - Original Message - From: "Edward A. Berry" To: CCP4BB@JISCMAIL.AC.UK Sent: Saturday, 2 May, 2015 23:30:29 Subject: Re: [ccp4bb] Alexander Rich passed away Monday April 27, 2015 On 05/02/2015 12:23 PM, Imre Berger wrote: > Dear Edward - > > Would you be so kind and explain why you went ahead to post that comment > about Alex Rich on CCP4, in a thread which announced the sad news of his > passing away? Yes- I realized after posting it that it was inappropriate. If there is any way to remove a post, I will be glad to do so. In any case an apology is due. As for the explanation, I did not intend it to be in any way derogatory. I have never met Alex Rich, but Prof Sung-Hou Kim was my mentor in crystallography, and I have no doubt that their actions were completely honorable. As explained on the page I linked, it was all a misunderstanding based on poor communications between Kim and Rich, and rapid progress on the part of Kim that Rich was not aware of at the previous meeting. There was no evidence of actual misconduct on the part of Rich or Kim, as grudgingly acknowledged in the final letter from Cambridge. If only I had pointed that out in the email, instead of linking to that first accusatory message, it wouldn't have looked so bad. I had forgotten how inflammatory that first letter was! I was thinking this followed in the lines of Bob Sweet's post, that Rich was a hard-driving man and maybe not afraid of stepping on some peoples toes in order to achieve his goals. I never meant to imply misconduct, although after reading back on my post I can see that interpretation. My sincere apologies to the community and to the memory of professor Rich, Ed Berry > > I have checked your home page and your CV and it is not obvious to me at > all what motivation or stake you could possibly have. > > Besides, knowing both Alex Rich and Aaron Klug and having discussed > with them years ago, I think it is fair to say that only those two are > concerned with the issue, and one of them has - very sadly - just died. > > In any case - in my view it is highly inappropriate indeed that you > placed those comments on CCP4. > > Maybe you could be so kind and remove your contribution from the thread > - it would be greatly appreciated. > > "De mortuis nihil nisi bonum" > > Imre > > -- > > Imre Berger PhD HDR > Professor of Biochemistry > Wellcome Trust Senior Investigator > Coordinator, EC FP7 ComplexINC project > The School of Biochemistry, University of Bristol UK > The European Molecular Biology Laboratory EMBL > imre.ber...@bristol.ac.uk > iber...@embl.fr > >
[ccp4bb] 3D graphics linux compatibility question
Dear BB, We are still a bit confused about compatibility of graphics cards with 3D Coot/PyMol in Linux: (a) In previous CCP4bb discussions, it was stated that only Quadro cards are compatible with Linux setups. But could someone tell me what the minimum standard really is: is it Quadro FX380, 2000, 3800 or something else ? The nVidia site lists Quadro 3700 and 3800 as the two lowest (cheapest) options compatible with Linux 3D. However, different CCP4ers have in the past mentioned the other two options as working "perfectly" or "with little trouble". (b) If a monitor such as the ASUS VG278H , which has an in-built nVidia 3D vision emitter which takes its stereo synch from a DVI cable is used, can we even use the simpler GeForce GTX670 or 680 ? As you might imagine, we are on a rather tight budget. Any info would be greatly appreciated! Emmanuel Saridakis N.C.S.R. "DEMOKRITOS" Athens 15 310 Greece esari...@chem.demokritos.gr tel. +30-210-6503793
Re: [ccp4bb] Temperature and crystallization
Dear Acoot, In the website of the company Centeo, you can find the slides of a short presentation I had given three years ago on temperature and macromolecular crystalllisation. You may find some info there: http://www.centeo.com/_fileupload/Temperature%20Control%20in%20PXTL.pdf There is a lot more on the centeo.com site. Best, Emmanuel Saridakis - Original Message - From: Acoot Brett To: CCP4BB@JISCMAIL.AC.UK Sent: Monday, November 19, 2012 7:08 AM Subject: [ccp4bb] Temperature and crystallization Dear All, Will you please give a comment on how the temperature influences on the possibility to get protein crystal, and how the temperatures used to get the protein crystals of the same protein influences the protein 3-D structures of the same protein got based on the crystals of the same protein got at different temperatures? Cheers, Acoot
Re: [ccp4bb] do you think it is interesting?
Of course, "oligomer" (pure Greek) usually does that kind of job, but not in this specific case, since oligo means few and in this case we have "endless" chains. I can only think of the neologism "myriomer" for this particular case, if you want to stick to Greek. Myrioi can mean 1 or countless, depending on where you accent the word! If that catches on, remember you (probably) saw it here first! Cheers, Emmanuel - Original Message - From: "Tim Gruene" To: Sent: Monday, June 18, 2012 5:43 PM Subject: Re: [ccp4bb] do you think it is interesting? -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 [...] of monomers is called a multimer, not a polymer. [...] shiver - what a terrible mixture of languages. 'multi-' has got latin origin, whereas both poly and mer have got greek origin, and I don't think one should mix these. Please!!! think of a different _GREEK_ syllable to express what you describe as 'multimer'. Cheers, Tim On 06/18/12 16:21, David Schuller wrote: Certainly it's interesting, but I think your description is inaccurate. "Endless linear polymers" - Each monomer is a polymer, but a collection of monomers is called a multimer, not a polymer. I don't suppose there are any knots? That would be really interesting. On 06/18/12 09:49, anna anna wrote: Hi all! I'd like your opinion about a structure I solved. Apart from protein structure itself, I think that my protein xtallized in an odd way! The biological unit is a dimer while the asymmetric unit is a tetramer (red cartoon in the figure) resulting from domain swapping between two dimers. The strange thing is that swapping connects infinite monomers and, rather than a xtal, my diffracting object seems a multilayer of endless linear polymers, a kind of papyrus with greek fret-like fibers. The figure shows the orientation of the polymers in each layer. I'd like to know if some of you have already seen a similar pattern or it is weird as I think! I'm further racking my brain to figure out a biological implication of this behaviour, I thought something like plaque formation but I can't find support in literature. All suggestions are welcome!! Cheers, Anna - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFP3z51UxlJ7aRr7hoRAqviAKDJXxXkeOE3Z0M14+RT8dznQhpD3gCcDKEP o034eyZnadpwyQRGXI4FV9w= =Q5GJ -END PGP SIGNATURE-
[ccp4bb] Pointless problems
Dear All, I am having problems when trying to run Pointless with input from Denzo/Scalepack. (1) Pointless refuses to work from the .sca file. The error message is: CCP4 library signal mtz:File not identified as MTZ (Error) CCP4MTZfile: open_read - File missing or corrupted: rn7e222test.sca or The program run with command: /programs/CCP4/ccp4-6.1.1/bin/pointless has failed with error message child process exited abnormally (when run from ccp4i) (2) Scalepack2mtz refuses to convert a Scalepack file produced using the command: "NO MERGE original index" (i.e. as instructed by the Pointless instructions). It fails with the rather tactless message: * Resolution Range : 0.002020.00485 ( 22.256 - 14.357 A ) * Sort Order : 0 0 0 0 0 * Space group = 'P 2 2 2' (number 16) SCALEPACK2MTZ: Check your data! And, no my resolution range is not 22.2-14.3 A!! (3) Pointless refuses to work with an .mtz file produced by Scalepack2mtz from a .sca file obtained with the simple "NO MERGE" instruction (remember the "NO MERGE original index" instruction is a no-go for Scalepack2mtz). The error message in this case is quite simply: HKLIN is merged and no HKLREF file is defined, SPACEGROUP or REINDEX. I know the orthodox ccp4 reply would be "stop whining and use Mosflm!", but is there an alternative if I really want to use Denzo/Scalepack? If not, is there another way to check my point group/spacegroup starting from Denzo/Scalepack? Thanks a lot! Emmanuel
[ccp4bb] DTU vs DTT ?
Dear All, Possibly a trivial question but your experience would be much appreciated: I recently submitted a structure to PDB containing 3 DTT (dithiothreitol) molecules, or so I thought. The molecules had been imported and fitted with Coot using the Get Monomer... instruction with the code DTT. The Annotator responded, quite rightly as it turns out, as follows: Please note DTT in your coordinates has been changed to DTU since it >> has incorrect stereochemistry as DTT. >> Please review the stereochemistory in the attached validation report >> summary. >> >> You can send me corrected stereochemistry for DTT if you want it >> changed back. >> >> DTU (2R,3S)-1,4-disulfanylbutane-2,3-diol >> C4 H10 O2 S2 >> >> DTT (2R,3R)-1,4-disulfanylbutane-2,3-diol >> C4 H10 O2 S2 So, is the "DTT" monomer of Coot in fact its stereoisomer known as dithioerythritol? Should I import the correct DTT from elsewhere and re-refine or is there something else behind this? Thanks a lot for any suggestions! Emmanuel
Re: [ccp4bb] How to distinguish microcrystalline, quasicystalline and precipitation?
Hi Joy, Yes, I agree that it is very difficult to distinguish those and it is even more difficult to put it in words or in writing: experts have been talking about shininess, transparency (rather than brown colour) and birefringence as far as I know. All these methods have some grain of truth in them, yet none is as simple let alone as accurate as we would like to believe. So, it seems to me that the only way to distinguish is what I would call the "operational" way, i.e. to streak seed from that precipitate into a couple of drops set at very similar conditions but that are just below the spontaneous nucleation level of supersaturation: if something grows along the streak line, the precipitate was microcrystalline. However, if it doesn't, that doesn't mean that it was not microcrystalline? Dilemma? Another interesting question that you are raising is what are quasicrystalline or "ordered precipitates" really worth, in terms of ultimate success near the relevant conditions... Finally, how about these fluorescent pens? I have not had a chance to use one of these, but my feeling is that they would only really work on good-sized crystals. It would be very interesting to hear members' experiences with these on smaller stuff. Best, Emmanuel - Original Message - From: joybeiyang To: CCP4BB@JISCMAIL.AC.UK Sent: Thursday, June 10, 2010 9:06 AM Subject: [ccp4bb] How to distinguish microcrystalline, quasicystalline and precipitation? Hi everyone, I am preparing a "crystallization manual" for our group, however, I found that it is very difficult to distinguish microcrystalline, quasicrystalline and precipitation, especially when the precipitation was shiny, like the grit on the beach. Is there a way to distinguish the three? Comments and suggestions will be greatly appreciated! -- Joy
Re: [ccp4bb] Off-topic: hollow protein crystals
Dear Andre, Yes, hollow crystals are not very uncommon. We have recently also solved a structure at very high resolution using long hollow crystals. Initially the walls were very thin; we managed to make them thicker (and the hole correspondingly smaller) by standard fine-tuning of conditions. I didn't see any "special" effects arising from the hollowness. We just got higher resolution as we got more material to fill in some of the hole. Saridakis E; Giastas P; Efthymiou G; Thoma V; Moulis J-M; Kyritsis P; Mavridis I. M J Biol.Inorg. Chem. 2009;14(5):783-99. Best, Emmanuel - Original Message - From: Andre Ambrosio To: CCP4BB@JISCMAIL.AC.UK Sent: Wednesday, June 02, 2010 10:07 PM Subject: [ccp4bb] Off-topic: hollow protein crystals Dear all, We have recently obtained crystals from a small protein, and interestingly, at least for me, they are hollow trigonal rods (please see pictures attached). Just out of curiosity, has anybody ever seen such feature for protein crystals before? Regards, -Andre.
Re: [ccp4bb] Setting Microbatch trays !!
Dear Rashmi, The original standard for microbatch crystallisation is paraffin oil (from Sigma or elsewhere). Drops set under paraffin oil lose almost no water, so it works like a well-sealed batch experiment, in other words you need to have your conditions right and you do get crystals. Paraffin oil is the only case where the reported conditions are the true ones. Al's oil allows slow water evaporation through the oil, so the drops get slowly concentrated, something like a vapour diffusion, except that you don't have a well-defined end-point, i.e. a reservoir solution. Douglas Instruments I think sell some microbatch plates with a channel around them which can be used as a reservoir for such cases. Al's oil may thus give you more hits, since the supersaturation of the drops gets progressively higher. Of course, you don't know what the true crystallisation conditions are. Silicone oil allows a great deal of evaporation through it, so it may actually give you even more hits but you also may end up with drops drying out before having the chance to produce any crystals, unless you use the plates I talked about before, in which case it works a lot like a vapour diffusion experiment. Have a look at Douglas Instruments' web page: there is a lot of relevant info in there. Cheers, Emmanuel Saridakis - Original Message - From: rashmi panigrahi To: CCP4BB@JISCMAIL.AC.UK Sent: Friday, April 23, 2010 5:35 AM Subject: [ccp4bb] Setting Microbatch trays !! Hi, While setting up microbatch trays (under oil crystallization), 1. Has anybody used mineral oil (sigma M8410) and obtained some crystal hits? 2. Has anybody used anything other than Al's oil from Hampton, as Parafin oil from sigma or silicone oil from sigma and obtained some crystal hits? Thanks -- rashmi
[ccp4bb] PhD position in protein crystallography
PhD position in crystallization and structure solution of natural and appropriate variants of the sponge protein silicatein and nanobiotechnology applications TOPIC: Research in the field of biomineralization and applications in nanobiotechnology. Biomineralization is the formation of minerals by living cells and organisms. To understand the processes involved in biomineralization (at the cutting edge between inorganic and organic world)and for nanobiotechnology applications, the structure determination of natural and appropriate variants of silicatein from marine demosponge Suberites domuncula is required. The prospective student will carry out European funded research (Marie Curie ITN network BIOMINTEC) in two of the partner institutions, NCSR Demokritos in Greece and Johannes Gutenberg-Universitaet, Mainz in Germany and will operate within a network of institutions highly specialized in biomineralisation. The project includes participation in workshops and summer schools. Motivation to travel and adapt to a different country and to integrate efficiently in a new working team is fundamental. TYPE OF APPOINTMENT-DURATION-STARTING DATE: Full-time contracts in the two institutions (overall period 36 months), starting April 2010 at NCSR Demokritos. PROFILE-ELIGIBILITY Applicants should have a BS or MSc degree in chemistry, biological sciences or related sciences and £4 years research experience at the time of hiring. They can be nationals of European Union or Associated Countries, other than the country of the host organisations (Greece & Germany). Candidates from countries outside EU are also eligible. Greek or German citizens who have resided in Greece or Germany for less than 12 months in the 3 years prior to the hiring dates are also eligible. BENEFITS The successful candidate as a Marie Curie fellow will enjoy high salary (according to the Marie Curie guidelines with social security benefits) and additionally a mobility allowance covering family obligations, travel allowance and career exploratory allowance. HOW TO APPLY Applicants should forward electronically (a) their detailed CV, (b) copies of published articles, (c) names, e-mails/phone numbers of two referees to: Dr. I. M. Mavridis Institute of Physical Chemistry National Center for Scientific Research "Demokritos" Aghia Paraskevi 1520, Athens -Greece mavr...@chem.demokritos.gr
[ccp4bb] Post-doctoral opening in macromolecular crystallography, Athens Greece
Laboratory of Structural and Supramolecular Chemistry, Institute of Physical Chemistry, National Center for Scientific Research "DEMOKRITOS" ,Terma Patriarhou Gregoriou, Aghia Paraskevi 15310, Athens-Greece Opening for a position of Experienced Researcher (4-10 years) in production, crystallisation and X-ray crystallography of biological macromolecules TOPIC: TOPCRYST, an academia-industry (IAPP) FP7 Marie Curie project, will use Dual Polarimetric Interferometry, pioneered by Farfield Scientific Ltd., to probe crystallisation at its earliest, most crucial stages. Transfer of knowledge between academia and industry will tackle the problem of detecting crystal nucleation phenomena at the very earliest stages of crystallisation and holds a number of promises that will be investigated in its course. The post doctoral, experienced researcher (4-10 years after the bachelor's degree) will be mainly occupied with production and/or crystallisation of macromolecules (by the method to be developed and by conventional methods), as well as with determination of their molecular structures according to the needs. Additional activity: the structure-based drug design project, specifically on complexes of antibiotics synthesized in-situ with A-site ribosomal RNAs (http://lssc.chem.demokritos.gr/). TYPE OF APPOINTMENT-DURATION-STARTING DATE: Full-time contract - 24 months - Salary, that of an "experienced researcher" (> 55000/annum gross) according to the Marie Curie projects guidelines - Any time up to March 1st 2010. PROFILE-ELIGIBILITY Applicants should have a PhD degree, experience in production, crystallisation of proteins and X-ray crystallography and 4-10 years research experience at the time of hiring. They can be nationals of any country other than the country of the host organisation (Greece), preferably citizens of EU Member States or Associated Countries, as long as they have not resided or carried out their main activity in Greece for more than 12 months in the last 3 years. Candidates from countries outside the EU are also eligible. Greek citizens who have resided in third countries for at least 3 years in the 4 years prior to this hiring date are also eligible. HOW TO APPLY Applicants should forward electronically (a) their detailed CV (b) copies of published articles, (c) names, e-mails/phone numbers of two referees to: Dr. Emmanuel Saridakis or Dr Irene Mavridis esaridak"at"chem.demokritos.gr mavridi"at"chem.demokritos.gr Tel. +30-210-6503658 Tel. +30-210-6503793
