[ccp4bb] Open Group Leader position at Grenoble Outstation of EMBL
Dear All, The Grenoble Outstation of the European Molecular Biology Laboratory is seeking to recruit a Group Leader in Structural Biology of Complexes. The appointed Group Leader will be an ambitious structural biologist with an original multidisciplinary research programme oriented towards structure-function relationships of macromolecular complexes in eukaryotic systems. Particular, but not exclusive, areas of interest are host-pathogen interactions, RNA biology or computational biology/modelling. He/she will benefit from the world-class environment of the EMBL Grenoble Outstation within the Partnership for Structural Biology (www.psb-grenoble.eu) which gives access to integrated state-of-the-art structural biology technologies, including ESRF synchrotron X-ray beamlines for MX and SAXS, cryo-EM/tomography and NMR as well as protein expression screening, insect cell, biophysics, confocal microscopy and high-throughput crystallization platforms. Applicants should have a Ph.D. and at least 3 years post-doctoral experience and a strong record of achievement in structural, molecular or cell biology. Further information about research at EMBL Grenoble can be found on http://www.embl.fr/index.php Further information about the position can be found on http://www.embl.fr/aboutus/jobs/searchjobs/index.php?loc=4list=1 Stephen Cusack -- ** Dr. Stephen Cusack, Head of Grenoble Outstation of EMBL Group leader in structural biology of protein-RNA complexes and viral proteins Joint appointment in EMBL Genome Biology Programme Director of CNRS-UJF-EMBL International Unit (UMI 3265) for Virus Host Cell Interactions (UVHCI) ** Email: cus...@embl.fr Website: http://www.embl.fr Tel:(33) 4 76 20 7238Secretary (33) 4 76 20 7123 Fax:(33) 4 76 20 7199 Postal address: EMBL Grenoble Outstation, 6 Rue Jules Horowitz, BP181, 38042 Grenoble Cedex 9, France Delivery address: EMBL Grenoble Outstation, Polygone Scientifique, 6 Rue Jules Horowitz, 38042 Grenoble, France **
[ccp4bb] PDRA Position Manchester
Dear All, please find below details of a PDRA position available at the University of Manchester. All enquiries should be made to Dr. Lydia Tabernero, lydia.tabern...@manchester.ac.ukmailto:lydia.tabern...@manchester.ac.uk. Thanks, Colin Postdoctoral Position in X-ray Crystallography Structure of the endosomal ESCRT-I core complex Faculty of Life Sciences, University of Manchester Manchester, UK A postdoctoral position is available in the laboratory of Dr Lydia Tabernero to study the structural basis for the assembly of a protein complex that is essential for mitogenic receptor down regulation. The project will focus on understanding the core structure of the endosomal-sorting complex, ESCRT-I (Stefani et al., 2011, Curr. Biol. 21, 1245050). The position is part of an ongoing research collaboration between Dr Lydia Tabernero and Professor Philip Woodman directed towards understanding the molecular basis for the down-regulation of the epidermal growth factor receptor. This is a high-impact fast-moving basic research area with direct implications for bettering our understanding of a key cellular process that is disrupted in several diseases. The successful applicant will join a collaborative team, also involving the laboratories of Professor Philip Woodman and Dr Alan Roseman, and will use X-ray crystallography and other structural techniques. The ideal candidate will have (or expect to gain shortly) a PhD in structural biology, and will have experience in recombinant protein expression and X-ray crystallography. The post is full time for up to 24 months and can be available immediately. Salary: £29,541 to £36,298 depending on experience Closing date :19/03/2013 Reference :LSX-02347 Further particulars and a full description of the project and job responsibilities can be found at: www.jobs.manchester.ac.ukhttp://www.jobs.manchester.ac.uk Informal enquiries Informal enquiries can be made to Dr Lydia Tabernero, Lecturer: Email: lydia.tabern...@manchester.ac.ukmailto:lydia.tabern...@manchester.ac.uk Telephone: 0161 275 7794 The University of Manchester values a diverse workforce and welcomes applications from all sections of the community.
[ccp4bb] postdoc position at Jozef Stefan Institute, Ljubljana, Slovenia
Dear All, We are looking for a postdoctoral researcher for our Structural Biology Group at the Dept. of Biochemistry and Molecular and structural Biology at Jozef Stefan Institute, Ljubljana, Slovenia. We are studying human and mouse endosomal enzymes involved in protein degradation and immune response and proteins at the surface of pathogenic bacteria such as S. aureus and C. difficile. We are looking for a self-initiative person, with a background in molecular biology, protein biochemistry, and macromolecular crystallography. Managing and communication skills for running a scientific project in a group environment are expected. Tentative start is January 1st, 2014. We offer excellent research opportunities and a stimulating environment for structural biology. Our laboratory is a member of a recently established Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins and is equipped with state-of-the-art equipment for protein expression and biochemistry, X-ray crystallography, and mass spectrometry. Applications (including CV with publication list, research experience, copy of PhD certificate, and two persons with contact information for references) and contact information (E-mail, phone, or Skype) should be sent by mail or E-mail to Prof. Dr. Dusan Turk Jozef Stefan Institute Dept. of Biochemistry and Molecular and Stuctural Biology Jozef Stefan Instiutute Jamova 39 1000 Ljubljana, Slovenia Dr. Dusan Turk, Prof. Head of Structural Biology Group Head of Centre for Protein and Structure Production Centre of excellence for Integrated Approaches in Chemistry and Biology of Proteins, Scientific Director Professor of Structural Biology at IPS Jozef Stefan e-mail: dusan.t...@ijs.sihttp://bio.ijs.si/sbl/ phone: +386 1 477 3857 Dept. of Biochem. Mol. Struct. Biol. fax: +386 1 477 3984 Jozef Stefan Institute Jamova 39, 1 000 Ljubljana,Slovenia Skype: dusan.turk (voice over internet: www.skype.com
[ccp4bb] tNCS: indexing and EP problems
Dear experts, I am dealing at the moment with a case involving translated NCS copies of my asymmetric unit along one axis of the unit cell (3 clear non-origin peaks in the native Patterson). I could get Mosflm to find the corresponding big unit cell only after restricting the max deviation from integral hkl parameter to 0.1 and thus get the majority of the spots under prediction boxes (although the cell parameters don't look very accurate sometimes). I have 2 questions about it : 1) Do you know whether it would be possible to configure XDS the same way, to make it find this enlarged unit cell ? (no success so far...) 2) Are you aware of any experimental phasing program making use of the information provided by the Patterson for finding the substructure? Many thanks in advance, Nicolas
Re: [ccp4bb] tNCS: indexing and EP problems
Hi Boaz, I'm looking for one or several XDS keyword(s) to configure, in order to find the same unit cell that Mosflm found. Thanks, Nicolas On 23/09/2013 15:04, Boaz Shaanan wrote: Hi, I'm not sure what you mean by 'configuring XDS the same way', do you mean that you tried to use the results from Mosflm as input to XDS? If not, it's worth trying. Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Nicolas Soler [nso...@mrc-lmb.cam.ac.uk] Sent: Monday, September 23, 2013 5:04 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] tNCS: indexing and EP problems Dear experts, I am dealing at the moment with a case involving translated NCS copies of my asymmetric unit along one axis of the unit cell (3 clear non-origin peaks in the native Patterson). I could get Mosflm to find the corresponding big unit cell only after restricting the max deviation from integral hkl parameter to 0.1 and thus get the majority of the spots under prediction boxes (although the cell parameters don't look very accurate sometimes). I have 2 questions about it : 1) Do you know whether it would be possible to configure XDS the same way, to make it find this enlarged unit cell ? (no success so far...) 2) Are you aware of any experimental phasing program making use of the information provided by the Patterson for finding the substructure? Many thanks in advance, Nicolas -- Nicolas Soler Roger Williams group MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge CB2 0QH United Kingdom phone : +44(0) 1223 26 76 20 mail : nso...@mrc-lmb.cam.ac.uk
Re: [ccp4bb] tNCS: indexing and EP problems
Hi, I'm not sure what you mean by 'configuring XDS the same way', do you mean that you tried to use the results from Mosflm as input to XDS? If not, it's worth trying. Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Nicolas Soler [nso...@mrc-lmb.cam.ac.uk] Sent: Monday, September 23, 2013 5:04 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] tNCS: indexing and EP problems Dear experts, I am dealing at the moment with a case involving translated NCS copies of my asymmetric unit along one axis of the unit cell (3 clear non-origin peaks in the native Patterson). I could get Mosflm to find the corresponding big unit cell only after restricting the max deviation from integral hkl parameter to 0.1 and thus get the majority of the spots under prediction boxes (although the cell parameters don't look very accurate sometimes). I have 2 questions about it : 1) Do you know whether it would be possible to configure XDS the same way, to make it find this enlarged unit cell ? (no success so far...) 2) Are you aware of any experimental phasing program making use of the information provided by the Patterson for finding the substructure? Many thanks in advance, Nicolas
Re: [ccp4bb] tNCS: indexing and EP problems
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Nicolas, shelxd is one answer to question 2 (http://shelx.uni-ac.gwdg.de/SHELX/shelxd_mm_keywords.php: PATS). I am sure there are others. You can provide the cell from mosflm to XDS. If you want XDS to find the cell without this information, there are plenty of keywords to tweak, although in my experience it is often sufficient to find a decent set of images to collect spots from, play with the things you let XDS refine (REFINE(...)) and finding the correct ORGX and ORGY. In difficult cases I use adxv to get an estimate for the cell dimensions to judge whether or not XDS found the correct one. Best, Tim On 09/23/2013 04:04 PM, Nicolas Soler wrote: Dear experts, I am dealing at the moment with a case involving translated NCS copies of my asymmetric unit along one axis of the unit cell (3 clear non-origin peaks in the native Patterson). I could get Mosflm to find the corresponding big unit cell only after restricting the max deviation from integral hkl parameter to 0.1 and thus get the majority of the spots under prediction boxes (although the cell parameters don't look very accurate sometimes). I have 2 questions about it : 1) Do you know whether it would be possible to configure XDS the same way, to make it find this enlarged unit cell ? (no success so far...) 2) Are you aware of any experimental phasing program making use of the information provided by the Patterson for finding the substructure? Many thanks in advance, Nicolas - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.14 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFSQE6XUxlJ7aRr7hoRAnUEAJ9l0CNtIOuFytwWO1+MY7zYijcRKQCbBibF 0RJPhc5dGV0LJlzsRozjy6c= =7JHE -END PGP SIGNATURE-
Re: [ccp4bb] tNCS: indexing and EP problems
In difficult cases I use adxv to get an estimate for the cell dimensions to judge whether or not XDS found the correct one. The new XDS gui can also serve for that these days, I guess. Boaz
[ccp4bb] השב: Re: [ccp4bb] tNCS: indexing and EP problems
Hi Nicolas, You may want to make sure that all other parameters in XDS are the same as in mosflm and particularly the origin. Otherwise, how does the xds indexing/integration look? Perhaps pointless will give a clue about the relation between the xds and mosflm cells/spacegroup? Cheers, Boaz הודעה מקורית מאת Nicolas Soler nso...@mrc-lmb.cam.ac.uk תאריך: 23/09/2013 18:40 (GMT02:00) אל CCP4BB@JISCMAIL.AC.UK נושא Re: [ccp4bb] tNCS: indexing and EP problems Thanks for your answers, I realized too late that my question number 2 was misleading. I wondered in fact whether shelxd or another program could handle tNCS fine. Otherwise for my indexing concerns, I have been trying to feed xds with the unit cell parameters found by mosflm via the UNIT_CELL_CONSTANTS keyword in XDS.INP but I didn't find them back in the solution list proposed by IDXREF.LP. Has anybody had similar issues? Cheers, Nicolas On 23/09/2013 15:22, Tim Gruene wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Nicolas, shelxd is one answer to question 2 (http://shelx.uni-ac.gwdg.de/SHELX/shelxd_mm_keywords.php: PATS). I am sure there are others. You can provide the cell from mosflm to XDS. If you want XDS to find the cell without this information, there are plenty of keywords to tweak, although in my experience it is often sufficient to find a decent set of images to collect spots from, play with the things you let XDS refine (REFINE(...)) and finding the correct ORGX and ORGY. In difficult cases I use adxv to get an estimate for the cell dimensions to judge whether or not XDS found the correct one. Best, Tim On 09/23/2013 04:04 PM, Nicolas Soler wrote: Dear experts, I am dealing at the moment with a case involving translated NCS copies of my asymmetric unit along one axis of the unit cell (3 clear non-origin peaks in the native Patterson). I could get Mosflm to find the corresponding big unit cell only after restricting the max deviation from integral hkl parameter to 0.1 and thus get the majority of the spots under prediction boxes (although the cell parameters don't look very accurate sometimes). I have 2 questions about it : 1) Do you know whether it would be possible to configure XDS the same way, to make it find this enlarged unit cell ? (no success so far...) 2) Are you aware of any experimental phasing program making use of the information provided by the Patterson for finding the substructure? Many thanks in advance, Nicolas - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.14 (GNU/Linux) Comment: Using GnuPG with Mozilla -http://enigmail.mozdev.org/ iD8DBQFSQE6XUxlJ7aRr7hoRAnUEAJ9l0CNtIOuFytwWO1MY7zYijcRKQCbBibF 0RJPhc5dGV0LJlzsRozjy6c= =7JHE -END PGP SIGNATURE-
Re: [ccp4bb] tNCS: indexing and EP problems
Thanks for your answers, I realized too late that my question number 2 was misleading. I wondered in fact whether shelxd or another program could handle tNCS fine. Otherwise for my indexing concerns, I have been trying to feed xds with the unit cell parameters found by mosflm via the UNIT_CELL_CONSTANTS keyword in XDS.INP but I didn't find them back in the solution list proposed by IDXREF.LP. Has anybody had similar issues? Cheers, Nicolas On 23/09/2013 15:22, Tim Gruene wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Nicolas, shelxd is one answer to question 2 (http://shelx.uni-ac.gwdg.de/SHELX/shelxd_mm_keywords.php: PATS). I am sure there are others. You can provide the cell from mosflm to XDS. If you want XDS to find the cell without this information, there are plenty of keywords to tweak, although in my experience it is often sufficient to find a decent set of images to collect spots from, play with the things you let XDS refine (REFINE(...)) and finding the correct ORGX and ORGY. In difficult cases I use adxv to get an estimate for the cell dimensions to judge whether or not XDS found the correct one. Best, Tim On 09/23/2013 04:04 PM, Nicolas Soler wrote: Dear experts, I am dealing at the moment with a case involving translated NCS copies of my asymmetric unit along one axis of the unit cell (3 clear non-origin peaks in the native Patterson). I could get Mosflm to find the corresponding big unit cell only after restricting the max deviation from integral hkl parameter to 0.1 and thus get the majority of the spots under prediction boxes (although the cell parameters don't look very accurate sometimes). I have 2 questions about it : 1) Do you know whether it would be possible to configure XDS the same way, to make it find this enlarged unit cell ? (no success so far...) 2) Are you aware of any experimental phasing program making use of the information provided by the Patterson for finding the substructure? Many thanks in advance, Nicolas - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.14 (GNU/Linux) Comment: Using GnuPG with Mozilla -http://enigmail.mozdev.org/ iD8DBQFSQE6XUxlJ7aRr7hoRAnUEAJ9l0CNtIOuFytwWO1+MY7zYijcRKQCbBibF 0RJPhc5dGV0LJlzsRozjy6c= =7JHE -END PGP SIGNATURE-
[ccp4bb] tricky mr problem
Hi all, I have been attempting to find a MR solution for a low resolution data set (3.9A), with pretty poor merging stats of a 22 strand membrane beta barrel I'm working on. I've created a trimmed poly-alanine from a structure of 17% identity, that gives a solution with a Tfz of 14.3 with two molecules per asu (llg is around 900). I'm guessing this in a genuine solution, but the map is too poor to build into. Does anyone have any advice as to proceed from here? It may be just a case of needing better resolution data to work with, but would this indicate that Selenomet derivative crystals won't be needed for this structure? Cheers, Rhys
Re: [ccp4bb] tricky mr problem
Taking Tfz of 14.3 I assume that you have used Phaser, and according to what authors say, it is most probably the solution. Maybe map is not yet good, but you can try to refine using modern approaches for refinement of low resolution structures which are recently implemented in Refmac and Phenix. Your map will look better after refinement, as model can move quite significant distance into better position. Phase extension into better resolution data is a method which is developed already the late 80's. So you are in… Good luck 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 Sep 24, 2013, at 24:01 , RHYS GRINTER r.grinte...@research.gla.ac.uk wrote: Hi all, I have been attempting to find a MR solution for a low resolution data set (3.9A), with pretty poor merging stats of a 22 strand membrane beta barrel I'm working on. I've created a trimmed poly-alanine from a structure of 17% identity, that gives a solution with a Tfz of 14.3 with two molecules per asu (llg is around 900). I'm guessing this in a genuine solution, but the map is too poor to build into. Does anyone have any advice as to proceed from here? It may be just a case of needing better resolution data to work with, but would this indicate that Selenomet derivative crystals won't be needed for this structure? Cheers, Rhys
Re: [ccp4bb] tricky mr problem
On Monday, 23 September, 2013 22:01:32 RHYS GRINTER wrote: Hi all, I have been attempting to find a MR solution for a low resolution data set (3.9A), with pretty poor merging stats of a 22 strand membrane beta barrel I'm working on. I've created a trimmed poly-alanine from a structure of 17% identity, that gives a solution with a Tfz of 14.3 with two molecules per asu (llg is around 900). I'm guessing this in a genuine solution, but the map is too poor to build into. Does anyone have any advice as to proceed from here? It may be just a case of needing better resolution data to work with, but would this indicate that Selenomet derivative crystals won't be needed for this structure? Apart from whether you need SeMet for phasing, when you are having trouble fitting into poor maps it can help a lot to have the location of methionines pinned down by peaks in an anomalous difference Fourier map. Ethan
Re: [ccp4bb] tricky mr problem
Rhys, Having worked on a number of these structures using both MR and SAD/MAD, my advice is to continue to make experimental phasing a priority since building into a poor density map at this resolution can take months to years to finish while building into a nice experimental map can take a few hours to days, depending on how good your phases are. With that being said, I fully support pursuing the MR route, just keep in mind though it won't easy at this resolution, even if you had awesome data. And yes, your results seem to indicate that you have a nice solution, but i wonder how much of the overall structure does your model cover? You mention this is a 22-stranded beta-barrelmembrane protein? A tonB-dept transporter maybeand if so, do you get a solution with the plug domain or are you just playing with the barrel domain currently? A good check to see if you have a real solution if you are only using the barrel domain is to check to see if you have any difference density for the plug domain. So, my 2 cents, keep chugging along with the MR, but I would put more energy into the experimental phasing, esp if you are able to express it ok and can crystallize using the same conditions as native. Also, both MR and experimental phasing would benefit greatly if you were able to increase your resolution closer to 3 angstroms (ughi know...easier said than done!). Again, if this is indeed a membrane protein, that could just mean that you end up screening a few hundred crystals to find that one crystal with that one sweet spot that gives you that one really good dataset. Good luck with your project, sounds like you are almost there! Cheers, Nick +++ Nicholas Noinaj Laboratory of Molecular Biology NIDDK, NIH 50 South Drive, Room 4505 Bethesda, MD 20892-8030 Phone (+1) 301-594-9230 Web: http://www-mslmb.niddk.nih.gov/buchanan/index.html From: RHYS GRINTER [r.grinte...@research.gla.ac.uk] Sent: Monday, September 23, 2013 5:01 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] tricky mr problem Hi all, I have been attempting to find a MR solution for a low resolution data set (3.9A), with pretty poor merging stats of a 22 strand membrane beta barrel I'm working on. I've created a trimmed poly-alanine from a structure of 17% identity, that gives a solution with a Tfz of 14.3 with two molecules per asu (llg is around 900). I'm guessing this in a genuine solution, but the map is too poor to build into. Does anyone have any advice as to proceed from here? It may be just a case of needing better resolution data to work with, but would this indicate that Selenomet derivative crystals won't be needed for this structure? Cheers, Rhys
[ccp4bb] Fwd: [ccp4bb] tricky mr problem
I would try phase improvement, especially since you have two molecules per a.u. In other words averaging, solvent flattning, histogram matching. The best way is to start at low(er) resoltuion and extend to the highest resolution vailable. The best criterium for success is a improved and interpretable map. I had quite some success with this appraoch with MR solutions, but uninterpretable or difficult to build maps. Good luck, Klaus Dr. Klaus Piontek Albert-Ludwigs University Freiburg Institute of Organic Chemistry and Biochemistry, Room 401 H Albertstrasse 21 D-79104 Freiburg Germany Phone: ++49-761-203-6036 Fax: ++49-761-203-8714 Email: klaus.pion...@ocbc.uni-freiburg.de --- the forwarded message follows --- ---BeginMessage--- Hi all, I have been attempting to find a MR solution for a low resolution data set (3.9A), with pretty poor merging stats of a 22 strand membrane beta barrel I'm working on. I've created a trimmed poly-alanine from a structure of 17% identity, that gives a solution with a Tfz of 14.3 with two molecules per asu (llg is around 900). I'm guessing this in a genuine solution, but the map is too poor to build into. Does anyone have any advice as to proceed from here? It may be just a case of needing better resolution data to work with, but would this indicate that Selenomet derivative crystals won't be needed for this structure? Cheers, Rhys---End Message---
Re: [ccp4bb] Fwd: [ccp4bb] tricky mr problem
I've had good luck using the CCP4 DM program PARROT to improve poor initial MR maps with twinned data. (Based on some suggestions from this bb.) I think it works especially well if you have a lot of NCS symmetry, but it's worth a try, and doesn't take long. Cheers, ___ Roger S. Rowlett Gordon Dorothy Kline Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu On 9/23/2013 9:01 PM, Klaus Piontek wrote: I would try phase improvement, especially since you have two molecules per a.u. In other words averaging, solvent flattning, histogram matching. The best way is to start at low(er) resoltuion and extend to the highest resolution vailable. The best criterium for success is a improved and interpretable map. I had quite some success with this appraoch with MR solutions, but uninterpretable or difficult to build maps. Good luck, Klaus Dr. Klaus Piontek Albert-Ludwigs University Freiburg Institute of Organic Chemistry and Biochemistry, Room 401 H Albertstrasse 21 D-79104 Freiburg Germany Phone: ++49-761-203-6036 Fax: ++49-761-203-8714 Email: klaus.pion...@ocbc.uni-freiburg.de --- the forwarded message follows ---
[ccp4bb] Docking models into low-res SAD map - summary
Many thanks for all the replies - I haven't yet tried all of them, but they all look worth following up on, much food for thought here: * Several people suggested SITUS COLORES, which I shall certainly try and had not heard of until now. * The program ESSENS, from the Uppsala software factory, can perform a phased molecular replacement search which may be suitable for this kind of problem. * There were a couple of votes for the use of FFEAR, which I have tried unsuccessfully, although it is likely that I am not employing it correctly, it seems like a very versatile program. * The use of UCSF Chimera was suggested - I use chimera all the time for making figures, but had not thought of using it for docking, thanks for the suggestion. *Randy Read suggested a procedure involving cutting out the density that forms the search space, converting it to structure factors, then performing a rotation search in PHASER and a phased translation search using FFT to dock the model into the density. Cheers, Oliver.
Re: [ccp4bb] tricky mr problem
We often use a S-SAD type data collection (there would be no need for enormous redundancy) which, if your model is correct, should show up the S positions in the same way as a Se-met would show up the Se positions. Good way of validating your model and a help to tracing. Cheers Andy De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de Ethan A Merritt [merr...@u.washington.edu] Envoyé : lundi 23 septembre 2013 23:25 À : CCP4BB@JISCMAIL.AC.UK Objet : Re: [ccp4bb] tricky mr problem On Monday, 23 September, 2013 22:01:32 RHYS GRINTER wrote: Hi all, I have been attempting to find a MR solution for a low resolution data set (3.9A), with pretty poor merging stats of a 22 strand membrane beta barrel I'm working on. I've created a trimmed poly-alanine from a structure of 17% identity, that gives a solution with a Tfz of 14.3 with two molecules per asu (llg is around 900). I'm guessing this in a genuine solution, but the map is too poor to build into. Does anyone have any advice as to proceed from here? It may be just a case of needing better resolution data to work with, but would this indicate that Selenomet derivative crystals won't be needed for this structure? Apart from whether you need SeMet for phasing, when you are having trouble fitting into poor maps it can help a lot to have the location of methionines pinned down by peaks in an anomalous difference Fourier map. Ethan
