Re: [ccp4bb] Two Postdoc positions at the University of Oxford, SGC
Gentle reminder of the following openings at SGC Oxford (deadline 7th February noon). Thanks. On 14 January 2013 17:51, Wyatt W. Yue yuewai...@googlemail.com wrote: Dear all, We are seeking two post-doc scientists in the Metabolic Rare Diseases group at the Structural Genomics Consortium (SGC), University of Oxford: 1. *Protein crystallographer*, driving multiple gene-to-structure projects to understand inborn errors of metabolism: https://www.recruit.ox.ac.uk/pls/hrisliverecruit/erq_jobspec_version_4.jobspec?p_id=106057 2. Industry-funded *Protein biochemist/structural biologist*, working on mechanism and small molecule development for protein misfolding disorders: https://www.recruit.ox.ac.uk/pls/hrisliverecruit/erq_jobspec_version_4.jobspec?p_id=106055 The successful candidates will - benefit from the SGC high-throughput platform for structural/biochemical characterization - work closely with an established network of geneticists, clinicians and drug developers - have regular access to the nearby Diamond synchrotron for data collection Visit the SGC Metabolic Rare Diseases group: http://www.thesgc.org/wyatt Informal enquiries to: wyatt@sgc.ox.ac.uk Application deadline:* Noon 7th Feb 2013 (GMT)* * * * * Dr Wyatt W. Yue Principal Investigator, Metabolic Rare Diseases Structural Genomics Consortium University of Oxford UK OX3 7DQ +44 (0)1865 617757 http://www.thesgc.org/wyatt
Re: [ccp4bb] generating electron density from PDB and structure factor file
Just to add some more possibilities: - You can download maps from EDS or models and maps from PDB_REDO straight into CCP4mg. - You can download PDB_REDO maps and models into PyMOL using this plugin (http://www.cmbi.ru.nl/pdb_redo/pymol.html) for which we should thank Ed Pozharski. Note that this does require a working and sourced CCP4 installation to convert mtz files into maps. Cheers, Robbie Date: Mon, 4 Feb 2013 05:15:40 -0800 From: jan_i...@yahoo.com Subject: [ccp4bb] generating electron density from PDB and structure factor file To: CCP4BB@JISCMAIL.AC.UK Dear All, I would like to know what is the best possible way to generate the density from the published pdb file. thanks, Bhat
[ccp4bb] Pilatus 300K CBF to Oxford Diffraction format convert
Dear all, sorry for the semi-off-topic but I'm trying to help convert some diffraction images and this seemed like a good place to ask. We are trying to process some images collected on a Pilatus 300K with the Crysalis Pro software (small molecule) but it seems to only be able to read Pilatus 6M frames. Is there an easy way to convert the 300K dbf files to something readable by Crysalis? (Oxford Diffraction, marCCD, Rigaku or Bruker AXS-SAXI). Thanks! Jose This email and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorized recipient of the addressee, please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to this email. Any views or opinions presented are solely those of the author and do not necessarily represent those of the Research Complex at Harwell. There is no guarantee that this email or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. We use an electronic filing system. Please send electronic versions of documents, unless paper is specifically requested. This email may have a protective marking, for an explanation, please see: http://www.mrc.ac.uk/About/informationandstandards/documentmarking/index.htm.
Re: [ccp4bb] Pilatus 300K CBF to Oxford Diffraction format convert
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Jose, it is odd the software should read 6M but not 0.3M Pilatus files - the format is probably the same, only the dimensions would differ - at least that's my guess. While you are waiting you might start processing your data with XDS, which is well suited also for small molecules crystals. If your cell is small, I recommend turning of refinement during the integration step (REFINE(INTEGRATE)=!) and only refine all parameters during the CORRECT step. You need to make sure the spots are correctly predicted on the FRAME.cbf, i.e. the cell from indexing is close enough to the correct one. Best wishes, Tim On 02/06/2013 11:35 AM, Jose Trincao wrote: Dear all, sorry for the semi-off-topic but I'm trying to help convert some diffraction images and this seemed like a good place to ask. We are trying to process some images collected on a Pilatus 300K with the Crysalis Pro software (small molecule) but it seems to only be able to read Pilatus 6M frames. Is there an easy way to convert the 300K dbf files to something readable by Crysalis? (Oxford Diffraction, marCCD, Rigaku or Bruker AXS-SAXI). Thanks! Jose This email and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorized recipient of the addressee, please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to this email. Any views or opinions presented are solely those of the author and do not necessarily represent those of the Research Complex at Harwell. There is no guarantee that this email or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. We use an electronic filing system. Please send electronic versions of documents, unless paper is specifically requested. This email may have a protective marking, for an explanation, please see: http://www.mrc.ac.uk/About/informationandstandards/documentmarking/index.htm. - -- - -- 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/ iD8DBQFREjxFUxlJ7aRr7hoRAnT6AJoCPwjWp5eDrIQ0JevYl/98Bh2ixQCglIQ+ 7e+OerAR3x+GVUejoXmVcQM= =ZDOJ -END PGP SIGNATURE-
Re: [ccp4bb] Pilatus 300K CBF to Oxford Diffraction format convert
Hi Tim I've looked at these images and they differ from the normal 6M images (miniCBF) in that they are a stab at writing fullCBF, i.e. with imgCIF style data content - unfortunately, there are a few syntax errors which need fixing before programs that use the header information (like Crysalis Pro, inter alia;-)) can do much useful with them. XDS (and any other programs that ignore header information) should be able to process these provided the correct beamline values are supplied. On 6 Feb 2013, at Wed6 Feb 11:19, Tim Gruene wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Jose, it is odd the software should read 6M but not 0.3M Pilatus files - the format is probably the same, only the dimensions would differ - at least that's my guess. While you are waiting you might start processing your data with XDS, which is well suited also for small molecules crystals. If your cell is small, I recommend turning of refinement during the integration step (REFINE(INTEGRATE)=!) and only refine all parameters during the CORRECT step. You need to make sure the spots are correctly predicted on the FRAME.cbf, i.e. the cell from indexing is close enough to the correct one. Best wishes, Tim On 02/06/2013 11:35 AM, Jose Trincao wrote: Dear all, sorry for the semi-off-topic but I'm trying to help convert some diffraction images and this seemed like a good place to ask. We are trying to process some images collected on a Pilatus 300K with the Crysalis Pro software (small molecule) but it seems to only be able to read Pilatus 6M frames. Is there an easy way to convert the 300K dbf files to something readable by Crysalis? (Oxford Diffraction, marCCD, Rigaku or Bruker AXS-SAXI). Thanks! Jose This email and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorized recipient of the addressee, please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to this email. Any views or opinions presented are solely those of the author and do not necessarily represent those of the Research Complex at Harwell. There is no guarantee that this email or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. We use an electronic filing system. Please send electronic versions of documents, unless paper is specifically requested. This email may have a protective marking, for an explanation, please see: http://www.mrc.ac.uk/About/informationandstandards/documentmarking/ index.htm. - -- - -- 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/ iD8DBQFREjxFUxlJ7aRr7hoRAnT6AJoCPwjWp5eDrIQ0JevYl/98Bh2ixQCglIQ+ 7e+OerAR3x+GVUejoXmVcQM= =ZDOJ -END PGP SIGNATURE- Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 0QH Chairman of European Crystallographic Association SIG9 (Crystallographic Computing)
Re: [ccp4bb] COOT v. 0.7
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hello Xavier, if you look at the downloaded file, you'll notice the source of the error: The pdbe download link has changed, i.e. this is not a PDB-file. You'll have to download the PDB file manually until it is fixed in the latest coot-code. Cheers, Tim On 02/06/2013 01:37 PM, F.Xavier Gomis-Rüth wrote: Dear CCP4ers, We managed to install COOT version 0.7 on a MacBookPro Retina with Mountain Lion and there seems to be an issue that did not appear with the Linux version when trying to retrieve coordinates directly from the PDB by givin the code: (get-ebi-pdb 4aw6) DEBUG:: in get-url-str: 4aw6 http://www.ebi.ac.uk/msd-srv/oca/oca-bin/save-pdb?id=4AW6; pdb (handle-read-draw-molecule-with-recentre coot-download/4aw6.pdb 1) Reading coordinate file: coot-download/4aw6.pdb There was an error reading coot-download/4aw6.pdb. ERROR 20 READ: Attempt to read unknown-type file. No Spacegroup found for this PDB file Cell: 1 1 1 90 90 90 There was a coordinates read error Any hints on how to circumvent this? Best wishes, Xavier -- - -- - -- 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/ iD8DBQFRElRDUxlJ7aRr7hoRAvolAJsEFvLl0WNvwi6FcM5Gbik4luBdKwCfS1YL zh+WaXVf9gesubCioI5SEe0= =UYHk -END PGP SIGNATURE-
[ccp4bb] Off Topic- Cystine Detection
Dear All, I am trying to probe the existence of a disulfide bond on the surface of my protein. I have attempted Ellman´s and my results were not as clear as I would have hoped for. I am not a sulfur/cysteine chemist and would appreciate the advice on what experiments to try! Thanks a bunch YAP
Re: [ccp4bb] Off Topic- Cystine Detection
I never done such experiments but N-Ethylmaleimide labeling and Mass-Spec could be the solution. Le 6 févr. 2013 à 17:10, Yuri Pompeu yuri.pom...@ufl.edu a écrit : Dear All, I am trying to probe the existence of a disulfide bond on the surface of my protein. I have attempted Ellman´s and my results were not as clear as I would have hoped for. I am not a sulfur/cysteine chemist and would appreciate the advice on what experiments to try! Thanks a bunch YAP Xavier Brazzolotto, PhD Département de Toxicologie Institut de Recherche Biomédicale des Armées 24 Av des Maquis du Grésivaudan 38702 La Tronche Cedex France
[ccp4bb] Beamtime @ SLS
=== SYNCHROTRON BEAM TIME FOR MACROMOLECULAR CRYSTALLOGRAPHY AT SLS === Proposal application deadline: Friday, February 15, 2013 Periods: May 1, 2013 - August 31, 2013 (Normal / Test proposals) May 1, 2013 - April 30, 2015 (Long-term proposals) Proposal submission: http://www.psi.ch/sls/px-beamlines-call-for-proposals Travel support: http://www.psi.ch/useroffice/sls-elisa-biostruct PSI DUO application for iphone: http://itunes.apple.com/ch/app/psi-duo/id375328818?mt=8 What's New? - PILATUS detectors at three PX beamlines - X06DA Multi-axis goniometer (PRIGO) - X06DA In-situ X-ray diffraction screening for any SBS format plate - X10SA Micro-beam with apertures (10 x 10, 30 x 30 micrometer) - Faster Sample changer (CATS) operation X06SA Beamline features (http://www.psi.ch/sls/pxi/pxi) - Undulator beamline with flux of 2x10^12 photons/sec at 12.4 keV (1Å) and fully tunable from 6.0 to 17.5 keV (2.07 - 0.71 Å) - Focused beam size and divergency: HRD - 85x10 microns and 0.35x0.06 mrad; MD2 - 25x5 microns and 0.5x0.4 mrad - PILATUS 6M pixel detector at the High Resolution Diffractometer, allowing continuous, fine phi-sliced data acquisition (25 frames per second) with 20 bit dynamic range (see http://pilatus.web.psi.ch/ or www.dectris.com for further information) - MAR225 CCD at Micro-Diffractometer MD2, allowing data collection with a focussed beam size of 25 x 5 micrometers, and smaller beam size with triple-aperture assembly ( 5 x 5, 10 x 10, 20 x 20 micrometer). X06DA Beamline features (http://www.psi.ch/sls/pxiii/pxiii) - Super-bending magnet beamline with flux of 5x10¹¹ photons/sec at 12.4 keV (1Å) and fully tunable from 6.0 to 17.5 keV (2.07 - 0.71 Å) - Focused beam size and divergency: 80x45 microns and 2x0.5 mrad (with possibility to reduce horizontal divergency to 0.4 mrad) - Mini-hutch design for fast manual mounting - PILATUS 2M (60 Hz, 450 um Si sensor) - Multi-axis goniometer (PRIGO) for crystal re-orentation - In-situ X-ray diffraction screening (with any SBS format plate) available during users shifts (R. Bingel-Erlenmeyer, et al., Crystal Growth Design 2011, 11, 916) X10SA Beamline features (http://www.psi.ch/sls/pxii/pxii) - Undulator beamline with flux of 2x10^12 photons/sec at 12.4 keV (1Å) and fully tunable from 6.0 to 20 keV (2.07 - 0.62 Å) - Focused beam size and divergency: 50x10 microns and 0.6x0.1 mrad - Micro-beam with apertures (10 x 10, 30 x 30 micrometer) - PILATUS 6M pixel detector Best regards, The MX group at SLS __ Meitian Wang Swiss Light Source at Paul Scherrer Institut CH-5232 Villigen PSI - http://www.psi.ch/sls/ Phone: +41 56 310 4175
Re: [ccp4bb] Off Topic- Cystine Detection
Hi, to my knowledge, Ellman's reagent detects free thiols only. (Or am I wrong?) In contrast, with the method of Thannhauser (Thannhauser [1987], Methods Enzymol. 143, 115-9) you can determine the total amount of thiols (free and in disulfide bonds). Any difference between the two methods should indicate the presence of disulfide bonds, but will probably not allow for their actual quantification. Regards, Joern ** Address: Joern Krausze Molecular Structural Biology Helmholtz Centre for Infection Research Inhoffenstrasse 7 38124 Braunschweig Germany Email: joern.krau...@helmholtz-hzi.de Phone: +49 (0)531 6181 7023 (office) +49 (0)531 6181 7020 (lab) ** On Wed, 6 Feb 2013, Yuri Pompeu wrote: Dear All, I am trying to probe the existence of a disulfide bond on the surface of my protein. I have attempted Ellman´s and my results were not as clear as I would have hoped for. I am not a sulfur/cysteine chemist and would appreciate the advice on what experiments to try! Thanks a bunch YAP
Re: [ccp4bb] Off Topic- Cystine Detection
Couldn't you just run reducing/non-reducing SDS-PAGE lanes and see the difference? JPK On Wed, Feb 6, 2013 at 11:10 AM, Yuri Pompeu yuri.pom...@ufl.edu wrote: Dear All, I am trying to probe the existence of a disulfide bond on the surface of my protein. I have attempted Ellman´s and my results were not as clear as I would have hoped for. I am not a sulfur/cysteine chemist and would appreciate the advice on what experiments to try! Thanks a bunch YAP -- *** Jacob Pearson Keller, PhD Postdoctoral Associate HHMI Janelia Farms Research Campus email: j-kell...@northwestern.edu ***
Re: [ccp4bb] need some suggestions for crystallization
Does that CA have a metal center (I think they all do)? If so, doesn't the citrate compete for the metal? JPK On Mon, Feb 4, 2013 at 2:25 PM, Roger Rowlett rrowl...@colgate.edu wrote: Human carbonic anhdyrase II can be easily crystallized from 1.3 M sodium citrate/0.1 M TrisCl pH 8.5 at 10 mg/mL protein concentration. Crystals are P21 and easily diffract to beyond 2.0 A on a home source. We cryopreserve in ML + 30% glucose. Sulfonamide ligands are easy to soak into the crystals in a few minutes during cryopreservation, and provide teaching opportunities for protein-ligand model building and refinement. Cheers, __**_ Roger 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 02/04/2013 12:31 PM, Jim Pflugrath wrote: A number of protein crystal recipes are available on the Rigaku web site: http://www.rigaku.com/**products/protein/recipeshttp://www.rigaku.com/products/protein/recipes Lysozyme is nice because it is so cheap, grows quickly, cryoprotectants in a straightforward way, and the unit cells are not large nor are the crystals fragile. One can get triclinic, monoclinic, orthorhombic, and tetragonal crystals relatively quickly. With hen egg white lysozyme if you are not up for sulfur-SAD phasing, then co-crystallizing or quick-soaking in iodide (say 100 mM) gives a very nice anomalous signal at just about any wavelength. That is, no need to worry about going to a so-called edge. While there are many other easy-to-go crystals, I have found that none of them combine all the properties of hen egg white lysozyme has a good teaching tool. Jim == Can you all suggest some protein crystallization conditions (along with cryo conditions) for some commercially available proteins? I'm looking to get 6-8 different ones (and we'll just take them and see how it goes). I wouldn't mind knowing unit cell parameters as well (just a citation works, I can have them figure it out). I have about 7 weeks to get everything grown and frozen and ready to go. Any help would be greatly appreciated. It always amazes me how helpful this group is. Thank you very much. Dave -- *** Jacob Pearson Keller, PhD Postdoctoral Associate HHMI Janelia Farms Research Campus email: j-kell...@northwestern.edu ***
Re: [ccp4bb] Off Topic- Cystine Detection
*** This message has been scanned by the InterScan for CSC SSM by IICT security policy and found to be free of known security risks. *** Dear Yuri, If you have access to mass spec, this should be a straight forward experiment. Find the reference here. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2291582/pdf/v010p00017.pdf What was the result in the Ellman´s reaction? Unless you have other reactive cysteines in your protein protein, you should not see any color if the pair of cysteines on surface form disulfide. Anthony - Dr. Anthony Addlagatta Center for Chemical Biology Indian Institute of Chemical Technology [IICT] Tarnaka, Hyderabad AP-500 607, INDIA Tel:91-40-27191812 Web: https://sites.google.com/site/chembioliict/home/dr-anthony-addlagatta-1 -- Original Message --- From: Yuri Pompeu yuri.pom...@ufl.edu To: CCP4BB@JISCMAIL.AC.UK Sent: Wed, 6 Feb 2013 16:10:35 + Subject: [ccp4bb] Off Topic- Cystine Detection *** This message has been scanned by the InterScan for CSC SSM at IICT and found to be free of known security risks. *** Dear All, I am trying to probe the existence of a disulfide bond on the surface of my protein. I have attempted Ellman´s and my results were not as clear as I would have hoped for. I am not a sulfur/cysteine chemist and would appreciate the advice on what experiments to try! Thanks a bunch YAP --- End of Original Message --- This Mail Scanned by ClamAV and Spammassassin
