Re: [ccp4bb] ccp4MG- selecting h-bonds
Kendall Nettles wrote: I have a question about how to show certain h-bonds with CCP4MG. I’d like to show a specific bond between an Arg and Glu, but not other H-bonds made by the Arg. How can I do this? Thanks! Kendall Dear Kendall, In the first and third columns in the display table you can specify atom selections. These can be anything, so in one selection specify one of your residues and in the other column the other residue. You can do this by using eg. the ..of residue ranges.. option and selecting just one residue. Best Wishes, Stuart McNicholas
[ccp4bb] EMBL Grenoble Team Leader: Synchrotron Methods for Structural Biology
*EMBL Grenoble Team Leader: Synchrotron Methods for Structural Biology Job Description*: We are looking for a structural biologist who has a focus on advanced crystallographic methods and instrumentation, particularly with relation to synchrotron radiation. The appointed Team Leader will manage, together with the Head of Outstation, the long-term collaboration between the EMBL Grenoble Outstation and the European Synchrotron Radiation Facility (ESRF) concerning the development and operation of the automated protein crystallography beamlines. He/she will oversee the activities of the three existing EMBL beamline scientists currently responsible for the dedicated microfocus beamline ID23-2, the MAD beamline ID14-EH4 and the CRG beamline BM14 (co-operated with MRC-France) as well as a SAXS beamline scientist currently under recruitment. He/she will collaborate in particular with the Outstation Diffraction Instrumentation team led by Florent Cipriani, which has developed state-of-the-art sample handling equipment currently installed on all ESRF MX beamlines (microdiffractometer, sample changer, minikappa) and with the ESRF MX group led by Sean McSweeney. He/she will develop a research programme focused on advanced crystallographic methods and instrumentation coupled to structural biological problems or more generally on new synchrotron techniques that might have an impact in biology and which take advantage of the unique environment at the world-leading 3rd generation synchrotron site in Grenoble. *Commencing date:* As soon as possible following the closing date* Contract:* An initial contract of 3 years will be offered to the successful candidate. This can be renewed, depending on circumstances at the time of review.* Closing date:* 8 July 2007 * Web page:* http://www.embl-grenoble.fr/ *To apply, please email a curriculum vitae, three references and a* *concise description of research interests and future plans quoting ref.* *no. W/07/065 in the subject line, to: [EMAIL PROTECTED] mailto:[EMAIL PROTECTED]* *Informal enquiries to me* *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 Gene Expression Programme ** Email: [EMAIL PROTECTED] Website: http://www.embl-grenoble.fr Tel: (33) 4 76 20 7238 Secretary (33) 4 76 20 7306 Fax: (33) 4 76 20 7786 or (33) 4 76 20 7199 Postal address: EMBL c/o ILL, BP181, 38042 Grenoble Cedex 9, France Delivery address: EMBL c/o ILL, Polygone Scientifique, 6 Rue Jules Horowitz, 38042 Grenoble, France **
[ccp4bb] EMBL Grenoble Staff Scientist : New SAXS Beamline on ID14-EH3 at the ESRF
*EMBL Grenoble Staff Scientist : New SAXS Beamline on ID14-EH3 at the ESRF Job description:* A scientist is required to join a team within the Partnership for Structural Biology (EMBL, ESRF, ILL and IBS, http://psb.esrf.fr/) which is establishing a unique and integrated SAXS-SANS platform, making use of the intense synchrotron X-ray and neutron beams of respectively the ERSF and ILL. The successful candidate will be responsible for construction, commissioning and user support of a new state-of-the-art SAXS beamline, dedicated to biology, to be built on undulator beamline ID14-EH3 at the ESRF. The beamline will cater to the growing needs of the European structural biology community who wish to combine SAXS studies with crystallography and other techniques. He/She will benefit from strong technical support from the ESRF MX and Soft Condensed Matter groups and other ESRF services as well as the EMBL Grenoble diffraction instrumentation group. In addition there will be a strong collaboration with the SAXS scientists from the EMBL Hamburg Outstation both to transfer expertise and to provide test facilities during the conception and construction phase of the future SAXS beamline at Petra III in Hamburg. * Qualifications and experience:* Applicants for this position are expected to hold a PhD in a related specialization, as well as have postdoctoral experience in instrumentation and software for small-angle scattering in physics, chemistry or biology, preferably at a synchrotron. At least some knowledge of, and demonstrable interest in, biology is required. Commencing date: As soon as possible following the closing date *Contract:* An initial contract of 3 years will be offered to the successful candidate. This can be renewed, depending on circumstances at the time of review. *Closing date*: 8 July 2007 *Web page*: http://www.embl-grenoble.fr/ To apply, please email a curriculum vitae, three references and a concise description of research interests and future plans quoting ref. no. W/07/065 in the subject line, to: [EMAIL PROTECTED] Informal enquiries to me Stephen Cusack * * http://www.embl-grenoble.fr/ ** 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 Gene Expression Programme ** Email: [EMAIL PROTECTED] Website: http://www.embl-grenoble.fr Tel:(33) 4 76 20 7238Secretary (33) 4 76 20 7306 Fax:(33) 4 76 20 7786 or (33) 4 76 20 7199 Postal address: EMBL c/o ILL, BP181, 38042 Grenoble Cedex 9, France Delivery address: EMBL c/o ILL, Polygone Scientifique, 6 Rue Jules Horowitz, 38042 Grenoble, France **
Re: [ccp4bb] refmac fails on iodine ions
Two things I think 1) I is a metal so you need to move the atom name 1 space to the left - more like this: ATOM 2838 O HOH W 102 6.018 39.720 31.127 1.00 21.43 O ATOM 2839 I I B 1 19.956 22.770 18.597 1.00 30.00 I And the monomer library calls this IOD so I guess you need ATOM 2838 O HOH W 102 6.018 39.720 31.127 1.00 21.43 O ATOM 2839 IIOD B 1 19.956 22.770 18.597 1.00 30.00 I Eleanor [EMAIL PROTECTED] wrote: Dear All, I am having trouble with refmac dictionaries when refining a structure that contains an iodine ion. the PDB entry should be correct and according to the convention (water added for comparison): - ATOM 2838 O HOH W 102 6.018 39.720 31.127 1.00 21.43 O ATOM 2839 I I B 1 19.956 22.770 18.597 1.00 30.00 I - refmac hovever comes up with the following error: - .. Number of chains : 3 I am reading library. Please wait. mon_lib.cif Open failed: Unit: 7, File: /xray/CCP4-6.0.1/ccp4-6.0.1/lib/data/monomers/i/IR.cif (logical: /xray/CCP4-6.0.1/ccp4-6.0.1/lib/data/monomers/i/IR.cif) * Refmac_5.2.0019: Open failed: File: /xray/CCP4-6.0.1/ccp4-6.0.1/lib/data/monomers/i/IR.cif * *Times: User: 1.4s System:0.0s Elapsed: 0:01 * - I figured that it tries to read the wrong dictionary (although the correct one ( I.cif) is present in the same directory). Explicitly supplying I.cif with a LIB_IN card does not help thanks for your help alex PS:probably this has been on the bb in the past, but I could not dig it out Dr. Alexander Pautsch Protein Crystallography /Structural Research Boehringer Ingelheim Pharma GmbH Co. KG Deutschland Birkendorferstrasse 65 88400 BIBERACH, Germany tel. +49 - (0)7351 - 54 4683 fax. +49 - (0)7351 - 83 4683 email [EMAIL PROTECTED]
Re: [ccp4bb] refmac fails on iodine ions
Residue name of iodine should IOD. Otherwsie there is a clash of names with some other residue names (ionisine) Garib On 6 Jun 2007, at 16:56, [EMAIL PROTECTED] wrote: Dear All, I am having trouble with refmac dictionaries when refining a structure that contains an iodine ion. the PDB entry should be correct and according to the convention (water added for comparison): - ATOM 2838 O HOH W 102 6.018 39.720 31.127 1.00 21.43 O ATOM 2839 I I B 1 19.956 22.770 18.597 1.00 30.00 I - refmac hovever comes up with the following error: - .. Number of chains : 3 I am reading library. Please wait. mon_lib.cif Open failed: Unit: 7, File: /xray/CCP4-6.0.1/ccp4-6.0.1/lib/data/ monomers/i/IR.cif (logical: /xray/CCP4-6.0.1/ccp4-6.0.1/lib/data/ monomers/i/IR.cif) Refmac_5.2.0019: Open failed: File: /xray/CCP4-6.0.1/ccp4-6.0.1/ lib/data/monomers/i/IR.cif Times: User: 1.4s System:0.0s Elapsed: 0:01 - I figured that it tries to read the wrong dictionary (although the correct one ( I.cif) is present in the same directory). Explicitly supplying I.cif with a LIB_IN card does not help thanks for your help alex PS:probably this has been on the bb in the past, but I could not dig it out Dr. Alexander Pautsch Protein Crystallography /Structural Research Boehringer Ingelheim Pharma GmbH Co. KG Deutschland Birkendorferstrasse 65 88400 BIBERACH, Germany tel. +49 - (0)7351 - 54 4683 fax. +49 - (0)7351 - 83 4683 email [EMAIL PROTECTED]
[ccp4bb] Drug Discovery Workshop, Oxford, September 10-14
I am pleased to announce that we will be holding the hands-on eCheminfoDrug Discovery Workshop week a second time this year in Oxford the weekof 10-14 September. First option on places will go to the waiting list fromthe June workshop but there nevertheless still are additional places available. If interested in attending, please see links below for further information, and use the contact information provided there to register. (Do not try to register by replying to my email. Thanks!)best regardsBarry HardyCommunity of Practice ManagerDouglas ConnectSwitzerlandTel: +41 61 851 0170Latest Advances in Drug Discovery Design Planning Methodsa Hands-on 5 Day eCheminfo Advanced Training Workshop Week25-29 June 2007 (registration closed) AND 10-14 September 2007Chemistry Research Laboratory, Oxford University, Oxford, UKBrochure: http://www.douglasconnect.com/files/eChemProgramOxford07-Sept-v1web.PDFAbstracts and Bios on Website: http://echeminfo.colayer.net/COMTY_trainingPhotos from Class of 2006: http://www.echeminfo.com/COMTY_oxfordphotos06Feedback from Class of 2006: http://www.echeminfo.com/COMTY_oxfordfeedback06
Re: [ccp4bb] refmac fails on iodine ions
Dear refmac experts, following on from the iodide ion question, If I ask coot to get IOD, it lines up the I with C of CA in pdb file. Good. But to tell refmac that it is an iodide ion (not a metal) and get the correct scattering factor, presumably the atom type should be changed to I- ?? or have I misunderstood horribly ? J -- Dr Judith Murray-Rust Structural Biology Lab Cancer Research UK London WC2A 3PX -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Garib Murshudov Sent: 06 June 2007 17:14 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] refmac fails on iodine ions Residue name of iodine should IOD. Otherwsie there is a clash of names with some other residue names (ionisine) Garib On 6 Jun 2007, at 16:56, [EMAIL PROTECTED] wrote: Dear All, I am having trouble with refmac dictionaries when refining a structure that contains an iodine ion. the PDB entry should be correct and according to the convention (water added for comparison): - ATOM 2838 O HOH W 102 6.018 39.720 31.127 1.00 21.43 O ATOM 2839 I I B 1 19.956 22.770 18.597 1.00 30.00 I - refmac hovever comes up with the following error: - .. Number of chains : 3 I am reading library. Please wait. mon_lib.cif Open failed: Unit: 7, File: /xray/CCP4-6.0.1/ccp4-6.0.1/lib/data/monomers/i/IR.cif (logical: /xray/CCP4-6.0.1/ccp4-6.0.1/lib/data/monomers/i/IR.cif) Refmac_5.2.0019: Open failed: File: /xray/CCP4-6.0.1/ccp4-6.0.1/lib/data/monomers/i/IR.cif Times: User: 1.4s System:0.0s Elapsed: 0:01 - I figured that it tries to read the wrong dictionary (although the correct one ( I.cif) is present in the same directory). Explicitly supplying I.cif with a LIB_IN card does not help thanks for your help alex PS:probably this has been on the bb in the past, but I could not dig it out Dr. Alexander Pautsch Protein Crystallography /Structural Research Boehringer Ingelheim Pharma GmbH Co. KG Deutschland Birkendorferstrasse 65 88400 BIBERACH, Germany tel. +49 - (0)7351 - 54 4683 fax. +49 - (0)7351 - 83 4683 email [EMAIL PROTECTED]
