Re: [ccp4bb] Checking for gremlins in deposited diffraction data] (fwd)
I am not sure what is meant by recent change in CCP4 default naming of mtz columns. The point of the LABIN mechanism is that mtz columns can have any user-defined labels. Yes there are conventions, but since CCP4 consists of many different programs written by many different authors with many different opinions, it seems highly dangerous to make assumptions about column naming. This has been true throughout the history of MTZ and I believe also for LCF (before my time!). Following the link below below, through to the online conversion tool http://pdb-extract.rcsb.org/auto-check/index-ext.html there is an option Semi-automatic MTZ Conversion to mmCIF which allows you to select the correct MTZ column. This seems a safer way to go, and it seems to work fine on one MTZ file with non-standard naming. Cheers Martyn P.S. posting problems are invariably due to subscribing and posting from different email addresses On Sun, 2009-03-08 at 16:04 +, Gerard Bricogne wrote: Dear all, I am forwarding to the BB this message from Maksymilian Chruszcz (with his permission), given that his own attempt at posting it directly was not successful. With best wishes, Gerard. - Forwarded message from Maksymilian Chruszcz m...@cms.mail.virginia.edu - Date: Sat, 07 Mar 2009 11:56:55 -0500 From: Maksymilian Chruszcz m...@cms.mail.virginia.edu Subject: Re: Checking for gremlins in deposited diffraction data To: g...@globalphasing.com, ccp4bb@jiscmail.ac.uk Cc: Dauter, Zbigniew zdau...@anl.gov, Zbyszek Otwinowski zbys...@work.swmed.edu, Wladek Minor wla...@iwonka.med.virginia.edu X-Mailer: CommuniGate Pro WebUser v5.1.14 Dear Gerard, Thank you very much for turning our attention to structure factors deposited for 3FTT. Preliminary check of our data confirmed your suggestion about F_calc and ph_calc being reported instead of F_meas_au and F_meas_sigma_au respectively. This error was introduced during the conversion from MTZ to CIF file. We are currently discussing with PDB source of such error. Currently I do not know why these particular column were extracted, and I am guessing that maybe PDB scripts handling new mtz files have problems. From: http://pdb-extract.rcsb.org/auto-check/help/checksform.html#conversions 'An automatic conversion is used to convert one standardized SF format to another. If you are using one of the accepted formats (column labels, etc.), and you have made no manual changes to the structure file format yourself, then this method will work for you. Our tool is programmed to recognize which columns correspond to each parameter (depending on the program's format) and automatically converts the data to the new format accordingly.' Looks that automatic conversion by PDB was broken by recent change in CCP4 default naming of mtz columns. Please note that authors of a deposit do not get file with structure factors converted from mtz to cif format. They are asked if pdb and mmcif files with coordinates are correct, but this is not a case for structure factors. Maybe it is worth to change PDB policy and ask PDB to send structure factors together with coordinates for authors’ approval. I will let you know what was source of the error when it will be clarified with PDB. Your suggestion to deposit diffraction images is very good. Actually CSGID puts the server that will make accessible all diffraction images for PDB deposits. You (and all intrested persons) will get access to 3ftt diffraction images next week. Best regards, Maks Chruszcz I do not know if it will be posted on CCP4BB. I have problem with authorization. - End forwarded message - -- *** * * * Dr. Martyn Winn * * * * STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. * * Tel: +44 1925 603455E-mail: martyn.w...@stfc.ac.uk* * Fax: +44 1925 603825Skype name: martyn.winn * * URL: http://www.ccp4.ac.uk/martyn/ * ***
[ccp4bb] postdoctoral position at King's College London
Dear ccp4bb readers, --- King's College London Cardiovascular Division and Randall Division of Cell and Molecular Biophysics A postdoctoral position is immediately available for a highly motivated molecular biologist/biochemist with an interest in structural biology (macromolecular crystallography and NMR) to perform structure-function studies of proteins and protein complexes involved in control of reactive oxygen species (ROS) in redox signalling. The position is supported by a British Heart Foundation Centre of Excellence scheme and is part of a research collaboration between the groups of Drs Sasi Conte and Roberto Steiner (Randall Division of Cell and Molecular Biophysics) and Professor Ajay Shah (Cardiovascular Division). Excellent infrastructure support is available to carry out the project. The salary is Grade 6, SP31 which translates into: £30,594 plus £3,323 (London weighting). The position is initially funded for 18 months. For informal enquiries please contact: roberto.stei...@kcl.ac.uk http://www.kcl.ac.uk/schools/medicine/research/cardio/pi/shah-a.html http://www.kcl.ac.uk/schools/biohealth/research/randall/ --- Roberto Steiner Randall Division of Cell and Molecular Biophysics New Hunt's House King's College London Guy's Campus London, SE1 1UL Phone +44 (0)20-7848-8216 Fax +44 (0)20-7848-6435 e-mail roberto.stei...@kcl.ac.uk
[ccp4bb] postdoctoral position at King's College London (2)
Dear ccp4bb readers, £1,000 worth correction on my previous postdoc ad: London weighting is £2,323 and not £3,323. Apologies (all the rest is correct..), Roberto On 9 Mar 2009, at 09:49, Roberto Steiner wrote: Dear ccp4bb readers, --- King's College London Cardiovascular Division and Randall Division of Cell and Molecular Biophysics A postdoctoral position is immediately available for a highly motivated molecular biologist/biochemist with an interest in structural biology (macromolecular crystallography and NMR) to perform structure-function studies of proteins and protein complexes involved in control of reactive oxygen species (ROS) in redox signalling. The position is supported by a British Heart Foundation Centre of Excellence scheme and is part of a research collaboration between the groups of Drs Sasi Conte and Roberto Steiner (Randall Division of Cell and Molecular Biophysics) and Professor Ajay Shah (Cardiovascular Division). Excellent infrastructure support is available to carry out the project. The salary is Grade 6, SP31 which translates into: £30,594 plus £3,323 (London weighting). The position is initially funded for 18 months. For informal enquiries please contact: roberto.stei...@kcl.ac.uk http://www.kcl.ac.uk/schools/medicine/research/cardio/pi/shah-a.html http://www.kcl.ac.uk/schools/biohealth/research/randall/ --- Roberto Steiner Randall Division of Cell and Molecular Biophysics New Hunt's House King's College London Guy's Campus London, SE1 1UL Phone +44 (0)20-7848-8216 Fax +44 (0)20-7848-6435 e-mail roberto.stei...@kcl.ac.uk --- Roberto Steiner Randall Division of Cell and Molecular Biophysics New Hunt's House King's College London Guy's Campus London, SE1 1UL Phone +44 (0)20-7848-8216 Fax +44 (0)20-7848-6435 e-mail roberto.stei...@kcl.ac.uk
Re: [ccp4bb] missing carboxyl oxygen
CCP4 bulletin board CCP4BB@JISCMAIL.AC.UK wrote on 03/07/2009 07:11:20 PM: Hi All, Sorry if this is a trivial question. I'm refining my first structure at 2.1 A resolution. There is no density for the main chain carboxyl oxygen of a residue even at 0.5 sigma level in 2FoFc map. The FoFc map shows a negative density when I place the oxygen, satisfying the standard geometry condition. Could someone tell me what to do in this situation. Should I make the occupancy of the oxygen zero. Any comments would be gratefully appreciated. Thanks very much. John Peter Hi John Peter - Is there a positive density peak on the other side of the peptide group? It's quite common to have the peptide bond flipped 180 degrees from the way it should be. The nitrogen atom doesn't move much, so you usually don't see difference density for it, but the oxygen atom moves a good deal and gives difference density peaks. (As others have noted, I'm assuming you meant carbonyl oxygen - the one in a peptide bond - not carboxylate oxygen - the one at the C terminus.) I don't really know about other refinement programs except O, but there should be some sort of flip peptide command - if not, you'll need to move things manually. Just so we're clear, I'm talking about turning this: H Ca-N-C-Ca O into: O Ca-N-C-Ca H Check hydrogen bonding patterns to see if the flipped peptide group makes sense chemically, of course. - Matt -- Matthew Franklin , Ph.D. Senior Scientist, ImClone Systems, a wholly owned subsidiary of Eli Lilly Company 180 Varick Street, 6th floor New York, NY 10014 phone:(917)606-4116 fax:(212)645-2054 Confidentiality Note: This e-mail, and any attachment to it, contains privileged and confidential information intended only for the use of the individual(s) or entity named on the e-mail. If the reader of this e-mail is not the intended recipient, or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that reading it is strictly prohibited. If you have received this e-mail in error, please immediately return it to the sender and delete it from your system. Thank you.
