Re: [ccp4bb] How to make an unnatural amino acid ligand?
Your solution sounds good. However, another way to skin this cat could be to define the unnatural residue as an amino acid residue and link it up to the other amino acid residues using the standard peptide bond description -- which, I believe, should be picked up automatically if the unconventional residue is defined as D-peptide in the _chem_comp.group in the cif dictionary file and has its backbone atoms named conventionally (or defining a TRANS link in the pdb file should fix that), i.e treat the ligand as a polypeptide chain with a nonconventional residue in it. Might be more fiddly to start with but cleaner on the long run? As for the text editing solution: JLigand seems to be the fashionable tool of choice for defining links between residues these days. > -- AstraZeneca UK Limited is a company incorporated in England and Wales with registered number: 03674842 and a registered office at 2 Kingdom Street, London, W2 6BD. Confidentiality Notice: This message is private and may contain confidential, proprietary and legally privileged information. If you have received this message in error, please notify us and remove it from your system and note that you must not copy, distribute or take any action in reliance on it. Any unauthorised use or disclosure of the contents of this message is not permitted and may be unlawful. Disclaimer: Email messages may be subject to delays, interception, non-delivery and unauthorised alterations. Therefore, information expressed in this message is not given or endorsed by AstraZeneca UK Limited unless otherwise notified by an authorised representative independent of this message. No contractual relationship is created by this message by any person unless specifically indicated by agreement in writing other than email. Monitoring: AstraZeneca UK Limited may monitor email traffic data and content for the purposes of the prevention and detection of crime, ensuring the security of our computer systems and checking Compliance with our Code of Conduct and Policies. -Original Message- > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of > Ian Clifton > Sent: 09 January 2013 12:44 > To: CCP4BB@JISCMAIL.AC.UK > Subject: [ccp4bb] How to make an unnatural amino acid ligand? > > I need to make dictionaries for a ligand that includes an unnatural > amino acid (D chirality, and unnatural side‐chain) amongst a short > sequence of natural amino acids. Sounds easy, but how to do it? I’m > thinking of first making my unnatural amino acid in isolation, then > using an editor to fix up the generated dictionaries to have the > correct > partial charges etc. for the main‐chain atoms, using standard > dictionary > entries as a template. Is there a better or sounder way to do it? > > Thanks, > -- > Ian ◎
[ccp4bb] How to make an unnatural amino acid ligand?
I need to make dictionaries for a ligand that includes an unnatural amino acid (D chirality, and unnatural side‐chain) amongst a short sequence of natural amino acids. Sounds easy, but how to do it? I’m thinking of first making my unnatural amino acid in isolation, then using an editor to fix up the generated dictionaries to have the correct partial charges etc. for the main‐chain atoms, using standard dictionary entries as a template. Is there a better or sounder way to do it? Thanks, -- Ian ◎
[ccp4bb] EMBO Practical Course in “High throughput Protein Production and Crystallization"
Dear All, A gentle reminder that the deadline for the practical course in "High-troughtput Protein Production and Crystallisation" is 31st January. For more details, please see below. For information: http://events.embo.org/13-htp-protein/index.html For Registration:http://events.embo.org/13-htp-protein/application.html With best Regards, Isabel On 14 Oct 2012, at 13:09, Dr. Isabel De Moraes wrote: > Apologies for the previous email, almost impossible to read. Hopefully, > this one looks better. > > > Dear All, > > We are happy to announce an EMBO Practical Course in “High throughput > Protein Production and Crystallisation” > > The overall aim of the course will be to review the state-of-the-art in HTP > structural biology with an emphasis on methods to study complex targets, > including membrane proteins. > > The course is aimed at early career post-doctoral scientists and PhD students > in their second or third year of study. > > > Practical training will be provided in: > Structural bioinformatics > High throughput cloning & expression in E. coli and mammalian cells > Protein purification and biophysical characterisation > High throughput protein crystallization > High throughput data collection at synchrotrons > > Speakers: > Lawrence Kelley - Imperial College London > David Drew - Imperial College London > Imre Berger - EMBL Grenoble > Chris Tate - University of Cambridge > Naomi Chayen Imperial College London > Opher Gileadi - University of Oxford > Renaud Vincentelli - AFMB, Marseille > Rob Meijers - EMBL, Hamburg > Robert Gilbert - University of Oxford > Scott Lesley - Genomics Institute of the Novartis Research Foundation- USA > Joanne Nettleship - University of Oxford > Louise Bird - University of Oxford > Jon Diprose - University of Oxford > Martin Walsh - Diamond Light Source > Isabel De Moraes - Imperial College, London > > > Venue: Research Complex at Harwell – UK > Date: 15-23 May 2013 > Registration deadline: JANUARY 31ST, 2013 > Total Number of Participants limited to: 20 participants > For information: http://events.embo.org/13-htp-protein/index.html > For Registration: http://events.embo.org/13-htp-protein/application.html > > The organizers > Ray Owens (OPPF-UK) > Isabel Moraes (MPL) > Martin Walsh (Diamond) > > > > > -- > > This e-mail 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 authorised 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 the > e-mail. > > Any opinions expressed within this e-mail are those of the individual and not > necessarily of Diamond Light Source Ltd. > > Diamond Light Source Ltd. cannot guarantee that this e-mail 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. > > Diamond Light Source Limited (company no. 4375679). Registered in England and > Wales with its registered office at Diamond House, Harwell Science and > Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom > > > > > > > > > -- This e-mail 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 authorised 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 the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail 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. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom
Re: [ccp4bb] A FREE course in High-throughput Protein Production and Crystallisation
Dear All, I would like to retract this post since the information is wrong. My sincerely apologies. I will send the right information shortly. Isabel On 9 Jan 2013, at 11:16, Dr. Isabel De Moraes wrote: > Dear All, > > A gentle reminder that the deadline for the practical course in > "High-troughtput Protein Production and Crystallisation" is 20th January. > > For more details, please see below. > > http://www.oppf.ox.ac.uk/OPPF/public/courses/oppfmpl2011.jsp > > With best Regards, > Isabel > > > > > On 2 Dec 2010, at 15:52, Dr. Isabel De Moraes wrote: > >> >> Dear Structural Biologists, >> >> The Oxford Protein Production Facility (OPPF-UK) and The Membrane Protein >> Laboratory (MPL) at Diamond are offering a >> "hands-on" course in "High-throughput Protein Production and >> Crystallization". >> >> The course runs from 30th March to 7th April 2011 at and its aim is the >> review of the state-of-the-art in HTP structural biology >> with an emphasis on methods to study complex and 'difficult' targets, >> including membrane proteins. >> >> The course is FREE for participants from UK Academic Institutions. See flyer >> attached. >> >> For more information please look into the following link: >> http://www.oppf.ox.ac.uk/OPPF/public/courses/oppfmpl2011.jsp >> >> Deadline for applications is: 20th Janaury 2011. >> >> With Best Regards, >> Isabel Moraes >> >> >> >> >> Dr. Isabel De Moraes, MRSC >> >> Membrane Protein Laboratory Facilities Coordinator/Group Leader >> Membrane Protein Laboratory, >> Diamond Light Source Ltd, >> Harwell Science and Innovation Campus, >> Chilton, Didcot, Oxfordshire, >> OX11 ODE, UK >> >> Tel: 01235 778664 >> email: isabel.de-mor...@diamond.ac.uk >> --- >> >> >> > > > > > -- > > This e-mail 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 authorised 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 the > e-mail. > > Any opinions expressed within this e-mail are those of the individual and not > necessarily of Diamond Light Source Ltd. > > Diamond Light Source Ltd. cannot guarantee that this e-mail 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. > > Diamond Light Source Limited (company no. 4375679). Registered in England and > Wales with its registered office at Diamond House, Harwell Science and > Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom > > > > > > > > > -- This e-mail 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 authorised 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 the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail 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. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom
[ccp4bb] A FREE course in High-throughput Protein Production and Crystallisation
Dear All, A gentle reminder that the deadline for the practical course in "High-troughtput Protein Production and Crystallisation" is 20th January. For more details, please see below. http://www.oppf.ox.ac.uk/OPPF/public/courses/oppfmpl2011.jsp With best Regards, Isabel On 2 Dec 2010, at 15:52, Dr. Isabel De Moraes wrote: > > Dear Structural Biologists, > > The Oxford Protein Production Facility (OPPF-UK) and The Membrane Protein > Laboratory (MPL) at Diamond are offering a > "hands-on" course in "High-throughput Protein Production and > Crystallization". > > The course runs from 30th March to 7th April 2011 at and its aim is the > review of the state-of-the-art in HTP structural biology > with an emphasis on methods to study complex and 'difficult' targets, > including membrane proteins. > > The course is FREE for participants from UK Academic Institutions. See flyer > attached. > > For more information please look into the following link: > http://www.oppf.ox.ac.uk/OPPF/public/courses/oppfmpl2011.jsp > > Deadline for applications is: 20th Janaury 2011. > > With Best Regards, > Isabel Moraes > > > > > Dr. Isabel De Moraes, MRSC > > Membrane Protein Laboratory Facilities Coordinator/Group Leader > Membrane Protein Laboratory, > Diamond Light Source Ltd, > Harwell Science and Innovation Campus, > Chilton, Didcot, Oxfordshire, > OX11 ODE, UK > > Tel: 01235 778664 > email: isabel.de-mor...@diamond.ac.uk > --- > > > -- This e-mail 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 authorised 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 the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail 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. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom
[ccp4bb] Post-doctoral position at York Structural Biology Laboratory / Closing date: 15 January 2013
Dear All, a Postdoctoral Research Fellow position in structural biology / biochemistry of DNA-translocating molecular motors is available from February/March 2013. The position is funded by the Wellcome Trust, for 3 years, with potential extension, with the starting salary of £29,541 per year. Closing date for this post is Tuesday 15 January. Additional information and full details about the application process can be found at https://jobs.york.ac.uk/ Please don't hesitate to contact me directly for further information. Fred Antson / YSBL
[ccp4bb] Acta Cryst., Section A - Bragg centennial
http://journals.iucr.org/services/promotions/bragg.html
[ccp4bb] PhD and post-doc positions in Structural Biology at the Biozentrum Basel
PhD and post-doc positions in Structural Biology at the Biozentrum (University of Basel) Several positions are open in the Focal Areas of Structural Biology/Biophysics and Infection Biology. We are studying the molecular mechanisms of • c-di-GMP mediated signaling (diguanylate cyclases, phosphodiesterases, novel receptors) • FIC domain mediated AMP transfer (regulation, novel targets) in a comprehensive approach combining in vivo studies with X-ray structure analyses and biochemical/biophysical characterizations. For further information please consult http://www.biozentrum.unibas.ch/open-positions/ and the web pages of the participating groups (Jenal, Dehio, Schirmer). Highly motivated candidates with a strong interest in structural biology and with experience in molecular biology and protein chemistry are encouraged to apply. Experience in biophysical methods and protein crystallography is of advantage. Starting date by arrangement. Salary according to institutional guidelines. The Biozentrum is an internationally renowned Institute for basic Life Science Research. With over 400 employees from 30 countries, it is the largest Natural Science department of the University of Basel. About 30 research groups engage in interdisciplinary research and are in close contact with local Life Sciences industries. The working language at the institution is English. Please, send your CV, a brief description of previous research experience and the names of two references to: Prof. Tilman Schirmer Structural Biology, Biozentrum University of Basel Klingelbergstrasse 50-70 CH-4056, Basel, Switzerland tilman.schir...@unibas.ch
