[ccp4bb] Off topic: multidisciplinary international PhD program in Bolzano, Italy
Dear All, on behalf of the Faculty of Science and Technology of the Free University of Bolzano, I would like to announce our new multidisciplinary international PhD program The PhD official language is English. The research projects cover several scientific fields: ecology, hydrology, fruit science, agricultural chemistry, biology, structural biology, microbiology, etc., More information are available at the following links: PhD Programme in Management of Mountain Environment: http://www.unibz.it/en/sciencetechnology/progs/phdmountainenvironment/default.html http://www.unibz.it/en/sciencetechnology/progs/phdmountainenvironment/default.html topics of PhD Thesis: http://www.unibz.it/en/sciencetechnology/progs/phdmountainenvironment/thesis/default.html http://www.unibz.it/en/sciencetechnology/progs/phdmountainenvironment/thesis/default.html study program: http://www.unibz.it/en/sciencetechnology/progs/phdmountainenvironment/studyplan/default.html http://www.unibz.it/en/sciencetechnology/progs/phdmountainenvironment/studyplan/default.html application forms: http://www.unibz.it/en/public/research/phd/prospectivePhdstudents.html http://www.unibz.it/en/public/research/phd/prospectivePhdstudents.html The Free University of Bolzano: http://www.unibz.it/en/public/university/default.html Bolzano is located in the north of Italy not far from the best slopes for alpine ski, hiking and climbing and the Dolomites (UNESCO heritage site http://whc.unesco.org/en/list/1237/). please do not reply to this email but if you are interested please refer to the links provided or contact: science.technol...@unibz.it mailto:science.technol...@unibz.it Faculty of Science and Technology piazza Università, 5 39100 Bolzano Italy T: +39 0471 017000 F: +39 0471 017009 With my best regards Stefano Benini, Ph.D. Assistant Professor http://pro.unibz.it/staff2/sbenini/ http://pro.unibz.it/staff2/sbenini/ Bio-organic Chemistry Laboratory Faculty of Science and Technology Free University of Bolzano-Bozen Piazza Università, 1 39100 Bolzano, Italy ***
[ccp4bb] Lactose refinement
We are attempting REFMAC refinement of a protein structure which is complexed with lactose. One of the rings (the one oriented away from the protein) loses the chair conformation which is flagged as a problem by COOT check chiral volumes. Is there anything we can do to restrain the ring as a chair and would this necessarily be a valid move? ie why can't the conformation deviate from the norm? Rex Palmer Birkbeck College
Re: [ccp4bb] Lactose refinement
If your resolution is high enough to support a deviation, then I don't see why not. I would probably stick with a chair conformation unless you are at high resolution or have convincing other evidence for the deviation. What often works well (and is easiest) is to define the 4 atoms that are the seat of the chair as a plane in your restraints file. Manually position the outer atoms in the up and down positions of the chair, and then refine. Simple, and pretty effective. Good luck- Steve From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Rex Palmer Sent: Monday, August 16, 2010 12:45 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Lactose refinement We are attempting REFMAC refinement of a protein structure which is complexed with lactose. One of the rings (the one oriented away from the protein) loses the chair conformation which is flagged as a problem by COOT check chiral volumes. Is there anything we can do to restrain the ring as a chair and would this necessarily be a valid move? ie why can't the conformation deviate from the norm? Rex Palmer Birkbeck College Notice: This e-mail message, together with any attachments, contains information of Merck Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates Direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.
Re: [ccp4bb] Method to calculate the axis of an alpha helix
Fitting a helix is not trivial. If you have access to windows and mathematica, then you might try helfit. (Otherwise, you could implement the algorithm yourself and then share your code with the rest of us ;-) http://dx.doi.org/10.1016/j.compbiolchem.2008.03.012 James On Aug 15, 2010, at 12:29 AM, 商元 wrote: Dear all, I want to compare the conformational change of two similar structures, using one alpha helix as the reference. Then, how can I get a vector that can represent both the position and direction of the helix? Is there any well-known software can do this？ Or, should I build a cylinder model, with parameters [radius,bottom center(x1,y1,z1),top center(x1,y2,z2)], using the coordinates of C,C(alpha) and N to fit these parameters? Thanks for any suggestions Regards, Yuan SHANG
Re: [ccp4bb] Lactose refinement
Hello Rex, Just a few biologically-related ideas that may support modeling the planar conformation. I'm not sure if the protein you're working with has enzymatic activity, but is it possible that the ring strain is indeed real and may be a part of the reaction mechanism? Are any parts of the protein in contact with the flattened ring in such a way that they might be pushing or pulling the ring into the planar conformation? Best, Mike - Original Message - From: Rex Palmer rex.pal...@btinternet.com To: CCP4BB@JISCMAIL.AC.UK Sent: Monday, August 16, 2010 9:44:39 AM GMT -08:00 US/Canada Pacific Subject: [ccp4bb] Lactose refinement We are attempting REFMAC refinement of a protein structure which is complexed with lactose. One of the rings (the one oriented away from the protein) loses the chair conformation which is flagged as a problem by COOT check chiral volumes . Is there anything we can do to restrain the ring as a chair and would this necessarily be a valid move? ie why can't the conformation deviate from the norm? Rex Palmer Birkbeck College -- Michael C. Thompson Graduate Student Biochemistry Molecular Biology Division Department of Chemistry Biochemistry University of California, Los Angeles mi...@chem.ucla.edu
[ccp4bb] Postdoctoral position in Houston
A position has become available for a Post-doctoral Research Fellow in the Department of Pharmacology, at Baylor College of Medicine in Houston. The focus of our work is on structural and biochemical characterization of Serine/Threonine protein kinases. The successful candidate will be involved in the complete process of the project, solving the structure of proteins, as well as biochemically characterizing them. The ideal applicant will have a PhD in a biological science, or the equivalent in professional qualifications and experience, and have experience in molecular cloning, protein purification and x-ray crystallography. The laboratory is located in Texas Medical Center campus which provides an excellent environment for academia and research. The lab is well-equipped including robotics to facilitate overproduction and crystallization of proteins and has access to the Berkeley ALS beamline in the framework of the molecular biology consortium. Interested candidates must send three references and a resume to: d...@bcm.edu Update: There are two positions to be filled, one for an experienced crystallographer and a second for an experienced structural biologist interested in learning advanced crystallography techniques. Candidates with relevant knowledge are valued, and those applicants with excellent letters of recommendation are also highly regarded. Please do not reply to this email address; reply to d...@bcm.edu
