[ccp4bb] Postdoctoral position in computational structural biology
Postdoctoral position in computational structural biology Dept. of Medical Biochemistry and Biophysics, Karolinska Institutet A postdoctoral position is available immediately in the Molecular Structural Biology group at the Karolinska Institutet in Stockholm (http://phillips.mbb.ki.se/). The position is initially available until 31 Dec. 2015 (approx. 1 1/2 years) with the possibility of extension. We are seeking a motivated scientist to join an ongoing research project on development new tools for real space refinement, description of model dynamics, ligand binding and validation in macromolecular crystallography. This project is carried out in close collaboration with scientists in Germany (BESSY, Berlin). Applicants should have a background in computational biology, bioinformatics, computational science or a related field with knowledge of structural biology and X-ray crystallography. Programming skills and a genuine interest in structural biology are required. The successful candidate must have a doctoral degree, and should possess good written and oral communication skills. For further enquiries please contact Bernhard Lohkamp by email. Interested candidates should apply before the 14th March 2014, by sending a cover letter, CV, and names and e-mail addresses of two references to: Dr. Bernhard Lohkamp Div. of Molecular Structural Biology Dept. of Medical Biochemistry and Biophysics Karolinska Institutet SE-17177 Stockholm Sweden e-mail: Bernhard.Lohkamp(at)ki.se phone: +46 8 5248 7651, fax: +46 8 32 7626 -- *** Dr. Bernhard Lohkamp Associate Professor/Docent Div. Molecular Structural Biology Dept. of Medical Biochemistry and Biophysics (MBB) Karolinska Institutet S-17177 Stockholm Sweden phone: (+46) 08-52487651 fax: (+46) 08-327626 email: Bernhard.Lohkamp(at)ki.se
[ccp4bb] Post with Jane Endicott and Martin Noble at Newcastle University
Dear BBers, I’d like to draw your attention to a post available from immediately until March 2016 working on interdisciplinary structural biology of CDK-containing complexes involved in regulating transcription and/or the cell-cycle. The post, which will be held at the Northern Institute for Cancer Research, provides an opportunity to blend X-ray crystallography with techniques spanning the biophysical to the cell biological. The closing date for applications, which should deb made therough the Newcastle University website, is 2nd March 2014. Job details are available at: https://www15.i-grasp.com/fe/tpl_newcastle02.asp?newms=jjid=52465aid=14216 I found this by googling “A1762R” and Newcastle Informal enquiries can be made to me offline. Best wishes, Martin
Re: [ccp4bb] I/sigmaI or I/sigmaI
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Calculate_average_I/sigma_from_.sca_file Qixu Cai Email: caiq...@gmail.com School of Life Sciences, Xiamen University, Fujian, China **from thunderbird** On 02/13/2014 12:20 AM, Ronald E Stenkamp wrote: How did people get I/sigmI when using HKL2000? Ron On Wed, 12 Feb 2014, Phil Evans wrote: I/sigmaI On 12 Feb 2014, at 11:43, Cai Qixu caiq...@gmail.com wrote: Dear all, Does the I/sigmaI in “Table 1” mean for I/sigmaI or I/sigmaI ? Thanks for your answer. Best wishes, Qixu Cai
[ccp4bb] Postdoctoral position in structural biology at Stockholm University
I'm posting this on behalf of Prof. Pål Stenmark. Please direct all correspondence regarding this position to the email specified below (struct...@dbb.su.se). Cheers, Ronnie Berntsson The Stenmark group study novel cancer targets involved within human nucleotide metabolism. This project is part of a large interdisciplinary research collaboration, with the goal to develop new therapeutics and take them all the way to human trials. This ambitious, but also achievable, goal depends on the joint efforts of several research groups, spanning all the way from basic science to the clinic. We use structure based drug design and fragment based drug discovery, in close collaboration with the organic chemistry team. Furthermore we elucidate the substrate specificity and catalysis of these enzymes using biochemistry, biophysics and structural biology. We now have an opening for a talented postdoc with expertise in macromolecular crystallography. The successful applicant will join a young team to take on these challenging tasks in a stimulating environment. The ideal candidate holds a PhD in structural biology, biochemistry, or a related field, with a proven track record in macromolecular crystallography. Experience in structure based drug design is advantageous. Fluency in English, both written and spoken and an ability to work in close collaborations, as well as individually, will be expected. Interested candidates are encouraged to apply by sending CV, a brief statement describing research experience, scientific interests and the names of at least two professional references to struct...@dbb.su.se. Informal inquiries can also be made to the same email address. --- Pål Stenmark, PhD Associate Professor Department of Biochemistry and Biophysics Stockholm University 10691 Stockholm Sweden Phone: +46-8-163729 www.dbb.su.se
[ccp4bb] Table in NSMB
Dear all, I'm filling out my table for NSMB, about a structure of protein ligand bound to a receptor. They ask for 3 different lines regarding number of atoms bfactor. 1) Protein 2) Ligand/Ion 3) Water. Does my protein ligand belong to Protein or Ligand/Ion? Thanks,
Re: [ccp4bb] Table in NSMB
On Tue, Feb 18, 2014 at 8:19 AM, Jan van Agthoven janc...@gmail.com wrote: I'm filling out my table for NSMB, about a structure of protein ligand bound to a receptor. They ask for 3 different lines regarding number of atoms bfactor. 1) Protein 2) Ligand/Ion 3) Water. Does my protein ligand belong to Protein or Ligand/Ion? Why not list them each explicitly? In my experience the recommended table of crystallography statistics for most journals is just a suggestion, not a strict format. If you leave out information they might complain, but surely they won't object if you include additional details. (They usually just exile it to the unformatted supplementary materials anyway.) -Nat
Re: [ccp4bb] Table in NSMB
Hi Jan - I believe that ligand in this case refers to small molecule ligands, e.g. ATP or NADPH. If your ligand is a protein or even a peptide, I think it belongs in the protein category. (Thus, you may have no ligand atoms, unless you have bound sulfate, PEG, etc.) - Matt On 2/18/14 11:19 AM, Jan van Agthoven wrote: Dear all, I'm filling out my table for NSMB, about a structure of protein ligand bound to a receptor. They ask for 3 different lines regarding number of atoms bfactor. 1) Protein 2) Ligand/Ion 3) Water. Does my protein ligand belong to Protein or Ligand/Ion? Thanks, -- Matthew Franklin, Ph. D. Senior Scientist New York Structural Biology Center 89 Convent Avenue, New York, NY 10027 (212) 939-0660 ext. 9374
Re: [ccp4bb] Table in NSMB
I would have thought that ligands are ligand/ion?. What I have just done with a recent structure and I await the reviewers noticing or not is include the ethylene glycol from the cryo that I can (probably) see in a solvent (rather than water) atom number and bfactor line along with water (which probably includes sodium/chloride ions etc misassigned as water) rather than as ligand. I would suggest that Protein, Ligand, Solvent/Ion is probably a better break down than Protein, Ligand/Ion and Water alhtough if I had an ion associated with a ligand Mg on my ATP I would have that in ligand rather than ion. What then should you do if there are waters then visible on the ion??? I guess the question that this is really asking is whether the Bfactor of what you are describing as a significant ligand in your discussion is well ordered compared to the surrounding protein. Gubbins filling out density peaks in the solvent area probably should not be included in that line. Best wishes Nick -- Prof Nicholas H. Keep Executive Dean of School of Science Professor of Biomolecular Science Crystallography, Institute for Structural and Molecular Biology, Department of Biological Sciences Birkbeck, University of London, Malet Street, Bloomsbury LONDON WC1E 7HX email n.k...@mail.cryst.bbk.ac.uk Telephone 020-7631-6852 (Room G54a Office) 020-7631-6800 (Department Office) Fax 020-7631-6803 If you want to access me in person you have to come to the crystallography entrance and ring me or the department office from the internal phone by the door
Re: [ccp4bb] Table in NSMB
Sorry misread the initial post. Yes a protein ligand should be in the protein but you could give B factor number for each chain- my comments about what goes in ligand and what in solvent may be of general interest/comment Nick -- Prof Nicholas H. Keep Executive Dean of School of Science Professor of Biomolecular Science Crystallography, Institute for Structural and Molecular Biology, Department of Biological Sciences Birkbeck, University of London, Malet Street, Bloomsbury LONDON WC1E 7HX email n.k...@mail.cryst.bbk.ac.uk Telephone 020-7631-6852 (Room G54a Office) 020-7631-6800 (Department Office) Fax 020-7631-6803 If you want to access me in person you have to come to the crystallography entrance and ring me or the department office from the internal phone by the door
[ccp4bb] AW: [ccp4bb] Table in NSMB
If the ligand is a bona fide protein (more than a few amino acids and its own stable fold), I would include it under protein. However it is a matter of taste and, as Nat says, it will probably be dumped in the supplementary materials to be never looked at again. Herman Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Nat Echols Gesendet: Dienstag, 18. Februar 2014 17:29 An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] Table in NSMB On Tue, Feb 18, 2014 at 8:19 AM, Jan van Agthoven janc...@gmail.commailto:janc...@gmail.com wrote: I'm filling out my table for NSMB, about a structure of protein ligand bound to a receptor. They ask for 3 different lines regarding number of atoms bfactor. 1) Protein 2) Ligand/Ion 3) Water. Does my protein ligand belong to Protein or Ligand/Ion? Why not list them each explicitly? In my experience the recommended table of crystallography statistics for most journals is just a suggestion, not a strict format. If you leave out information they might complain, but surely they won't object if you include additional details. (They usually just exile it to the unformatted supplementary materials anyway.) -Nat
[ccp4bb] Data Analysis Scientist Post at Diamond Light Source
We are looking for a high calibre software scientist to join our scientific software group to work on visualization and analysis of diffraction and spectral data. The group have the responsibility for the provision of advanced data evaluation, analysis and visualization software applications for users of Diamond. Full details can be found here: http://www.diamond.ac.uk/Home/Jobs/Current/DIA0905_CH.html Regards, Alun ___ Alun Ashton, alun.ash...@diamond.ac.uk Tel: +44 1235 778404 Group Leader - Data Analysis Software,www.diamond.ac.uk Diamond Light Source, Chilton, Didcot, Oxon, OX11 0DE, U.K. -- 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] AW: [ccp4bb] Table in NSMB
Thanks for all responses, Yes I'll keep my ligand in the protein section, and will add extra information regarding the ligand/receptor. They actually asked for separate b-factors during review, so I guess they'll be willing to see it in the final table. Jan 2014-02-18 11:39 UTC-05:00, herman.schreu...@sanofi.com herman.schreu...@sanofi.com: If the ligand is a bona fide protein (more than a few amino acids and its own stable fold), I would include it under protein. However it is a matter of taste and, as Nat says, it will probably be dumped in the supplementary materials to be never looked at again. Herman Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Nat Echols Gesendet: Dienstag, 18. Februar 2014 17:29 An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] Table in NSMB On Tue, Feb 18, 2014 at 8:19 AM, Jan van Agthoven janc...@gmail.commailto:janc...@gmail.com wrote: I'm filling out my table for NSMB, about a structure of protein ligand bound to a receptor. They ask for 3 different lines regarding number of atoms bfactor. 1) Protein 2) Ligand/Ion 3) Water. Does my protein ligand belong to Protein or Ligand/Ion? Why not list them each explicitly? In my experience the recommended table of crystallography statistics for most journals is just a suggestion, not a strict format. If you leave out information they might complain, but surely they won't object if you include additional details. (They usually just exile it to the unformatted supplementary materials anyway.) -Nat
Re: [ccp4bb] create a lower resolution data set by truncating a high resolution data
I agree that simple truncation is not a great way to create a lower-resolution dataset. However, neither is simply applying a B factor. It is harder than that to fool the downstream phasing programs you will probably be running. That said, the combination of a B factor with a resolution cutoff does effectively suppress Fourier ripples, which are always there, but the rms error they contribute to the map is just the rms value of all structure factors beyond the resolution limit, divided by the cell volume. So, if you apply a big enough B factor everything beyond the resolution limit will be essentially zero. I recommend as a rule of thumb combining a resolution cutoff of d with the B factor taken from the general trend of the PDB: B = 4*d^2+12 where B is the average atomic B factor from structures claiming resolution d. That is, if you download every PDB entry with a resolution of 2 A, and then take the average value of the B factor of all the atoms in all those files, you'll get ~28. So, if you start with a 1.8 A data set, chances are it will have an average atomic (aka Wilson) B factor of 25. If you apply a B-factor of 45 to the observed data with CAD, then the Wilson B will become 70, and the structure factors at 3.8 A will now be about the same average magnitude as the 1.8 A data were in the original set. So, you can now cut of the data at 3.8 A and not change the maps in any serious way. The maps will look like 3.8A data. This is actually how I made my resolution example movie: http://bl831.als.lbl.gov/~jamesh/movies/index.html#reso This treatment is fine for map calculation, but if you are trying to test the effect of resolution on something more complicated, like phasing or refinement, you will run into problems. For example, if you calculate the isomorphism of the old 1.8 A dataset to the new 3.8 A dataset with SCALEIT, you will find the R-factor between them is zero. This is because the standard procedure for calculating an R factor is to scale the two datasets together first, and scaling generally implies fitting a B factor as well as an overall scale. In this case the relative B factor (aka scaling B factor) will be 45, the number you gave to CAD above. So, if you take a coordinate file refined against the 1.8A data and refine it against your new 3.8A data, all the atomic B factors will simply increase by 45, the atoms will hardly move, and the R and Rfree will be a little better than they were with the 1.8A data (because the noisy high-angle stuff is now cut off).You will also find that the quality of the anomalous differences are largely unaffected by applying a B factor. This is because if you scale all the Fs and sigFs on a Harker diagram by a constant, it doesn't change the phase. Yes, the refined B factor of the heavy atom sites will increase by 45, but the phasing power, etc will be the same. I imagine this is not what you had in mind? Clearly, you have to add some noise in addition to applying the B factor and cutting off the resolution. But what sort of noise? You have the sigmas from the original dataset, but those are not noise, they are an estimate of the noise that is already there, hidden in the value of F itself. Nevertheless, it's all you've got, so it is helpful to consider where SIGF comes from. SIGF begins its life as the estimate of the number of photons that were counted in a given spot area on the detector. The error in the background-subtracted spot intensity is (at least) the square root of the _total_ number of photons that hit in the spot region. That is, background plus spot. You might have a hope of reconstructing the spot intensity using F^2 and some sort of overall scale factor (related to the illuminated crystal volume, beam intensity, etc), but the background level is lost in the scaling and mergeing process. After all, different observations of the same or symmetry-equivalent hkls will generally have different background levels. They also have different intensities, due to the Lorentz and polarization factors. This latter fact is often neglected, but if you take the average value of the Lp factor (Holton Frankel, 2010) vs resolution for a typical data collection situation (wavelength = 1A, resolution up to ~1.5A), you will find that it is a fairly straight line: L*p*frac_obs ~ 1.55*d where d is the d spacing of the spot. So, yes, high-angle spot intensities are weaker than low-angle spot intensities not just because F is smaller, but because d is smaller as well, and the actual spot intensities on the detector are not proportional to F^2, but rather d*F^2. On average. Most data sets have a few hkls that by chance are very close to the rotation axis and stay in contact with the Ewald sphere for the entire rotation range. These will accumulate a VERY large number of counts. On the other hand, a spot that appears on the equator won't register very many
[ccp4bb] High Salt Cryo
Hi all, I'm looking for a cryo condition for high NaCl (3+ M) crystallization condition. I would do it the proper way, but our beam/cryostream is down. I've tried a bunch of things at the moment. Ethylene glycol and PEG 400 nuke the crystals immediately even at low concentrations. Prolonged exposure to glycerol and sucrose starts to break them down so I'm thinking that the diffraction will probably suffer. I can't find any reports of NaCl's viability as a cryosalt. I've got Paratone/Paraffin oil/Mitegen's LV cryo oil on tap but I was hoping to not put all my eggs in one basket. I tried the ISRDB database through archive.com without any luck (no search function). I've gone to the PDB searching for similar crystallization conditions and looked up the papers for their cryos, but they are all glycerol. Google gives me the same. I thought I'd see if anyone on the bb has an anecdotal this worked for us story. I would love to hear it. Thank you for your time, Katherine -- Nil illegitimo carborundum* - *Didactylos
[ccp4bb] Symmetry problem
Dear, Does anyone know how to merge two molecules with different symmetry? I will explain: I have done the molecular replacement using the domains of the molecules separately, now I have to put all together, however they have a different symmetry. I will appreciate any kind of help. Regards, Mônika -- __o _`\,_ (*)/ (*) -+-+-+-+-+-+- * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * ...E tudo muda... * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
Re: [ccp4bb] High Salt Cryo
How about a short swish in well solution + 25-30% glucose? Doesn't take long to cryoprotect, just a quick sufrace coat. Sodium malonate? We just froze some really fragile crystals from 1.8 M sodium formate in 3 M sodium malonate and they held up really well. (Still didn't improve their diffraction, though--but at least they did not crack or disintegrate.) ___ Roger S. 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 2/18/2014 1:08 PM, Katherine Sippel wrote: Hi all, I'm looking for a cryo condition for high NaCl (3+ M) crystallization condition. I would do it the proper way, but our beam/cryostream is down. I've tried a bunch of things at the moment. Ethylene glycol and PEG 400 nuke the crystals immediately even at low concentrations. Prolonged exposure to glycerol and sucrose starts to break them down so I'm thinking that the diffraction will probably suffer. I can't find any reports of NaCl's viability as a cryosalt. I've got Paratone/Paraffin oil/Mitegen's LV cryo oil on tap but I was hoping to not put all my eggs in one basket. I tried the ISRDB database through archive.com http://archive.com without any luck (no search function). I've gone to the PDB searching for similar crystallization conditions and looked up the papers for their cryos, but they are all glycerol. Google gives me the same. I thought I'd see if anyone on the bb has an anecdotal this worked for us story. I would love to hear it. Thank you for your time, Katherine -- Nil illegitimo carborundum/- /Didactylos
[ccp4bb] stereo emitter
Colleagues, I was happily using my NuVision 60GX emitter with Quadro FX1400 graphics card for number of years on CRT and recently something went bad and image will flip regularly sending front to back and vice versa. First I thought the card went bad but after installing new one nothing changed. I'm suspecting the emitter now and wondering if now there are solutions better than those emitters. Hopefully it is not too off topic. Thanks in advance for suggestions. Vaheh Oganesyan, PhD Antibody development and protein engineering 1 MedImmune Way, Gaithersburg, MD 20878 www.medimmune.comhttp://www.medimmune.com/ [logo1] To the extent this electronic communication or any of its attachments contain information that is not in the public domain, such information is considered by MedImmune to be confidential and proprietary. This communication is expected to be read and/or used only by the individual(s) for whom it is intended. If you have received this electronic communication in error, please reply to the sender advising of the error in transmission and delete the original message and any accompanying documents from your system immediately, without copying, reviewing or otherwise using them for any purpose. Thank you for your cooperation. inline: image002.jpg
[ccp4bb] Reminder: International Summer School of Crystallography 2014 DESY Hamburg
Dear ccp4bb, this is a gentle reminder for the application deadline of the International Summer School of Crystallography, held in Hamburg, Germany. The deadline will be the 28th of February. For further information please visit our website: http://conferences.cfel.de/issc14 In case you are interested in applying, please do not forget about the two step process of registering on the INDICO website AND sending your CV via email. Thank you very much and sorry for the spam. With kind regards Cornelius Gati Original Invitation: We are pleased to announce the first International Summer School of Crystallography at the Center for Free-Electron Laser Science at DESY, Hamburg (D). As part of the International Year of Crystallography 2014, Prof. Carmelo Giacovazzo will lecture on the basics of crystallography, as well as, the basics of modern phasing methods in protein crystallography covering basic mathematical understanding of crystallographic point and space groups, diffraction experiments, structure factor calculations, systematic absences, determination of space groups and many additional topics. Participants will also learn modern applications of protein crystallography using advanced light sources, such as 3rd generation synchrotron and XFELs. The summer school program is geared for PhD students working in the field of crystallography, but exceptions for motivated PostDocs and MSc students can be made. The course will mostly cover mathematical background of crystallography, hence we are looking for students, having a (bio)physics background. This will NOT be a workshop covering protein crystallographic programs but rather will be theory oriented. Accepted applicants will be asked to pay a registration fee in the amount of 100 EUR (includes coffee breaks and lunch). In addition, participants will have to pay for their own travel costs, unfortunately, we do not have any travel grants. The application deadline is on the 28th of February, 2014. Notification of accepted applicants will be sent during March 2014. Places and accommodation are limited to 30 students in total. The application is a two step process: - Go to https://indico.desy.de//event/ISSC14 and complete the application form (located at the bottom of the page). - Applicants must provide a motivation letter, as well as, a CV, directly to the organizer Cornelius Gati (cornelius.g...@cfel.de). _ Cornelius Gati PhD student - Prof. Chapman Center for Free-Electron Laser Science / DESY Building 99, Room 03.073 22607 Hamburg
Re: [ccp4bb] stereo emitter
Did your OS/nvidia driver get upgraded? There's a bug in all of the modern nvidia drivers that cause this on the quadro 1300/1400 series. It works fine with the older nvidia drivers, e.g. 173.14.31 (note the legacy 9x.xx.xx drivers have the same problem). We're still able to use that version of the nvidia driver with centos/rhel 6.2. If you update past that version with 6, make sure not to update any of the xorg packages. The newer xorg packages have a new ABI which will only work with newer nvidia drivers, which will then cause the stereo flipping bug. On Tue, Feb 18, 2014 at 3:59 PM, Oganesyan, Vaheh oganesy...@medimmune.comwrote: Colleagues, I was happily using my NuVision 60GX emitter with Quadro FX1400 graphics card for number of years on CRT and recently something went bad and image will flip regularly sending front to back and vice versa. First I thought the card went bad but after installing new one nothing changed. I'm suspecting the emitter now and wondering if now there are solutions better than those emitters. Hopefully it is not too off topic. Thanks in advance for suggestions. *Vaheh Oganesyan, PhD* *Antibody development and protein engineering* *1 MedImmune Way, Gaithersburg, MD 20878* *www.medimmune.com http://www.medimmune.com/* *[image: logo1]* To the extent this electronic communication or any of its attachments contain information that is not in the public domain, such information is considered by MedImmune to be confidential and proprietary. This communication is expected to be read and/or used only by the individual(s) for whom it is intended. If you have received this electronic communication in error, please reply to the sender advising of the error in transmission and delete the original message and any accompanying documents from your system immediately, without copying, reviewing or otherwise using them for any purpose. Thank you for your cooperation. inline: image002.jpg
[ccp4bb] Number unique reflections (all)
Dear Users, Which value in scala log file indicate the Number of unique reflection (all) that needs to be entered during the deposition of structure in RCSB. Thank you Regards Kavya -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.
