[ccp4bb] BMC second edition - request for comments
Dear Fellows and faithful readers of BMC: Many thanks again to the members of the community who have contributed so generously to BMC either with original ideas and comments during its 60 month gestation period or by careful reading and correcting many mistakes and outright errors during post-publication review. An errata page of over 500 entries is quite a sign of community involvement (and less so of my attention to detail). There have been quite some exciting and developments and consolidations of opinions in the field in recent years, and after half a decade, an update of the books seems to be justified. Many of you have also used the book in courses, and now is your chance to voice your critique, comments, and wishes for the second edition. You might express this either informally through email to me or in a more structured response to a simple template I have available on my web site. http://www.ruppweb.org/garland/BMC_2nd_Ed_suggestions.docx ANYTHING you wish to express is fair game, from didactic pointers to subject additions, to offers for review of newly suggested chapters; any material you may have that is worthwhile of/for a better or new figure, and of course, still plenty of typos or poor English (copy editors are human, too). From the pool of useful suggestions I will draw a winner receiving a copy of BMC2. Best wishes, BR Bernhard Rupp k.-k. Hofkristallamt Vista, CA 92084 001 (925) 209-7429 mailto:b...@ruppweb.org b...@ruppweb.org mailto:b...@hofkristallamt.org b...@hofkristallamt.org http://www.ruppweb.org/ http://www.ruppweb.org/ ---
Re: [ccp4bb] Coot Performance on Intel HD Graphics 5000
On Friday, 28 March, 2014 12:35:57 mesters wrote: The OpenGL performance is rather poor on intel HD chips up to and including the HD 4600 My experience differs. I have not seen dramatically different performance in practice between coot running on nvidia and the same program version running on Intel HD4000. Yes the OpenGL benchmarks are radically different, but that doesn't seem to reflect what is acheived by programs of interest. I notice more of a difference in Pymol performance, but not such a huge difference as to be a problem. but with the appearance of HD 5000 series (Iris HD) the Cinebench OpenGL score increased dramatically and even challenges many nvidia cards in performance. With these kind of intel chips you should be able to run Coot and Pymol smoothly and operate a passive 3D screen without problems. HOWEVER Good 2-core chips would be Core i5-4258U http://ark.intel.com/products/75990 or Core i5-4288U http://ark.intel.com/products/75991 with plenty of performance and, no surprice, found in many Apple computers (not the mini model, too bad...). Have not yet seen one mini-pc with these chips but this is probably due to need for active (and sometimes loud) cooling. One mini PC with a 4-core and Iris Pro Graphics is the new Gigabyte Brix Pro. Already the model with the low end chip Core i5-4570R http://ark.intel.com/products/76640 is EXTREMELY loud. I'm running a fanless i7-3517UE (Ivy Bridge). Totally silent. Ethan Even the NUC D54250WYKH with the fast 2-core i5-4250U becomes VERY VERY noisy during video demanding operations (tested by Hardware). The NUC DN2820FYKH with the celeron chip and HD 5000 is the only quiet model but very slow otherwise (intended for video playback at home). All in all, a choise between big, fast, full with air and quiet (good old desktop) or, small and very noisy (D54250WYKH) or, small, quiet and slow (DN2820FYKH) or, the smallest but expensive iMac (so no box on your desk) with the i5-4250U (no other all-in-one PCs with Iris Pro).. - Jeroen - Am 27.03.14 19:25, schrieb Dale Tronrud: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi all, My lab desktop PC broke and I'm looking into replacements. Being tired of the enormous tower (full of air) occupying much of my desk I looking at systems like the Intel NUC. These systems are too small for video cards so I'd be working with the integrated Intel graphics. Is the 5000 version of their graphics good enough for Coot to work nice? I am not interested in stereo. Dale Tronrud -BEGIN PGP SIGNATURE- Version: GnuPG v2.0.22 (MingW32) Comment: Using GnuPG with Thunderbird - http://www.enigmail.net/ iEYEARECAAYFAlM0bRwACgkQU5C0gGfAG11raACgrYltSYvIbVrVVLHxMfMPgfyn MJEAn1i2cUEedyXeYOtjIAw7HvAB2qeL =YIfi -END PGP SIGNATURE-
Re: [ccp4bb] sorry, sort of off topic
Thanks everyone for the info coming in.. another related: is there such a thing as a trade fair for crystallography... or should I attend the biggest conferences? ta again Dean From: Dean Derbyshire Sent: 27 March 2014 13:35 To: CCP4BB@JISCMAIL.AC.UK Subject: sorry, sort of off topic I'm after suggestions as to where the best place(s) for obtaining info on latest equipment - advances in techniques etc. Oh, for protein crystallisation and screening ahead of data collection! cheers Dean
[ccp4bb] microscope for checking for crystal growth
Hi, can somebody recommend a not too expensive microscope for checking for crystal growth? Thanks Ruth -- Jun.-Prof. Dr. Ruth Brenk Johannes Gutenberg-Universität Mainz Institut für Pharmazie und Biochemie Staudinger Weg 5 D-55128 Mainz Phone: +49 (6131) 39-25726 Fax: +49 (6131) 39-25670 http://www.pharmazie.uni-mainz.de/AK-Brenk
[ccp4bb] OSX 10.9.2
Hi, Does the ccp4 suite work with the latest OSX 10.9.2 operating system? Are there any known problems? Mirek
[ccp4bb] CCP4-6.4.0 Update 012
Dear CCP4 Users An update for the CCP4-6.4.0 series has just been released, consisting of the following changes * crank2 - New SAD phasing pipeline * monomer library - Corrections to OXY, PO4 and URE * imosflm - Update to version 7.1.1 Note that auto-updates work only with CCP4 6.4.0 series, therefore please upgrade if necessary. The Update Manager is now included in the package so you do not need to install it separately. In addition, all available updates will be installed automatically if you are using Setup Manager for CCP4 installation. Please report any bugs to c...@stfc.ac.uk. Many thanks for using CCP4. The CCP4 Core Team -- Scanned by iCritical.
Re: [ccp4bb] Coot Performance on Intel HD Graphics 5000
The OpenGL performance is rather poor on intel HD chips up to and including the HD 4600 but with the appearance of HD 5000 series (Iris HD) the Cinebench OpenGL score increased dramatically and even challenges many nvidia cards in performance. With these kind of intel chips you should be able to run Coot and Pymol smoothly and operate a passive 3D screen without problems. I beg to differ too. My experience with Coot running on both HD 4000 and 5000 series couldn't be better. In fact, I generally switch to HD4000 on my Macbook Pro every time I load Coot, because the slight difference in performance doesn't justify the massive increase in both temperature and power consumption. Presentation software like CCP4mg or pymol are much more resource-hungry than Coot, and still the HD series hold themselves up quite decently. Jon -- Dr Jon Agirre York Structural Biology Laboratory / Department of Chemistry University of York, Heslington, YO10 5DD, York, England http://www.york.ac.uk/chemistry/research/ysbl/people/research/jagirre/ +44 (0) 1904 32 8253
[ccp4bb] Protein crystallographer position at Heptares Therapeutics
I would like to draw your attention to the fact that Heptares Therapeutics is hiring a protein crystallographer. Please send your application in pdf format, to: h...@heptares.commailto:h...@heptares.com quoting reference number 2014/2B. The closing date for applications is 18th April 2014. Protein Crystallographer Heptares is a Drug Discovery Company located in Hertfordshire UK, working on G protein-coupled receptors (GPCRs) involved in CNS and metabolic diseases. Our unique structure-based approach to discovering therapeutic agents for these diseases relies on a proprietary approach to stabilise GPCRs, enabling their purification for structural and biophysical studies. We are currently seeking an experienced protein crystallographer to join the crystallography group working on GPCR structure determination to enable drug discovery efforts. Applicants should have a PhD in protein crystallography or related discipline and be familiar with purification of proteins from recombinant expression systems such as E. coli or baculovirus/insect cells, setting up crystallisation experiments including Lipidic Cubic Phase crystallisation, X-ray data collection, data processing, structure solution and refinement of novel structures and follow on complexes. Experience working with GPCRs or other membrane proteins would be an advantage. Experience of working in a drug discovery environment where structural studies are used to drive compound design and medicinal chemistry would also be of benefit. The successful candidate will be expected to work independently and within a highly successful group to: Express and purify GPCRs for structural and biophysical methods; Set up and optimise vapour diffusion and LCP crystallisation experiments; Collect X-ray diffraction data at synchrotron sources; Solve and refine structures; Assist with interpretation of structural results for the design of new compounds; Present results (written and oral) to internal and external audiences. This is an exceptional opportunity to participate in pioneering science with an Industry-leading Drug Discovery company. Applicants must be able to demonstrate proof of the right to work in the United Kingdom. Further information can be found on our website (www.heptares.comhttp://www.heptares.com). Applications should include a covering letter with curriculum vitae including the names and contact details for two referees. Please send your application in pdf format, to h...@heptares.commailto:h...@heptares.com quoting reference number 2014/2B. The closing date for applications is 18th April 2014. No agencies, please. Thanks, Joao Dr Joao Dias Principal Scientist Heptares Therapeutics Ltd BioPark, Broadwater Road, Welwyn Garden City, Herts, AL7 3AX UK This document contains company confidential and/or proprietary information. It is intended for the exclusive attention of the addressee(s) above and should not be copied or disclosed to any other. If you have received this transmission in error, please make no use of its contents and contact the sender. [www.heptares.com]www.heptares.comhttp://www.heptares.com The information in this e-mail is confidential and may be legally privileged. It is intended for the exclusive attention of the addressee stated above and should not be copied or disclosed to any other. If you have received this transmission in error, please make no use of its contents and contact the sender. Contact and registered office address: Heptares Therapeutics Limited, BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire, AL7 3AX. Company No: 06267989 inline: d8a2d3.png
Re: [ccp4bb] OSX 10.9.2
On Mar 28, 2014, at 10:29 AM, Cygler, Miroslaw miroslaw.cyg...@usask.ca wrote: Hi, Does the ccp4 suite work with the latest OSX 10.9.2 operating system? Are there any known problems? Mirek As far as I can tell, it works fine. One problem I have heard (on the ccp4bb) with 10.9.X is that support for 3rd-party monitors may be problematic. Bill
Re: [ccp4bb] Coot Performance on Intel HD Graphics 5000
Coot and PyMol run fine on my HD4000. I believe I also have an HD3000 in the lab that is going strong. I look forward to running Coot on my Android before long. Ho Ho Leung Ng University of Hawaii at Manoa Assistant Professor, Department of Chemistry h...@hawaii.edu
