Re: [ccp4bb] N-terminal sequencing
Dear Daniel, You can get it here as well... University of Pittsburgh Department of Biological Sciences Fifth and Ruskin Aves Clapp Hall 301 Pittsburgh PA 15260 email: hem...@pitt.edu ph: 412.624.0106 or Jack Presley Laboratory Manager UC Davis Molecular Structure Facility http://msf.ucdavis.edu (530) 752-7327 With regards PAnkaj Thanks, On Wed, Feb 9, 2011 at 2:02 AM, Daniel Bonsor bon...@bbri.org wrote: We have used Alphalyse (http://www.alphalyse.com/picknpost.html). Dan
Re: [ccp4bb] Let's talk pseudotranslational symmetry (or maybe it's bad data).
Yees - a translation of 0.5 along x means you must consider SGs P212121 and P2 21 21 since the absences will be present (at least at low resolution) with either SG. I dont know how good Phenix would be at distinguishing between z=0.233 and z=0.25 However even if the exact peak is at z0.25, it is nowhere near equal to the origin peak, and pointless should be able to detect C centring pretty accurately.. So I would consider the possibility of P2 21 21 , but be surprised if it was a C /mmm symmetry.. On 02/08/2011 05:49 PM, Francis E Reyes wrote: Hi all I have a case of a dataset that indexed, integrated, and scaled well in P 21 21 21 (55.6410 81.6493 147.1294 90. 90. 90.) . The data has an Mn(i/sd) of 2.1 at 3.5 A with a Rpim of about 0.398 at the highest resolution shell (3.49-3.58). Analysis with phenix.xtriage warns of pseudotranslational symmetry (26% of origin). x y z height p-value(height) ( 0.500, 0.000, 0.233 ) : 26.344 (2.681e-03) ( 0.000, 0.338, 0.000 ) : 5.380 (8.476e-01) If the observed pseudo translationals are crystallographic the following spacegroups and unit cells are possible: space group operator unit cell of reference setting C 2 2 21 (b-1/4,c-1/4,2*a) x+1/2, y, z+1/4 (73.64, 55.47, 81.46, 90.00, 90.00, 90.00) From what I've read about pseudo c-centering via pseudotranslational symmetry, the problem exhibits itself with alternating weak and strong reflections at low resolution, but become consistent at high resolution. Inspection of the h+k parity groups via truncate does not show this behavior . Despite the fact the data was collected at the anomalous peak, I do not observe any anomalous signal (DelAnom correlation between half-sets is 0.013 for all data). Using a reasonably complete model (80%) I searched for two molecules in the ASU in space group P 21 21 21 and obtained a solution at TFZ=22.1 for two molecules related solely by a translation. However the electron density maps (after rigid body refinement) are not great (or maybe my expectations are too high). I am encouraged by the fact the density is weak for a region of the model which should have a different conformation, while strong density is maintained for the rest of the molecule. Is this the proper way to approach pseudotranslation (i.e. is there any reason to believe that the solution obtained by MR is not the correct solution?). Is the space group determined? (i.e. does the pseudo c-centering affect pointless's ability to analyze the systematic absences?). Is the lack of a pattern of alternating weak/strong reflections normal (would observing this behavior be dependent on the crystal orientation) ? any advice would be greatly appreciated! (especially from those who have had a case like this before) F - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D
[ccp4bb] The 2nd Advanced Protein Characterisation and Crystallisation Course in Helsinki, Finland
Dear all, I would like to draw your attention to the following protein crystallization and characterization course we are offering: 2nd Advanced Protein Characterisation and Crystallisation Course: May 2.- 6. 2011 The Biocenter Finland Protein crystallisation unit is again organising an advanced workshop in Protein Characterisation and Crystallisation. The dates are May 2nd to May 6th, 2011. The course will start at 9 am on Monday and end at 2 pm on Friday. The course will be held at the Institute of Biotechnology in Helsinki. We have again assembled a world-class team of international experts in protein crystallisation and characterisation, and the course will be appropriate for graduate students and also for postdoctoral fellows wishing to acquire new skills. for details: http://www.biocenter.helsinki.fi/bi/xray/automation/kurssi.htm Best regards, Tommi Kajander, Ph.D., Docent Macromolecular X-ray Crystallography Research Program in Structural Biology and Biophysics Institute of Biotechnology P.O. Box 65 (Street: Viikinkaari 1, 4th floor) University of Helsinki FIN-00014 Helsinki, Finland Tel. +358-9-191 58903 Fax +358-9-191 59940
Re: [ccp4bb] Ken Olsen, Founder of Digital Equipment Corporation, Died Sunday
At times DEC we innovative in ways that no hardware company today even comes close. But I guess innovation and commercial success do not go hand in hand. OK, this is abridged from Wikipedia, but much of it is true... Digital supported/developed the ANSI standards, especially the ASCII and multinational character sets. The first versions of the C language and the Unix operating system ran on Digital's PDP series of computers Digital produced the first pure 64-bit microprocessor, AlphAXP. Digital collaborated on the Ethernet standard and made the commercially success it is today. Digital, though their Hierarchical Storage Controllers, delivered the first hardware RAID. Digital was the primary sponsor for the X Window System project (project Athena). Digital was one of the first businesses connected to the Internet with dec.com, registered in 1985, being one of the very first .com domains. Digital was also the first computer vendor to open a public website, on October 1, 1993. AltaVista, created by Digital, was one of the first comprehensive Internet search engines. (Although Lycos was earlier, it was much more limited.) DEC invented Digital Linear Tape (DLT) which was so much more reliable than helical scan technologies such as DAT. Digital were even developing the forerunner of the iPod (a hard-disk based MP3 player) back in 1998 before the merger with Compaq. Regards, Robert -- Dr. Robert Esnouf, University Research Lecturer and Head of Research Computing, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK Emails: rob...@strubi.ox.ac.uk Tel: (+44) - 1865 - 287783 and rob...@esnouf.comFax: (+44) - 1865 - 287547
[ccp4bb] Fw: RE: Preliminary studies
--- On Wed, 9/2/11, geoffrey kamau genka...@hotmail.com wrote: From: geoffrey kamau genka...@hotmail.com Subject: RE: Preliminary studies To: rex.pal...@btinternet.com Date: Wednesday, 9 February, 2011, 9:03 Dear Dr. Rex Palmer, Thanks for the message. Yes, we have been using X-ray diffraction cameras, particularly with respect to oscillation and powder diffraction experiments, till last year September. This is when our X-ray generator broke down. We have been working on it with know success. In addition, we are looking for an inidvidual or institution, capable of donating a used, but operational X-ray generator. Therefore, we would be grateful if you could spread our request to others. Best regards, GN Kamau Date: Tue, 8 Feb 2011 12:43:00 + From: rex.pal...@btinternet.com Subject: Preliminary studies To: genka...@hotmail.com Dear Professor Genkamau John Helliwell suggested I might contact you regarding current usage of X-ray diffraction cameras eg precession/oscillation to screen crystals for quality/unit cell/space group prior to data collection. Any information you have will be greatly appreciated. Best wishes Rex Palmer Birkbeck College
[ccp4bb] group defs for refmac rigid body
Dear all, is there a short cut to define an entire chain as one group in the rigid body refinement of refmac, or do I have to explicitly name the starting and ending residues - that's a little tedious with several domains, and using a wild card would come very handy. Cheers, Tim -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen phone: +49 (0)551 39 22149 GPG Key ID = A46BEE1A signature.asc Description: Digital signature
[ccp4bb] Why 0.1% bandwidth?
Dear ccp4bb, I sometimes find the flux of x-ray sources reported in units of photons/s/0.1% bandwidth instead of simply photons/s. Where does the 1/0.1% bandwidth unit come from? I have also seen other percentages like 0.01% bw or 0.02% bw... Is it simply defining some degree of acceptance in energy (for example, the flux between 8 KeV +/- 8 eV for a given stored current)? Does it somehow have to do with energy resolution? Thank you in advance for your answers, -Andre Ambrosio
[ccp4bb] Application Scientist position at Agilent Technologies (formerly Oxford Diffraction), Yarnton, UK
The Agilent Technologies' X-ray Diffraction department, located in Yarnton near Oxford, is looking for an Application Scientist to join a small team of highly-skilled chemical and macromolecular crystallographers. Your principle activities within the team will include macromolecular X-ray data-collection and data-processing demonstrations to potential customers at our Yarnton lab and at external sites. You will also visit our new customers to provide user training to help them to get the most out of our X-ray equipment and software. You will also use your problem solving skills to solve their experimental and data-processing issues. You will be expected to carry out experiments to test new technologies and methods in the macromolecular X-ray data collection area in support of the Agilent Research and Development effort. You will be also involved in pre-sales and marketing activities, including demos and presentation at crystallographic conferences, and at potential customer sites. Extensive travelling within Europe and world-wide is an essential part of the job. Preference will be given to scientists who have hands-on experience in the use of X-ray systems and a high level of understanding of data collection and processing methods. Ph.D. in the field of chemical or macromolecular crystallography and a few years of experience involving X-ray data collection and processing are required. In addition to a solid scientific background, excellent communication and presentations skills as well as the ability to work efficiently with a team to tight schedules are essential. Interested? Send your CV to emma_dubaniew...@non.agilent.commailto:emma_dubaniew...@non.agilent.com. For informal enquiries contact tadeusz.skarzyn...@agilent.commailto:tadeusz.skarzyn...@agilent.com To find out more about Agilent X-ray products google: agilent crystallography Tadeusz Skarzynski Product Manager - Protein Crystallography Agilent Technologies Yarnton
[ccp4bb] Graduate Student Summer Internship at Merck
Hi Everyone, Merck Research Laboratories has an opening for a summer intern in the Structural Chemistry (X-ray crystallography) groups located in either Kenilworth, NJ or West Point, PA. The idea is to have someone comfortable with programming and mathematics to explore some computational ideas that can take advantage of the large parallel computing cluster at Merck ( 3000 cores). I am pasting the advertisement below - please note that the deadline is rapidly approaching. Interested applicants must apply through the link provided below. Thanks- Steve Stephen M. Soisson, Ph.D. Structural Chemistry Site Lead, WP Merck Research Laboratories 770 Sumneytown Pike, WP14-1101 West Point, PA 19486 Phone: (215) 652-6185 Fax:(215) 652-9051 stephen_sois...@merck.com Job Description Graduate Structural Chemistry Internship 2011:CHE002969 Description Merck is a global health care leader with a diversified portfolio of prescription medicines, vaccines and consumer health products, as well as animal health products. Today, we are building a new kind of healthcare company - one that is ready to help create a healthier future for all of us. Our ability to excel depends on the integrity, knowledge, imagination, skill, diversity and teamwork of people like you. To this end, we strive to create an environment of mutual respect, encouragement and teamwork. As part of our global team, you'll have the opportunity to collaborate with talented and dedicated colleagues while developing and expanding your career. The X-ray Crystallography group of the Global Structural Chemistry Department within Merck Research Laboratories is seeking graduate interns for their summer internship program. The intern will be embedded in the Structural Chemistry/X-ray Crystallography group and will conduct research on a project relevant to drug discovery. The intern will also attend group meetings to gain a wider perspective of the role of structural chemistry within the discovery process in the pharmaceutical industry. The Global Structural Chemistry Department is an industry-leading research group with world class laboratory, synchrotron, and computational facilities. A suitable candidate has a science background with interest in x-ray crystallography and drug discovery. Not required, but a plus, would be experience in one or more of the areas of protein crystallization, X-ray diffraction theory and x-ray crystallography. Preference will be given to candidates having a strong math and/or physical science background with expertise in computers and computer programming. We are seeking graduate student with strong academic performance, communication skills, teamwork, and the ability to work in a multi-functional environment. This internship is offered at either of our research facilities in Kenilworth, NJ or West Point, PA. It is a paid 10-12 week internship targeted to start in June 2011. A weekly stipend will be provided. Housing and transportation to and from work are available for those interns meeting the housing distance guideline. **Please note when applying for this position, the candidate MUST upload a cover letter or a personal statement letter and a copy of your unofficial transcript along with your resume. Qualifications * Candidate is currently pursuing a graduate degree in a relevant field (biochemistry, biophysics, applied math, computer science, etc.). * Science background with an interest in drug discovery * Must have experience in x-ray crystallography and knowledge of programming tools such as Python, Perl or C. * Applicants must be currently enrolled in an academic program. * Applicants must be available for full-time employment for 10 - 12 weeks during the months of June - August 2011. To be considered for this position, please visit our career site at www.merck.com/careers to create a profile and submit your resume for requisition #CHE002969. Merck is an equal opportunity employer, M/F/D/V - proudly embracing diversity in all of its manifestations. Primary Location:US-NJ-Kenilworth Job Type:Intern Employee Status:Regular Number of Openings:1 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] Ken Olsen, Founder of Digital Equipment Corporation, Died Sunday
I love hearing these types of stories, which have a few effects on me: -Admiration of those who worked with so little to produce so much -Thankfulness for the resources we have now -Excitement for the forthcoming technogies -Despair about using current technologies, knowing they will be supplanted in a few years Regarding the last point, does anybody have a good response to the Moore's law conundrum that some programs which will take, say, ten years to run now will take only ~1 year to run 8 years from now, making it futile to run the program now? Maybe it is never worth it to run such processes, assuming Moore's law will continue? Another question: Dale Tronrud mentioned the disconnect between clock speed and actual processor performance. Is there a simple way to understand this disconnect? I have wondered for a long time about this now, especially since it is often raised as a rationalization for using Mac's even though the dollar:processorHz is much higher in Mac's than PC's. Jacob Keller On Wed, Feb 9, 2011 at 4:16 AM, Robert Esnouf rob...@strubi.ox.ac.uk wrote: At times DEC we innovative in ways that no hardware company today even comes close. But I guess innovation and commercial success do not go hand in hand. OK, this is abridged from Wikipedia, but much of it is true... Digital supported/developed the ANSI standards, especially the ASCII and multinational character sets. The first versions of the C language and the Unix operating system ran on Digital's PDP series of computers Digital produced the first pure 64-bit microprocessor, AlphAXP. Digital collaborated on the Ethernet standard and made the commercially success it is today. Digital, though their Hierarchical Storage Controllers, delivered the first hardware RAID. Digital was the primary sponsor for the X Window System project (project Athena). Digital was one of the first businesses connected to the Internet with dec.com, registered in 1985, being one of the very first .com domains. Digital was also the first computer vendor to open a public website, on October 1, 1993. AltaVista, created by Digital, was one of the first comprehensive Internet search engines. (Although Lycos was earlier, it was much more limited.) DEC invented Digital Linear Tape (DLT) which was so much more reliable than helical scan technologies such as DAT. Digital were even developing the forerunner of the iPod (a hard-disk based MP3 player) back in 1998 before the merger with Compaq. Regards, Robert -- Dr. Robert Esnouf, University Research Lecturer and Head of Research Computing, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK Emails: rob...@strubi.ox.ac.uk Tel: (+44) - 1865 - 287783 and rob...@esnouf.com Fax: (+44) - 1865 - 287547 -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program cel: 773.608.9185 email: j-kell...@northwestern.edu ***
Re: [ccp4bb] Why 0.1% bandwidth?
Dear Andre For a continuum wavelength band source this unit is needed. A monochromator of a given type then extracts it's rocking curves worth of bandpass. Or in Laue diffraction a wide band is selected with eg a mirror cut off at short wavelengths and a filter or transmission mirror at long wavelengths. The sample crystal picks out it's rocking curves worth of bandpass. The source type can be xray or neutron. The synchrotron undulator is a special case where periodic magnets of low field create a gathering of wavelengths emitted from the SR source ie by constructive inteference into a narrow bandpass which can be say 0.02%. This is technical I realise but hope that sets you on the right track to consult a relevant textbook. Best wishes, John Prof John R Helliwell DSc On 9 Feb 2011, at 12:13, Andre Luis Berteli Ambrosio andre.ambro...@lnbio.org.br wrote: Dear ccp4bb, I sometimes find the flux of x-ray sources reported in units of “photons/s/0.1% bandwidth” instead of simply “photons/s”. Where does the “1/0.1% bandwidth” unit come from? I have also seen other percentages like 0.01% bw or 0.02% bw… Is it simply defining some degree of acceptance in energy (for example, the flux between 8 KeV +/- 8 eV for a given stored current)? Does it somehow have to do with energy resolution? Thank you in advance for your answers, -Andre Ambrosio
Re: [ccp4bb] Ken Olsen, Founder of Digital Equipment Corporation, Died Sunday
Hi Jacob, On Wed, 9 Feb 2011, Jacob Keller wrote: Regarding the last point, does anybody have a good response to the Moore's law conundrum that some programs which will take, say, ten years to run now will take only ~1 year to run 8 years from now, making it futile to run the program now? Maybe it is never worth it to run such processes, assuming Moore's law will continue? This assumes that the process stays running on the same machine. If you checkpoint it and migrate it to faster machine(s) as they become available, you may finish earlier. This depends on how processing throughput for the particular problem evolves between now and now + 8 years. If you choose to re-code/re-optimise to take full advantage of newer machines, the time involved in doing that must be factored in as well: that could be a fully-fledged research project in its own right. Regards, Peter. -- Peter Keller Tel.: +44 (0)1223 353033 Global Phasing Ltd., Fax.: +44 (0)1223 366889 Sheraton House, Castle Park, Cambridge CB3 0AX United Kingdom
Re: [ccp4bb] Why 0.1% bandwidth?
Andre The 0.1% bandwidth is a standard for flux/mrad/bandwidth or brightness (flux/mrad^2/mm^2/bandwidth) from the synchrotron source. It is an emittance rather than an acceptance. A typical perfect crystal monochromator might take (i.e. accept) a tenth of this. However, dependent on the range of angles on the mono the actual bandpass from the mono might be back at 0.1% or higher (but flux still down by a factor of 10). Undulator beamlines generally have a low divergence and the angular divergence term for the mono bandpass is often small. The best advice is to beware of any flux, brightness or bandpass numbers which you might see. Most facilities select some terms which might show their facility in a good light. FELs for example are keen on peak brightness. If you see brilliance it was probably a mis-translation from German in to English by a Frenchman. Yes it is all confusing! Regards Colin From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Andre Luis Berteli Ambrosio Sent: 09 February 2011 12:14 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Why 0.1% bandwidth? Dear ccp4bb, I sometimes find the flux of x-ray sources reported in units of photons/s/0.1% bandwidth instead of simply photons/s. Where does the 1/0.1% bandwidth unit come from? I have also seen other percentages like 0.01% bw or 0.02% bw... Is it simply defining some degree of acceptance in energy (for example, the flux between 8 KeV +/- 8 eV for a given stored current)? Does it somehow have to do with energy resolution? Thank you in advance for your answers, -Andre Ambrosio
[ccp4bb] image file extensions
Dear all, I'm trying to create some space on our server and want to compress all x-ray data files. I'm wondering what extensions I should search for. mccd and img come to mind easily. What other extensions are commonly used? Thanks. Andreas -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk
Re: [ccp4bb] image file extensions
.osc 2011/2/9 Andreas Förster docandr...@gmail.com: Dear all, I'm trying to create some space on our server and want to compress all x-ray data files. I'm wondering what extensions I should search for. mccd and img come to mind easily. What other extensions are commonly used? Thanks. Andreas -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program cel: 773.608.9185 email: j-kell...@northwestern.edu ***
Re: [ccp4bb] Why 0.1% bandwidth?
Andre I should have replaced flux in my email by photons/sec to be clear (or at least a bit clearer). Flux in magnetism is the strength of the magnetic field per unit area so it is confusing to use the term in the way I did. Different fields use the same term for different purposes. Technical (John's statement) or confusing (mine). Take your pick! Colin From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Colin Nave Sent: 09 February 2011 14:35 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Why 0.1% bandwidth? Andre The 0.1% bandwidth is a standard for flux/mrad/bandwidth or brightness (flux/mrad^2/mm^2/bandwidth) from the synchrotron source. It is an emittance rather than an acceptance. A typical perfect crystal monochromator might take (i.e. accept) a tenth of this. However, dependent on the range of angles on the mono the actual bandpass from the mono might be back at 0.1% or higher (but flux still down by a factor of 10). Undulator beamlines generally have a low divergence and the angular divergence term for the mono bandpass is often small. The best advice is to beware of any flux, brightness or bandpass numbers which you might see. Most facilities select some terms which might show their facility in a good light. FELs for example are keen on peak brightness. If you see brilliance it was probably a mis-translation from German in to English by a Frenchman. Yes it is all confusing! Regards Colin From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Andre Luis Berteli Ambrosio Sent: 09 February 2011 12:14 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Why 0.1% bandwidth? Dear ccp4bb, I sometimes find the flux of x-ray sources reported in units of photons/s/0.1% bandwidth instead of simply photons/s. Where does the 1/0.1% bandwidth unit come from? I have also seen other percentages like 0.01% bw or 0.02% bw... Is it simply defining some degree of acceptance in energy (for example, the flux between 8 KeV +/- 8 eV for a given stored current)? Does it somehow have to do with energy resolution? Thank you in advance for your answers, -Andre Ambrosio
Re: [ccp4bb] N-terminal sequencing
I think that this CRO can help you: Proteos 4717 Campus Drive Kalamazoo, Michigan 49008 269.372.3423 http://www.proteos.net Good luck! Bryan From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Junyu Xiao Sent: Tuesday, February 08, 2011 2:52 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] N-terminal sequencing Hi, Sorry for non-crystallography related questions. I am seeking protein N-terminal sequencing service. However, the facilities I have worked with previously (Michigan state and UCSD) were both closed. Does anyone know any companies or core facilities that can do this? Thanks, Junyu --- Junyu Xiao, Ph.D. University of California, San Diego Leichtag Room 283 9500 Gilman Drive, 0721 La Jolla, CA 92093-0721 Lab phone: 858-822-0684 -- Confidentiality Notice: This message is private and may contain confidential and proprietary 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 unauthorized use or disclosure of the contents of this message is not permitted and may be unlawful.
Re: [ccp4bb] Detaching crystals from glass cover slides
Cool the coverslip on the opposite side of the crystal with a chip of dry ice. Do not freeze the drop. I learned this from Gary Gilliland. Also I wonder if you can simply move the whole tray into a cooler temperature? You can imagine that the thermal expansion coefficient of the glass coverslip and the crystal are different. I have not tried heating, but maybe that works, too? Or bend the coverslip without breaking is by applying pressure from the opposite side. Jim ... Any suggestions for detaching crystals from cover slides will be greatly appreciated. Wataru
Re: [ccp4bb] Detaching crystals from glass cover slides
Hi Wataru, I second Bill's suggestion. Additionally, you might want to migrate to a sitting drop setup and use the vacuum grease with that. It worked for me. Happy Fishing, Chris -- Christopher L. Colbert, Ph.D. Assistant Professor Department of Chemistry and Biochemistry North Dakota State University P.O. Box 6050 Dept. 2710 Fargo, ND 58108-6050 PH: (701) 231-7946 FAX: (701) 231-8324 On 2/8/11 8:19 PM, William G. Scott wgsc...@ucsc.edu wrote: Hi Wataru: I hope all is well. For the ones you already have grown, try very gently prying them off with a wedge-shaped needle. If you can grow more, try using a very thin smooth layer of vacuum grease, and apply the drop to that. I managed to get RNA crystals to grow that way that otherwise irreversibly adhered to the surface. All the best, Bill On Feb 8, 2011, at 6:06 PM, Wataru Kagawa wrote: Hi all, I have crystals growing by the hanging-drop method, using 24-well VDX plates and Hampton Research siliconized glass cover slides. Most crystals are attached to the cover slide, and I am having difficulties detaching the crystals (using a cryoloop) without breaking them. There are few smaller crystals floating in the drop, and they diffract X-rays pretty well (clean spots, ~3.5A resolution using RAXIS). However, I would like to try the bigger ones, because they may diffract to a higher resolution. Any suggestions for detaching crystals from cover slides will be greatly appreciated. Wataru
Re: [ccp4bb] image file extensions
.ipf if you have files from (old) image plate detectors. clement Dear all, I'm trying to create some space on our server and want to compress all x-ray data files. I'm wondering what extensions I should search for. mccd and img come to mind easily. What other extensions are commonly used? Thanks. Andreas -- Andreas F#65533;ster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk Clement Angkawidjaja, Ph.D Specially appointed assistant professor Laboratory of Molecular Biotechnology (Kanaya Lab) Division of Advanced Science and Biotechnology Graduate School of Engineering, Osaka University 2-1 Yamadaoka, Suita-shi, Osaka 565-0871 Japan
Re: [ccp4bb] Why 0.1% bandwidth?
And before anyone else points out the mistake Flux in magnetism is the magnetic field (e.g. no. of lines) over a defined area. Some similarity to photons/sec over a defined area for x-ray sources Well I think this is right. From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Colin Nave Sent: 09 February 2011 15:06 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Why 0.1% bandwidth? Andre I should have replaced flux in my email by photons/sec to be clear (or at least a bit clearer). Flux in magnetism is the strength of the magnetic field per unit area so it is confusing to use the term in the way I did. Different fields use the same term for different purposes. Technical (John's statement) or confusing (mine). Take your pick! Colin From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Colin Nave Sent: 09 February 2011 14:35 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Why 0.1% bandwidth? Andre The 0.1% bandwidth is a standard for flux/mrad/bandwidth or brightness (flux/mrad^2/mm^2/bandwidth) from the synchrotron source. It is an emittance rather than an acceptance. A typical perfect crystal monochromator might take (i.e. accept) a tenth of this. However, dependent on the range of angles on the mono the actual bandpass from the mono might be back at 0.1% or higher (but flux still down by a factor of 10). Undulator beamlines generally have a low divergence and the angular divergence term for the mono bandpass is often small. The best advice is to beware of any flux, brightness or bandpass numbers which you might see. Most facilities select some terms which might show their facility in a good light. FELs for example are keen on peak brightness. If you see brilliance it was probably a mis-translation from German in to English by a Frenchman. Yes it is all confusing! Regards Colin From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Andre Luis Berteli Ambrosio Sent: 09 February 2011 12:14 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Why 0.1% bandwidth? Dear ccp4bb, I sometimes find the flux of x-ray sources reported in units of photons/s/0.1% bandwidth instead of simply photons/s. Where does the 1/0.1% bandwidth unit come from? I have also seen other percentages like 0.01% bw or 0.02% bw... Is it simply defining some degree of acceptance in energy (for example, the flux between 8 KeV +/- 8 eV for a given stored current)? Does it somehow have to do with energy resolution? Thank you in advance for your answers, -Andre Ambrosio
Re: [ccp4bb] Detaching crystals from glass cover slides
Hi Wataru, Have you tried Mitegen's polymer MicroTools? These tools have tips made from soft, flexible microfabricated polymer films and are specifically designed for this type of application. There is more information about them here ( http://mitegen.com/products/microtools/microtools.shtml). Best wishes, Ben Apker On Tue, Feb 8, 2011 at 9:06 PM, Wataru Kagawa wkag...@aoni.waseda.jpwrote: Hi all, I have crystals growing by the hanging-drop method, using 24-well VDX plates and Hampton Research siliconized glass cover slides. Most crystals are attached to the cover slide, and I am having difficulties detaching the crystals (using a cryoloop) without breaking them. There are few smaller crystals floating in the drop, and they diffract X-rays pretty well (clean spots, ~3.5A resolution using RAXIS). However, I would like to try the bigger ones, because they may diffract to a higher resolution. Any suggestions for detaching crystals from cover slides will be greatly appreciated. Wataru -- Product Development and Production Manager MiTeGen, LLC 95 Brown Rd - Suite 183 Ithaca, NY 14850 Phone: 607-266-8877 Fax: 607-697-0400 Disclaimer: The information contained in or attached to this e-mail is confidential, proprietary, and the sole property of MiTeGen, LLC. This e-mail is intended solely for the use of the intended recipient(s). If you have received this e-mail in error, please notify the sender immediately and then delete it. If you are not the intended recipient, you must not use, disclose or distribute this e-mail without the author's prior permission.
Re: [ccp4bb] Detaching crystals from glass cover slides
Dear Wataru check out the following entry on the CCP4-wiki on 'sticky crystals' which we compiled based on feeback from many crystallographers: http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Sticky_crystals Best regards Savvas Savvas Savvides Unit for Structural Biology @ L-ProBE Ghent University K.L. Ledeganckstraat 35, 9000 Ghent, Belgium Tel/SMS/texting +32 (0)472 928 519 Skype: savvas.savvides_skype http://www.LProBE.ugent.be/xray.html On 09 Feb 2011, at 16:11, Colbert, Christopher wrote: Hi Wataru, I second Bill's suggestion. Additionally, you might want to migrate to a sitting drop setup and use the vacuum grease with that. It worked for me. Happy Fishing, Chris -- Christopher L. Colbert, Ph.D. Assistant Professor Department of Chemistry and Biochemistry North Dakota State University P.O. Box 6050 Dept. 2710 Fargo, ND 58108-6050 PH: (701) 231-7946 FAX: (701) 231-8324 On 2/8/11 8:19 PM, William G. Scott wgsc...@ucsc.edu wrote: Hi Wataru: I hope all is well. For the ones you already have grown, try very gently prying them off with a wedge-shaped needle. If you can grow more, try using a very thin smooth layer of vacuum grease, and apply the drop to that. I managed to get RNA crystals to grow that way that otherwise irreversibly adhered to the surface. All the best, Bill On Feb 8, 2011, at 6:06 PM, Wataru Kagawa wrote: Hi all, I have crystals growing by the hanging-drop method, using 24-well VDX plates and Hampton Research siliconized glass cover slides. Most crystals are attached to the cover slide, and I am having difficulties detaching the crystals (using a cryoloop) without breaking them. There are few smaller crystals floating in the drop, and they diffract X-rays pretty well (clean spots, ~3.5A resolution using RAXIS). However, I would like to try the bigger ones, because they may diffract to a higher resolution. Any suggestions for detaching crystals from cover slides will be greatly appreciated. Wataru
Re: [ccp4bb] Ken Olsen, Founder of Digital Equipment Corporation, Died Sunday
On Tuesday, February 08, 2011 11:47:04 pm Dale Tronrud wrote: I see in the news that Ken Olsen has died. Although he was not a crystallographer I think we should stop for a moment to remember the profound impact the company that this man founded had on our field. My first experience in a crystallography lab was as an undergraduate in M. Sundaralingam's lab in Madison Wisconsin. While I never had the opportunity to use them, his two diffractometers were controlled by the ubiquitous PDP-8 computers. I had more experience with his main computer, which was either a PDP-11/34 or 35 (Ethan help me out!). http://skuld.bmsc.washington.edu/people/merritt/graphics/madgraph/pdp11.html This was connected to a Vector General graphics display running software called UWVG. http://skuld.bmsc.washington.edu/people/merritt/graphics/madgraph/madgraph.html Having the least stature in the lab I got the midnight to 4am time slot for model building. The computer took about 10 minutes to compute and contour each block of map, covering about three residues. While waiting I would crawl under the DECwriter and nap. http://upload.wikimedia.org/wikipedia/commons/c/c5/Decwriter.jpg Ah, Memory Lane! Ethan The computer would stop rattling when the map was up and that would wake me. When I joined the Matthews lab in Oregon they had a VAX 11/780. What an amazing machine! It had 1 MB of RAM and could run a million instructions in a second. It only took 48 hours to run a cycle of refinement with PROLSQ, that is, if no one else used the computer. These specs don't sound like much but this computer was really a revolution for computational crystallography. That a single lab could own a computer of such power was unheard of before this. It wasn't just that the computer had so much RAM (We later got it up to its max of 4 MB.) but the advent of virtual memory made program design so much easier. You could simply define an array of 100,000 elements and not have to worry about finding where in memory, mixed in with the operating system, utility programs, and other users' software, you could find an unused block that big. Digital didn't invent virtual memory, but the VAX made it achievable for regular crystallographers. Through most of the 1980's you didn't have to worry about getting your code to run on other computers - Everyone had access to a VAX. In the 1990's DEC came out with the alpha CPU chip which really broke ground for performance. These things screamed when in came to running crystallographic software. In 1999 the lab bought several of the 666 MHz models. It was about four years before Intel came out with a chip that would match these alphas on my crystallography benchmark and they had to be clocked at over 2 GHz to do it. Yes, Digital lost out in the competition of the marketplace, and Ken Olsen was pushed out of the company well before the end. But what a ride it was. What great computers they were and what great science was done on them! Dale Tronrud -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg University of Washington, Seattle 98195-7742
[ccp4bb] image file extensions
Harry Powell had the most comprehensive answer, giving me the extensions that are used in mosflm: .img .mar* (i.e. .mar1600, .mar2300, etc) .mccd .osc .SFRM .sfrm .image .ipf .cbf In addition, finding files larger than a certain cutoff might do the trick too - especially if the objective is economizing disk space. Thanks. Andreas -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk
Re: [ccp4bb] Ken Olsen, Founder of Digital Equipment Corporation, Died Sunday
Dear Jacob, Regarding your second question, I stumbled across a relevant article on Wikipedia recently: en.wikipedia.org/wiki/Megahertz_myth Cheers, David. On 9 Feb 2011 13:53, Jacob Keller j-kell...@fsm.northwestern.edu wrote: I love hearing these types of stories, which have a few effects on me: -Admiration of those who worked with so little to produce so much -Thankfulness for the resources we have now -Excitement for the forthcoming technogies -Despair about using current technologies, knowing they will be supplanted in a few years Regarding the last point, does anybody have a good response to the Moore's law conundrum that some programs which will take, say, ten years to run now will take only ~1 year to run 8 years from now, making it futile to run the program now? Maybe it is never worth it to run such processes, assuming Moore's law will continue? Another question: Dale Tronrud mentioned the disconnect between clock speed and actual processor performance. Is there a simple way to understand this disconnect? I have wondered for a long time about this now, especially since it is often raised as a rationalization for using Mac's even though the dollar:processorHz is much higher in Mac's than PC's. Jacob Keller On Wed, Feb 9, 2011 at 4:16 AM, Robert Esnouf rob...@strubi.ox.ac.uk wrote: At times DEC we innovative in ways that no hardware company today even comes close. But I guess innovation and commercial success do not go hand in hand. OK, this is abridged from Wikipedia, but much of it is true... Digital supported/developed the ANSI standards, especially the ASCII and multinational character sets. The first versions of the C language and the Unix operating system ran on Digital's PDP series of computers Digital produced the first pure 64-bit microprocessor, AlphAXP. Digital collaborated on the Ethernet standard and made the commercially success it is today. Digital, though their Hierarchical Storage Controllers, delivered the first hardware RAID. Digital was the primary sponsor for the X Window System project (project Athena). Digital was one of the first businesses connected to the Internet with dec.com, registered in 1985, being one of the very first .com domains. Digital was also the first computer vendor to open a public website, on October 1, 1993. AltaVista, created by Digital, was one of the first comprehensive Internet search engines. (Although Lycos was earlier, it was much more limited.) DEC invented Digital Linear Tape (DLT) which was so much more reliable than helical scan technologies such as DAT. Digital were even developing the forerunner of the iPod (a hard-disk based MP3 player) back in 1998 before the merger with Compaq. Regards, Robert -- Dr. Robert Esnouf, University Research Lecturer and Head of Research Computing, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK Emails: rob...@strubi.ox.ac.uk Tel: (+44) - 1865 - 287783 and rob...@esnouf.comFax: (+44) - 1865 - 287547 -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program cel: 773.608.9185 email: j-kell...@northwestern.edu ***
Re: [ccp4bb] Why 0.1% bandwidth?
That's approximately the bandwidth of a Si (111) monochromator. On Wed, 9 Feb 2011, Andre Luis Berteli Ambrosio wrote: Dear ccp4bb, I sometimes find the flux of x-ray sources reported in units of “photons/s/0.1% bandwidth” instead of simply “photons/s”. Where does the “1/0.1% bandwidth” unit come from? I have also seen other percentages like 0.01% bw or 0.02% bw… Is it simply defining some degree of acceptance in energy (for example, the flux between 8 KeV +/- 8 eV for a given stored current)? Does it somehow have to do with energy resolution? Thank you in advance for your answers, -Andre Ambrosio -- = Robert M. Sweet E-Dress: sw...@bnl.gov Group Leader, PXRR: Macromolecular ^ (that's L Crystallography Research Resource at NSLSnot 1) http://px.nsls.bnl.gov/ Biology Dept Brookhaven Nat'l Lab. Phones: Upton, NY 11973631 344 3401 (Office) U.S.A. 631 344 2741 (Facsimile) =
[ccp4bb] N-terminal sequencing facility summary
Dear all, Thanks for your hearty responses. Below is a summary for the information I received. Again, I really appreciate all the help. Best regards, Junyu 1. Yale University, University of Utah, and Wake Forest University are three that have core facilities which perform N-terminal sequencing. 2. A colleague here has had good results with the facility at Iowa state: http://www.biotech.iastate.edu/service_facilities/protein.html If you just want to identify the protein, mass spec may be cheaper. The same place will do that, or we have had excellent results with http://www.appliedbiomics.com/ If you need to confirm N-term construct, Edman degradation is probably still more cost effective. 3. I've gotten decent results from Rockefeller: http://proteomics.rockefeller.edu/edman/edmaninfo 4. We have used Alphalyse (http://www.alphalyse.com/picknpost.html). 5. There is one at the Johns Hopkins University. Synthesis and Sequening facility 6. You can get it here as well... University of Pittsburgh Department of Biological Sciences Fifth and Ruskin Aves Clapp Hall 301 Pittsburgh PA 15260 email: hem...@pitt.edu ph: 412.624.0106 or Jack Presley Laboratory Manager UC Davis Molecular Structure Facility http://msf.ucdavis.edu (530) 752-7327 7. Proteos 4717 Campus Drive Kalamazoo, Michigan 49008 269.372.3423 http://www.proteos.net --- Junyu Xiao, Ph.D. University of California, San Diego Leichtag Room 283 9500 Gilman Drive, 0721 La Jolla, CA 92093-0721 Lab phone: 858-822-0684
Re: [ccp4bb] Why 0.1% bandwidth?
By That's I presume Bob means the 0.01% bandwidth figure is approximately the intrinsic bandwidth of a Si (111) monochromator. The 0.1% bandwidth in the title of the email is the standard bandwidth often used to define the output of synchrotron sources. When defining flux within a certain bandwidth, the term spectral flux is useful. See also Journal of Synchrotron Radiation Volume 12, Part 3 (May 2005) http://scripts.iucr.org/cgi-bin/paper?es0344 This article ends with a plea to retain 0.1% bandwidth (and mm^2 etc.) as this is ensconced in the literature. This gets difficult if the source emits its radiation in to a bandwidth smaller than this. John gives an example in his response. When describing the output of a particular beamline with a monochromator then it is reasonable to give the flux in to a bandwidth relevant to the monochromator e.g. approx 0.01% for Si (111). However, this too has its complications as it might not correspond to the bandwidth one actually gets on the beamline. Colin -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Robert Sweet Sent: 09 February 2011 13:47 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Why 0.1% bandwidth? That's approximately the bandwidth of a Si (111) monochromator. On Wed, 9 Feb 2011, Andre Luis Berteli Ambrosio wrote: Dear ccp4bb, I sometimes find the flux of x-ray sources reported in units of “photons/s/0.1% bandwidth” instead of simply “photons/s”. Where does the “1/0.1% bandwidth” unit come from? I have also seen other percentages like 0.01% bw or 0.02% bw… Is it simply defining some degree of acceptance in energy (for example, the flux between 8 KeV +/- 8 eV for a given stored current)? Does it somehow have to do with energy resolution? Thank you in advance for your answers, -Andre Ambrosio -- === == Robert M. Sweet E-Dress: sw...@bnl.gov Group Leader, PXRR: Macromolecular ^ (that's L Crystallography Research Resource at NSLSnot 1) http://px.nsls.bnl.gov/ Biology Dept Brookhaven Nat'l Lab. Phones: Upton, NY 11973631 344 3401 (Office) U.S.A. 631 344 2741 (Facsimile) === ==
Re: [ccp4bb] image file extensions
Dear Andreas,
I had the same problem frequently and wrote a little python-script for
compressing our images on our server. It might help you and you can
easily modify the extension for which the script should search for...
Best Regards,
Georg
-- code starts below
#!/usr/bin/python
#
# script to compress all xray images (as specified in variables) downstream
# of a specfied directory using as many cores as available on the system
#
# requirement: python = 2.4, bzip2
# tested with systems: MacOS X (10.5.7), ubuntu 8.04.2 (LTS)
#
# USAGE AT YOUR OWN RISK
# georg.zoc...@gmx.de
#
#
# version 0.1
#
import os, sys, subprocess
# variables
# You can modify the data types here
imagetypes = [.ccd, .img, .cbf, mar2300]
# If you only want to get a file list without compressing anything
switch to 'on'
debug = 'off'
#
#
# do not modify anything below this line unless you know what you
are doing
images = []
usage =
\t usage: \t image_compressor directory \n
\t\t\t All image files downstream the specified directory will
'bzip2'-ed on several cores
\t\t\t USAGE AT YOUR OWN RISK\n
### check input
try :
sys.argv[1]
except:
print
print \t Please specify a directory to dive into...
print usage
sys.exit(0)
check = os.path.exists(sys.argv[1])
if check == True:
input = os.path.abspath(sys.argv[1])
if check == False:
print
print \t Specified directory not found...
print usage
sys.exit(0)
### functions
def __get_images():
Function to get all xray image files downstream of a specified
directory
return value is a list...
print \n\t generating file list
for dir, dirs, files in os.walk(sys.argv[1]):
for f in files:
if os.path.splitext(f)[1] in imagetypes :
images.append((os.path.join(dir, f)))
print \n\t\t\t...done
return images
def __get_ncpu():
Function to get the number of CPU-Cores on POSIX systems
try:
ncpu = int(os.sysconf('SC_NPROCESSORS_ONLN'))
if ncpu 0:
return ncpu
except (AttributeError,ValueError):
#pass
print \n\t System not POSIX compatible. Sys.exit...\n
sys.exit(0)
def run_bzip(ncpu, list):
dic = {}
j=0
list.sort()
while j = len(list):
for i in range(ncpu):
if j len(list):
break
if j = len(list):
print \t compressing image:, os.path.basename(list[j-1])
try:
if debug == off:
dic[i] = subprocess.Popen([rbzip2,-z9,
list[j]])
#for testing
if debug == on:
dic[i] = subprocess.Popen([rls,-l, list[j]])
except:
print
j+=1
dic[i].wait()
def main():
run_bzip(__get_ncpu(), __get_images())
### end functions
if __name__ =='__main__':
main()
code end above
Am 09.02.11 15:49, schrieb Andreas Förster:
Dear all,
I'm trying to create some space on our server and want to compress all
x-ray data files. I'm wondering what extensions I should search for.
mccd and img come to mind easily. What other extensions are commonly
used?
Thanks.
Andreas
--
Universität Tübingen
Interfakultäres Institut für Biochemie
Dr. Georg Zocher
Hoppe-Seyler-Str. 4
72076 Tuebingen
Germany
Fon: +49(0)-7071-2973374
Mail: georg.zoc...@uni-tuebingen.de
http://www.ifib.uni-tuebingen.de
Re: [ccp4bb] First images of proteins and viruses caught with an X-ray laser
As one of the people involved (I'm author #74 out of 88 on PMID 21293373), I can tell you that about half of the three million snapshots were blank, but we wanted to be honest about the number that were collected, as well as the minimum number that were needed to get a useful data set. The blank images were on purpose, since the nanocrystals were diluted so that there would be relatively few double-hits. As many of you know, multiple lattices crash autoindexing algorithms! Whether or not a blank image or a failed autoindexing run qualifies as conforming to our existing model or not I suppose is a matter of semantics. But yes, I suppose some details do get lost between the actual work and the press release! In case anyone wants to look at the data, it has been deposited in the PDB under 3PCQ, and the detailed processing methods published under PMID: 20389587. -James Holton MAD Scientist On 2/9/2011 10:38 AM, Thomas Juettemann wrote: http://www.nanowerk.com/news/newsid=20045.php http://home.slac.stanford.edu/pressreleases/2011/20110202.htm I think it is pretty exciting, although they only take the few datasets that conform to their existing model: The team combined 10,000 of the three million snapshots they took to come up with a good match for the known molecular structure of Photosystem I.
[ccp4bb] Max F. Perutz International PhD Program Vienna 2011
Dear All, I would like to point your attention to: *Max F. Perutz International PhD Program Vienna 2011* The Max F. Perutz Laboratories is inviting applications from talented students all over the world for our graduate program. The institute is located at the Vienna Biocenter Campus - a major European science hub - and will provide a rigorous and comprehensive PhD education. Our research covers the full range of the molecular biosciences, exploring life at a cellular, molecular and atomic level. The Perutz labs have an open, collaborative environment with PhD students already representing more than 40 nations. The working language is English, and no prior knowledge of German is required. The city of Vienna is currently ranked as the best in the world for quality of life (Mercer 2010 Quality of Living Survey). It is a city of exciting contrasts, with both a rich cultural heritage and a vibrant contemporary way of life. This year's summer selection is co-organized with the special doctoral programs in Cell Signaling, RNA Biology and Structural Biology. These are the flagships of MFPL PhD training and mentoring, with the goals of promoting creativity and fostering independence in young scientists. The Max F. Perutz Labs are a joint venture of the University of Vienna and the Medical University of Vienna. All PhD students are employed with a highly competitive salary according to the guidelines of the Austrian Research Fund (FWF). Applications to the program are open to holders of a Master's degree (or equivalent) in the biosciences, chemistry or medicine. Applicants from related fields will also be considered. Students will be selected following a 4-day interview process. *Application deadline: 27th March 2011. www.mfpl.ac.at/phdprogram* -- ** Department for Structural and Computational Biology Max F. Perutz Laboratories University of Vienna Campus Vienna Biocenter 5 A-1030 Vienna Austria e-mail: kristina.djino...@univie.ac.at Phone: +43-1-4277-52203/52201 Mobile: +43-664-602 77-522 03 Fax: +43-1-4277-9522
Re: [ccp4bb] image file extensions
On 02/09/11 09:49, Andreas Förster wrote: Dear all, I'm trying to create some space on our server and want to compress all x-ray data files. I'm wondering what extensions I should search for. mccd and img come to mind easily. What other extensions are commonly used? Thanks. Andreas /bin/ls -lR | sort -nk5 | tail -40 will list the largest files in the directory tree. Those are probably the ones you need to compress. -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
Re: [ccp4bb] First images of proteins and viruses caught with an X-ray laser
Thank you for clarifying this James. Those details are indeed often lost/misinterpreted when the paper is discussed in journal club, so your comment was especially helpful. Best wishes, Thomas On Wed, Feb 9, 2011 at 20:38, James Holton jmhol...@lbl.gov wrote: As one of the people involved (I'm author #74 out of 88 on PMID 21293373), I can tell you that about half of the three million snapshots were blank, but we wanted to be honest about the number that were collected, as well as the minimum number that were needed to get a useful data set. The blank images were on purpose, since the nanocrystals were diluted so that there would be relatively few double-hits. As many of you know, multiple lattices crash autoindexing algorithms! Whether or not a blank image or a failed autoindexing run qualifies as conforming to our existing model or not I suppose is a matter of semantics. But yes, I suppose some details do get lost between the actual work and the press release! In case anyone wants to look at the data, it has been deposited in the PDB under 3PCQ, and the detailed processing methods published under PMID: 20389587. -James Holton MAD Scientist On 2/9/2011 10:38 AM, Thomas Juettemann wrote: http://www.nanowerk.com/news/newsid=20045.php http://home.slac.stanford.edu/pressreleases/2011/20110202.htm I think it is pretty exciting, although they only take the few datasets that conform to their existing model: The team combined 10,000 of the three million snapshots they took to come up with a good match for the known molecular structure of Photosystem I.
Re: [ccp4bb] image file extensions
find . -name '*.osc' -or -name '*.img' -type f -size +3000 -print -exec
bzip2 '{}' \;
is a personal favorite, along those lines, with ample opportunities for
customization. (If the above command line wraps, it's all supposed to
be on one line)
Phil Jeffrey
Princeton
On 2/9/11 2:46 PM, David Schuller wrote:
/bin/ls -lR | sort -nk5 | tail -40
will list the largest files in the directory tree. Those are probably
the ones you need to compress.
Re: [ccp4bb] Let's talk pseudotranslational symmetry (or maybe it's bad data).
Just to add to Phil and Eleanor's response... I would NOT use Phaser for MR with PTS present. It doesn't handle it correctly yet, since the likelihood targets don't account for PTS. Others may be able to explain it better. Its probably not C-centered (as Eleanor mentions) and you should try the other primitive cell options. From what I understand about seeing (or not) the strong/weak reflection behavior... it is proportional to the size of your off-origin Patterson peak so it is more difficult to see when the off-origin peak is small (26% in your case). Crystal orientation, I guess, could also be a reason for not visualizing it on the diffraction image, but it still should be apparent in the stats since Xtriage found it. If it was me... If your off-origin peak was over 50% of the origin peak height AND after inspecting the Patterson map to see if it lies at z0.25, then you MIGHT be able to solve and refine the structure in C-centered orthorhombic cell. The advantage of this would be that you wouldn't be refining against a large portion of weak reflection data. In your case, however, since your weak reflections are not really that weak you shouldn't have too much of a problem refining. Hope this helps. Jon -- Jonathan P. Schuermann, Ph. D. Beamline Scientist NE-CAT, Building 436E Advanced Photon Source (APS) Argonne National Laboratory 9700 South Cass Avenue Argonne, IL 60439 email: schue...@anl.gov Tel: (630) 252-0682 Fax: (630) 252-0687 On 02/08/2011 11:49 AM, Francis E Reyes wrote: Hi all I have a case of a dataset that indexed, integrated, and scaled well in P 21 21 21 (55.6410 81.6493 147.1294 90. 90. 90.) . The data has an Mn(i/sd) of 2.1 at 3.5 A with a Rpim of about 0.398 at the highest resolution shell (3.49-3.58). Analysis with phenix.xtriage warns of pseudotranslational symmetry (26% of origin). x y zheight p-value(height) ( 0.500, 0.000, 0.233 ) : 26.344 (2.681e-03) ( 0.000, 0.338, 0.000 ) :5.380 (8.476e-01) If the observed pseudo translationals are crystallographic the following spacegroups and unit cells are possible: space groupoperator unit cell of reference setting C 2 2 21 (b-1/4,c-1/4,2*a) x+1/2, y, z+1/4 (73.64, 55.47, 81.46, 90.00, 90.00, 90.00) From what I've read about pseudo c-centering via pseudotranslational symmetry, the problem exhibits itself with alternating weak and strong reflections at low resolution, but become consistent at high resolution. Inspection of the h+k parity groups via truncate does not show this behavior . Despite the fact the data was collected at the anomalous peak, I do not observe any anomalous signal (DelAnom correlation between half-sets is 0.013 for all data). Using a reasonably complete model (80%) I searched for two molecules in the ASU in space group P 21 21 21 and obtained a solution at TFZ=22.1 for two molecules related solely by a translation. However the electron density maps (after rigid body refinement) are not great (or maybe my expectations are too high). I am encouraged by the fact the density is weak for a region of the model which should have a different conformation, while strong density is maintained for the rest of the molecule. Is this the proper way to approach pseudotranslation (i.e. is there any reason to believe that the solution obtained by MR is not the correct solution?). Is the space group determined? (i.e. does the pseudo c-centering affect pointless's ability to analyze the systematic absences?). Is the lack of a pattern of alternating weak/strong reflections normal (would observing this behavior be dependent on the crystal orientation) ? any advice would be greatly appreciated! (especially from those who have had a case like this before) F - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D
Re: [ccp4bb] Let's talk pseudotranslational symmetry (or maybe it's bad data).
Is there a program that does ? I was under the impression that they were all equally good/bad at this, because any solution that agrees with the PTS has quite a high score and any solution that doesn't has a low score, irrespective of the correctness of the placement of the molecules. In one case that ritually defeats me with quite strong pseudo-centering, this seems to be true for heavy atom searches also. Phil Jeffrey Princeton On 2/9/11 5:08 PM, Jon Schuermann wrote: I would NOT use Phaser for MR with PTS present. It doesn't handle it correctly yet, since the likelihood targets don't account for PTS. Others may be able to explain it better.
Re: [ccp4bb] Let's talk pseudotranslational symmetry (or maybe it's bad data).
molrep can deal with some of the PST cases. Garib On 9 Feb 2011, at 22:27, Phil Jeffrey wrote: Is there a program that does ? I was under the impression that they were all equally good/bad at this, because any solution that agrees with the PTS has quite a high score and any solution that doesn't has a low score, irrespective of the correctness of the placement of the molecules. In one case that ritually defeats me with quite strong pseudo-centering, this seems to be true for heavy atom searches also. Phil Jeffrey Princeton On 2/9/11 5:08 PM, Jon Schuermann wrote: I would NOT use Phaser for MR with PTS present. It doesn't handle it correctly yet, since the likelihood targets don't account for PTS. Others may be able to explain it better.
Re: [ccp4bb] First images of proteins and viruses caught with an X-ray laser
Any idea where then phases came from? BR -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Thomas Juettemann Sent: Wednesday, February 09, 2011 12:16 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] First images of proteins and viruses caught with an X-ray laser Thank you for clarifying this James. Those details are indeed often lost/misinterpreted when the paper is discussed in journal club, so your comment was especially helpful. Best wishes, Thomas On Wed, Feb 9, 2011 at 20:38, James Holton jmhol...@lbl.gov wrote: As one of the people involved (I'm author #74 out of 88 on PMID 21293373), I can tell you that about half of the three million snapshots were blank, but we wanted to be honest about the number that were collected, as well as the minimum number that were needed to get a useful data set. The blank images were on purpose, since the nanocrystals were diluted so that there would be relatively few double-hits. As many of you know, multiple lattices crash autoindexing algorithms! Whether or not a blank image or a failed autoindexing run qualifies as conforming to our existing model or not I suppose is a matter of semantics. But yes, I suppose some details do get lost between the actual work and the press release! In case anyone wants to look at the data, it has been deposited in the PDB under 3PCQ, and the detailed processing methods published under PMID: 20389587. -James Holton MAD Scientist On 2/9/2011 10:38 AM, Thomas Juettemann wrote: http://www.nanowerk.com/news/newsid=20045.php http://home.slac.stanford.edu/pressreleases/2011/20110202.htm I think it is pretty exciting, although they only take the few datasets that conform to their existing model: The team combined 10,000 of the three million snapshots they took to come up with a good match for the known molecular structure of Photosystem I.
Re: [ccp4bb] Let's talk pseudotranslational symmetry (or maybe it's bad data).
I have used phaser to successfully solve a structure in P2x2x2x that had pseudo-translational symmetry. It was unable to correctly choose the space group, but after running phaser in all 8 possible space groups and inspecting the best solutions in each the correct solution was clear. Furthermore, it was the only MR program that worked. Was I just lucky? Sue On 9 Feb 2011, at 22:27, Phil Jeffrey wrote: Is there a program that does ? I was under the impression that they were all equally good/bad at this, because any solution that agrees with the PTS has quite a high score and any solution that doesn't has a low score, irrespective of the correctness of the placement of the molecules. In one case that ritually defeats me with quite strong pseudo-centering, this seems to be true for heavy atom searches also. Phil Jeffrey Princeton On 2/9/11 5:08 PM, Jon Schuermann wrote: I would NOT use Phaser for MR with PTS present. It doesn't handle it correctly yet, since the likelihood targets don't account for PTS. Others may be able to explain it better. Dr. Sue A. Roberts Dept. of Chemistry and Biochemistry University of Arizona 1041 E. Lowell St., Tucson, AZ 85721 Phone: 520 621 8171 s...@email.arizona.edu http://www.biochem.arizona.edu/xray
Re: [ccp4bb] First images of proteins and viruses caught with an X-ray laser
This was molecular replacement from 1jb0, so the phases came from the model. Probably more properly called direct refinement since all we did was a few cycles of rigid body. Personally, I was quite impressed by how good the R factors were, all things considered. -James Holton MAD Scientist On Wed, Feb 9, 2011 at 2:56 PM, Bernhard Rupp (Hofkristallrat a.D.) hofkristall...@gmail.com wrote: Any idea where then phases came from? BR -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Thomas Juettemann Sent: Wednesday, February 09, 2011 12:16 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] First images of proteins and viruses caught with an X-ray laser Thank you for clarifying this James. Those details are indeed often lost/misinterpreted when the paper is discussed in journal club, so your comment was especially helpful. Best wishes, Thomas On Wed, Feb 9, 2011 at 20:38, James Holton jmhol...@lbl.gov wrote: As one of the people involved (I'm author #74 out of 88 on PMID 21293373), I can tell you that about half of the three million snapshots were blank, but we wanted to be honest about the number that were collected, as well as the minimum number that were needed to get a useful data set. The blank images were on purpose, since the nanocrystals were diluted so that there would be relatively few double-hits. As many of you know, multiple lattices crash autoindexing algorithms! Whether or not a blank image or a failed autoindexing run qualifies as conforming to our existing model or not I suppose is a matter of semantics. But yes, I suppose some details do get lost between the actual work and the press release! In case anyone wants to look at the data, it has been deposited in the PDB under 3PCQ, and the detailed processing methods published under PMID: 20389587. -James Holton MAD Scientist On 2/9/2011 10:38 AM, Thomas Juettemann wrote: http://www.nanowerk.com/news/newsid=20045.php http://home.slac.stanford.edu/pressreleases/2011/20110202.htm I think it is pretty exciting, although they only take the few datasets that conform to their existing model: The team combined 10,000 of the three million snapshots they took to come up with a good match for the known molecular structure of Photosystem I.
[ccp4bb] CCP4i doesn't run
Hi, I am using CCP4 6.1.13 in Windows 7. It worked fine after installation, but now stopped running after I moved CCP4-DATABASE to a subdirectory for consolidation. So I uninstalled the whole program and removed folders (CCP4-Packages and Ccp4Temp) from C: drive, and then I downloaded it again and reinstalled the program, however the problem doesn't go away. It did ask me to override a lock once. It stops with the following message: ERROR no project database directory: C:/Ccp4Temp/CCP4_DATABASE Please set up a project directory using the DirectoriesProjectDir window from the main CCP4i interface, and then rerun this job. In the assigned project directory, CCP4_DATABASE folder exists and contains 2 files: database (def file), and database (Lock file). C:/Ccp4Temp is empty. I shouldn't have messed up with the directories, but can anyone help? Thanks, Yong-Fu
Re: [ccp4bb] First images of proteins and viruses caught with an X-ray laser
According to the paper, the data was refined in REFMAC in 'twin mode' which, I believe, calculates the R-factor using a non-conventional R-factor equation which usually lower than the conventional R-factor. I believe this is dependent on the twin fraction which wasn't mentioned in the paper (or supplementary info) unless I missed it. Jon -- Jonathan P. Schuermann, Ph. D. Beamline Scientist NE-CAT, Building 436E Advanced Photon Source (APS) Argonne National Laboratory 9700 South Cass Avenue Argonne, IL 60439 email: schue...@anl.gov Tel: (630) 252-0682 Fax: (630) 252-0687 On 02/09/2011 05:11 PM, James Holton wrote: This was molecular replacement from 1jb0, so the phases came from the model. Probably more properly called direct refinement since all we did was a few cycles of rigid body. Personally, I was quite impressed by how good the R factors were, all things considered. -James Holton MAD Scientist On Wed, Feb 9, 2011 at 2:56 PM, Bernhard Rupp (Hofkristallrat a.D.) hofkristall...@gmail.com mailto:hofkristall...@gmail.com wrote: Any idea where then phases came from? BR -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Thomas Juettemann Sent: Wednesday, February 09, 2011 12:16 PM To: CCP4BB@JISCMAIL.AC.UK mailto:CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] First images of proteins and viruses caught with an X-ray laser Thank you for clarifying this James. Those details are indeed often lost/misinterpreted when the paper is discussed in journal club, so your comment was especially helpful. Best wishes, Thomas On Wed, Feb 9, 2011 at 20:38, James Holton jmhol...@lbl.gov mailto:jmhol...@lbl.gov wrote: As one of the people involved (I'm author #74 out of 88 on PMID 21293373), I can tell you that about half of the three million snapshots were blank, but we wanted to be honest about the number that were collected, as well as the minimum number that were needed to get a useful data set. The blank images were on purpose, since the nanocrystals were diluted so that there would be relatively few double-hits. As many of you know, multiple lattices crash autoindexing algorithms! Whether or not a blank image or a failed autoindexing run qualifies as conforming to our existing model or not I suppose is a matter of semantics. But yes, I suppose some details do get lost between the actual work and the press release! In case anyone wants to look at the data, it has been deposited in the PDB under 3PCQ, and the detailed processing methods published under PMID: 20389587. -James Holton MAD Scientist On 2/9/2011 10:38 AM, Thomas Juettemann wrote: http://www.nanowerk.com/news/newsid=20045.php http://home.slac.stanford.edu/pressreleases/2011/20110202.htm I think it is pretty exciting, although they only take the few datasets that conform to their existing model: The team combined 10,000 of the three million snapshots they took to come up with a good match for the known molecular structure of Photosystem I.
[ccp4bb] ctruncate - FP=0?
I observe under some conditions that ctruncate sets some reflections amplitudes to zero. AFAIU, this should not be happening as even negative intensities (there are none in this particular dataset) should produce FP0 upon truncation. 66 out of ~23000 reflections are zeros after ctruncate is applied. Nothing obvious comes up upon inspecting the corresponding hkl's, except that one and only one is always zero (sg is P21212, so these are not systematic absences). One curious thing is that the I/sigma for these reflections is close to the average I/sigma in the highest resolution range (but it varies and these reflections are in all resolution ranges). A bug? -- I'd jump in myself, if I weren't so good at whistling. Julian, King of Lemurs
Re: [ccp4bb] First images of proteins and viruses caught with an X-ray laser
I performed DEN-refinement with CNS using the same data and starting model, and obtained similar twinned R values and maps. The twin fraction is 0.5. Axel On Feb 9, 2011, at 3:29 PM, Jon Schuermann wrote: According to the paper, the data was refined in REFMAC in 'twin mode' which, I believe, calculates the R-factor using a non-conventional R-factor equation which usually lower than the conventional R-factor. I believe this is dependent on the twin fraction which wasn't mentioned in the paper (or supplementary info) unless I missed it. Jon -- Jonathan P. Schuermann, Ph. D. Beamline Scientist NE-CAT, Building 436E Advanced Photon Source (APS) Argonne National Laboratory 9700 South Cass Avenue Argonne, IL 60439 email: schue...@anl.gov Tel: (630) 252-0682 Fax: (630) 252-0687 On 02/09/2011 05:11 PM, James Holton wrote: This was molecular replacement from 1jb0, so the phases came from the model. Probably more properly called direct refinement since all we did was a few cycles of rigid body. Personally, I was quite impressed by how good the R factors were, all things considered. -James Holton MAD Scientist On Wed, Feb 9, 2011 at 2:56 PM, Bernhard Rupp (Hofkristallrat a.D.) hofkristall...@gmail.com wrote: Any idea where then phases came from? BR -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Thomas Juettemann Sent: Wednesday, February 09, 2011 12:16 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] First images of proteins and viruses caught with an X-ray laser Thank you for clarifying this James. Those details are indeed often lost/misinterpreted when the paper is discussed in journal club, so your comment was especially helpful. Best wishes, Thomas On Wed, Feb 9, 2011 at 20:38, James Holton jmhol...@lbl.gov wrote: As one of the people involved (I'm author #74 out of 88 on PMID 21293373), I can tell you that about half of the three million snapshots were blank, but we wanted to be honest about the number that were collected, as well as the minimum number that were needed to get a useful data set. The blank images were on purpose, since the nanocrystals were diluted so that there would be relatively few double-hits. As many of you know, multiple lattices crash autoindexing algorithms! Whether or not a blank image or a failed autoindexing run qualifies as conforming to our existing model or not I suppose is a matter of semantics. But yes, I suppose some details do get lost between the actual work and the press release! In case anyone wants to look at the data, it has been deposited in the PDB under 3PCQ, and the detailed processing methods published under PMID: 20389587. -James Holton MAD Scientist On 2/9/2011 10:38 AM, Thomas Juettemann wrote: http://www.nanowerk.com/news/newsid=20045.php http://home.slac.stanford.edu/pressreleases/2011/20110202.htm I think it is pretty exciting, although they only take the few datasets that conform to their existing model: The team combined 10,000 of the three million snapshots they took to come up with a good match for the known molecular structure of Photosystem I.
Re: [ccp4bb] First images of proteins and viruses caught with an X-ray laser
The twin fraction for REFMAC was exactly 0.5. The individual crystals were not twinned (or at least I would be VERY surprised if they were), but they do belong to the space group P63, and autoindexing will give you one of the two possible axis conventions at random. So, of the 15445 crystals that were merged, there were about ~7700 indexed one way and 7700 indexed the other way. It is hard to tell exactly. Mergeing the data blindly (which we did) will result in a twinned data set where each merged h,k,l has an equal contribution from k,h,-l. This was all discussed in the data processing paper PMID: 20389587. Obviously, there are a number of things you can think of for resolving this indexing ambiguity and removing the twinning effect, and in fact, this is what I thought was really cool about this particular kind of data collection and why I encouraged the people doing all the work (the other 87 authors) to go ahead with a twinnable space group. On the first pass, you can just take advantage of TWIN refinement in REFMAC, but in the future, when the indexing improves (probably using post-refinement) it may be possible to de-twin a crystal system that actually suffers from real twinning. That is, a twin domain cannot be smaller than a mosaic block (otherwise the h,k,l and -k,h,-l structure factors would add as phased Fs, not |F|^2). So, since nanocrystals are essentially single mosaic blocks (smaller than the coherence length of the beam), you could take your twinned crystals and either grind them up or re-optimize for smaller crystals (counterintuitive!), and then resolve the twin domains manually. Sort of like Louis Pasteur and his tartaric acid crystals. Anyway, I thought that was a cool idea, but like so many other cool things, it had to be cut from the Nature paper. Admittedly, the problem has not actually been solved yet. This is why we used REFMAC in TWIN mode. -James Holton MAD Scientist On Wed, Feb 9, 2011 at 3:29 PM, Jon Schuermann schue...@anl.gov wrote: According to the paper, the data was refined in REFMAC in 'twin mode' which, I believe, calculates the R-factor using a non-conventional R-factor equation which usually lower than the conventional R-factor. I believe this is dependent on the twin fraction which wasn't mentioned in the paper (or supplementary info) unless I missed it. Jon -- Jonathan P. Schuermann, Ph. D. Beamline Scientist NE-CAT, Building 436E Advanced Photon Source (APS) Argonne National Laboratory 9700 South Cass Avenue Argonne, IL 60439 email: schue...@anl.gov Tel: (630) 252-0682 Fax: (630) 252-0687 On 02/09/2011 05:11 PM, James Holton wrote: This was molecular replacement from 1jb0, so the phases came from the model. Probably more properly called direct refinement since all we did was a few cycles of rigid body. Personally, I was quite impressed by how good the R factors were, all things considered. -James Holton MAD Scientist On Wed, Feb 9, 2011 at 2:56 PM, Bernhard Rupp (Hofkristallrat a.D.) hofkristall...@gmail.com wrote: Any idea where then phases came from? BR -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Thomas Juettemann Sent: Wednesday, February 09, 2011 12:16 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] First images of proteins and viruses caught with an X-ray laser Thank you for clarifying this James. Those details are indeed often lost/misinterpreted when the paper is discussed in journal club, so your comment was especially helpful. Best wishes, Thomas On Wed, Feb 9, 2011 at 20:38, James Holton jmhol...@lbl.gov wrote: As one of the people involved (I'm author #74 out of 88 on PMID 21293373), I can tell you that about half of the three million snapshots were blank, but we wanted to be honest about the number that were collected, as well as the minimum number that were needed to get a useful data set. The blank images were on purpose, since the nanocrystals were diluted so that there would be relatively few double-hits. As many of you know, multiple lattices crash autoindexing algorithms! Whether or not a blank image or a failed autoindexing run qualifies as conforming to our existing model or not I suppose is a matter of semantics. But yes, I suppose some details do get lost between the actual work and the press release! In case anyone wants to look at the data, it has been deposited in the PDB under 3PCQ, and the detailed processing methods published under PMID: 20389587. -James Holton MAD Scientist On 2/9/2011 10:38 AM, Thomas Juettemann wrote: http://www.nanowerk.com/news/newsid=20045.php http://home.slac.stanford.edu/pressreleases/2011/20110202.htm I think it is pretty exciting, although they only take the few datasets that conform to their existing model: The team combined 10,000 of the three million snapshots they took to come up with a good match for the
Re: [ccp4bb] Ken Olsen, Founder of Digital Equipment Corporation, Died Sunday
Hi Dale, Thanks for posting this interesting piece of history. My non-PX initiation into PX was through DEC too. On a summer internship in 1996 after my junior year, I landed up at this institute which had just received their new DEC ALPHA2000. My project was to write up a C code (I had recently finished with PASCAL and wanted to try out something else) to read all the PDB CD-ROMs (that's how they were distributed back then, at least in India), extract out the parts of the loop regions from the coordinate files and build up a library of loop regions for modeling. There was hardly anyone using the computer at that time and so I got almost exclusive use of it for 2 months. (The previous summer I had been learning molecular dynamics simulations and theory to model the folding of a peptide under different dielectric environment, to simulate a cytoplasmic hydrophilic vs. membrane hydrophobic environment using another 2 legacy items: BIOSYM's INSIGHTDISCOVER running on a SG...I was driven after recently watching Jurassic Park and knowing that a lot of the graphics had been created on SGs). Too bad that they lost out to the competition despite all their innovations. I hope he and his company will be remembered for all their achievements. Regards, -Debanu. From: Dale Tronrud det...@uoxray.uoregon.edumailto:det...@uoxray.uoregon.edu Date: Tue, Feb 8, 2011 at 11:47 PM Subject: [ccp4bb] Ken Olsen, Founder of Digital Equipment Corporation, Died Sunday To: CCP4BB@jiscmail.ac.ukmailto:CCP4BB@jiscmail.ac.uk I see in the news that Ken Olsen has died. Although he was not a crystallographer I think we should stop for a moment to remember the profound impact the company that this man founded had on our field. My first experience in a crystallography lab was as an undergraduate in M. Sundaralingam's lab in Madison Wisconsin. While I never had the opportunity to use them, his two diffractometers were controlled by the ubiquitous PDP-8 computers. I had more experience with his main computer, which was either a PDP-11/34 or 35 (Ethan help me out!). This was connected to a Vector General graphics display running software called UWVG. Having the least stature in the lab I got the midnight to 4am time slot for model building. The computer took about 10 minutes to compute and contour each block of map, covering about three residues. While waiting I would crawl under the DECwriter and nap. The computer would stop rattling when the map was up and that would wake me. When I joined the Matthews lab in Oregon they had a VAX 11/780. What an amazing machine! It had 1 MB of RAM and could run a million instructions in a second. It only took 48 hours to run a cycle of refinement with PROLSQ, that is, if no one else used the computer. These specs don't sound like much but this computer was really a revolution for computational crystallography. That a single lab could own a computer of such power was unheard of before this. It wasn't just that the computer had so much RAM (We later got it up to its max of 4 MB.) but the advent of virtual memory made program design so much easier. You could simply define an array of 100,000 elements and not have to worry about finding where in memory, mixed in with the operating system, utility programs, and other users' software, you could find an unused block that big. Digital didn't invent virtual memory, but the VAX made it achievable for regular crystallographers. Through most of the 1980's you didn't have to worry about getting your code to run on other computers - Everyone had access to a VAX. In the 1990's DEC came out with the alpha CPU chip which really broke ground for performance. These things screamed when in came to running crystallographic software. In 1999 the lab bought several of the 666 MHz models. It was about four years before Intel came out with a chip that would match these alphas on my crystallography benchmark and they had to be clocked at over 2 GHz to do it. Yes, Digital lost out in the competition of the marketplace, and Ken Olsen was pushed out of the company well before the end. But what a ride it was. What great computers they were and what great science was done on them! Dale Tronrud
[ccp4bb] coot-scripting
Hi, I'm using COOT-0.6 following the manual,but while trying to use (calculatescripting)python or (calculatescripting)scheme to write any command (say,set_show_origin_marker 0) it shows BL WARNING:: Python syntax error! (Or you attempted to use an invalid guile command...) Python error: unexpected EOF while parsing (string, line 1) type 'exceptions.SyntaxError' Please suggest me the correction to run the command correctly. Thanking you, Seema Nath
Re: [ccp4bb] coot-scripting
Hi Seema, for python scripting in Coot (and syntax) you may want to refer to the WIKI: http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Coot#Python_Scripts or the manual: http://www.biop.ox.ac.uk/coot/doc/user-manual.html#Scripting I meant to complete a more comprehensive manual/tutorial on this, but it takes time... Hope this helps, B P.S. There is a specific Coot BB too: http://www.biop.ox.ac.uk/coot/mailing-list.html Hi, I'm using COOT-0.6 following the manual,but while trying to use (calculatescripting)python or (calculatescripting)scheme to write any command (say,set_show_origin_marker 0) it shows BL WARNING:: Python syntax error! (Or you attempted to use an invalid guile command...) Python error: unexpected EOF while parsing (string, line 1) type 'exceptions.SyntaxError' Please suggest me the correction to run the command correctly. Thanking you, Seema Nath
