Re: [ccp4bb] sftools and batch mode
Easier to use CAD for this! SFTOOLS is too clever.. Eleanor On 7 January 2015 at 03:45, Seth Harris set...@gmail.com wrote: Hi all, I have a heterogeneous collection of mtz files I'm trying to whip into some kind of standardized vocabulary shape, namely setting column names and types so that subsequent scripts can sensibly make maps and so forth. I have set up the ever-useful sftools to do most of this, but of course sftools scripts rely on one providing a series of answers to questions you think it is going to ask, and by its own admission it was designed to be used interactively and includes various protections which, also by its own admission, makes it harder to use it in batch mode... Because it finds files with interesting columns (e.g. only 1's and 0's) that prompt it to ask you unexpected questions (e.g. is this an X-plor Rfree column? despite the Rfree_flag title and the 5% population of 1's ; ). , for which your prescribed answers no longer apply (and my log files end up with inane computer v computer dialogues like You must answer Y or N! You must answer Y or N! You must answer...etc.) So, presumably the number of exceptional cases is finite (though tedious) and I can just carry on dealing with them one after the other and learn to be a better coder, but... My question: is there some way to turn off these protections (i.e. please just read in the file without question!), or some version of SFTOOLS that is more batch-friendly about which I'm not yet aware? It would be nice to have something that can more programmatically interrogate mtz column headers and respond sensibly rather than this kind of 20 questions you do when you have to read the header and then parse the names and then ask a series of is it Rfree? is it CV? is it bigger than a breadbox? type stuff. Again, I know the sftools documentation is clear that the design goal was for interactive use and humans have little trouble with such questions, but when there might be several thousand of them... Thanks for any pointers or alternatives! Seth
[ccp4bb] problems with wincoot 8.1 on windows 7 with multiple desktop
Dear CCP4 users, I just installed the latest CCP4 / wincoot on my windows 7 machine. This machine runs also the dexpot software in order to have multiples desktop. Wincoot runs fine as long as I don't switch to an other desktop. If I do and come back to the desktop where wincoot is displayed, I get a blank wincoot windows : menus and buttons are still available, but the graphic window is grey... Wincoot appears however to still run normally (I can see that hitting the barspace changes to the next residue, as indicated by the text as the bottom of the windows) but the graphic remains blank... Things were fine with wincoot 0.7.2... any ideas ?? thanks laurent -- -- Laurent Maveyraud laurent.maveyraud AT ipbs DOT fr P I C T --- Plateforme Intégrée de Criblage de Toulouse Université Paul Sabatier / CNRS / I.P.B.S. UMR 5089 Département BiologieStructurale et Biophysique http://cribligand.ipbs.fr http://www.ipbs.fr 205 route de Narbonne 31077 TOULOUSE Cedex FRANCE Tél: +33 (0)561 175 435 Fax : +33 (0)561 175 994 --
[ccp4bb] Postdoctoral Research Associate at Nottingham University
Job Title Research Associate Applications are invited for a Research Associate position funded by the Medical Research Council (MRC) for 3 years in the Centre for Biomolecular Sciences, Nottingham University. The project title is: ADAMTS13 structure and the molecular basis of VWF recognition and cleavage. You will join a well-established research group studying haemostatic proteins. Specifically, the project will explore the structure and biochemistry of ADAMTS13. ADAMTS13 is a multidomain plasma metalloprotease that regulates von Willebrand factor (VWF) platelet-tethering function through a single, highly specific proteolytic event. Deficiency in ADAMTS13 or VWF causes thrombotic and bleeding disorders, respectively. The activity and specificity of ADAMTS13 is manifest through the functional dependency upon multiple exosite interactions with its substrate (VWF). How these interactions are mediated and precisely what effect these have upon ADAMTS13 structure, conformation and function is unclear. This project will aim to probe the functionality of these ADAMTS13 exosites and key structural features of ADAMTS13 through biochemical and crystallographic analyses. There are two postdoctoral posts associated with the grant, one is required to have skills in protein crystallographic structure determination and analysis based in Nottingham. The second post is based at Imperial College using a wide range of techniques, ranging from recombinant protein _expression_ (mammalian, insect and bacteria), protein purification, protein biochemistry and enzyme kinetic analyses during the course of this project. We are looking highly motivated candidates preferably with an interest in haemostasis and a high standard of writing and presentation skills. You will have a PhD as a requirement. Salary starting salary up to £36,340 per annum Full-time, fixed-term available (3 years) from May 1st 2015 until April 30th 2018 Further information about the research activity of the nottingham and imperial college labs are http://www.nottingham.ac.uk/research/groups/structural-biology/index.aspx http://www1.imperial.ac.uk/departmentofmedicine/divisions/experimentalmedicine/haematology/coag/ For informal enquiries please contact: Dr Jonas Emsley jonas.ems...@nottingham.ac.uk ##Dr Jonas EmsleyProfessor of Macromolecular Crystallography,Division of Medicinal Chemistry Structural Biology,Centre for Biomolecular Sciences,School of Pharmacy,University of Nottingham,University Park,Nottingham.NG72RDTel: +44 1158467092Fax: +44 1158468002email:jonas.ems...@nottingham.ac.ukhttp://www.nottingham.ac.uk/research/groups/structural-biology/index.aspx This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system, you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.
[ccp4bb] Postdoctoral Position to work on membrane protein crystallography at the University of Western Australia
Structural Biology of Molecular Targets from Neisseria A postdoctoral research associate position is available to pursue crystallographic studies of membrane protein targets from Neisseria in Prof. Alice Vrielink’s laboratory at the University of Western Australia, Perth. The position will involve expression and purification of target proteins followed by downstream crystallographic studies. A number of target enzymes are already in crystal form and studies are being directed towards inhibitor design. Other targets will also be pursued. We are seeking applicants with a PhD in Biochemistry or a related discipline and with experience at macromolecular crystallography. A strong background in molecular biology, protein expression and purification of membrane proteins is also essential. The appointee will carry out research in the Vrielink laboratory but will also be part of a multidisciplinary team involving chemists and microbiologists with outstanding expertise at the study of Neisseria. As such this position offers excellent opportunities to interact across multiple disciplines and hence extend research expertise and career development. The Structural Biology Laboratory at the University of Western Australia has outstanding facilities for protein expression and purification as well as in-house X-ray facilities including a rotating anode generator and two MAR Imaging plate detectors. Crystallization and liquid handling robots are also available for crystallization experiments. The laboratory also houses state of the art protein facilities to study protein-protein and protein-ligand interactions include isothermal titration calorimetry, SEC-MALLS, and microscale thermophoresis. High resolution X-ray data collection will be carried out at the Australian Synchrotron. Perth is a thriving and vibrant city, which lies along the Indian Ocean and benefits from outstanding natural beauty and many opportunities for outdoor activities. Benefits include generous superannuation and salary packaging opportunities. Closing date: Friday 30 January 2015 Applications must be submitted online. Full details of the position's responsibilities and the selection criteria are outlined in the position description and applicants should clearly demonstrate they meet the selection criteria. Please see http://external.jobs.uwa.edu.au/cw/en/job/493825/research-associate-ref-493825 for further details and for information about applying. If you have any further questions about the position please contact me directly. Kind regards Alice Vrielink ** Alice Vrielink Professor of Structural Biology School of Chemistry and Biochemistry M310 University of Western Australia 35 Stirling Highway Crawley, WA, 6009 Australia Email: alice.vriel...@uwa.edu.aumailto:alice.vriel...@uwa.edu.au Phone: +61 08 6488 3162 Fax:+61 08 6488 1005 Webpage: http://crystal.bcs.uwa.edu.au/px/alice/ We are what we repeatedly do. Excellence, then, is not an act, but a habit. Aristotle **
[ccp4bb] Announcement: CCP4 crystallographic summer school in USA, at APS, June 16-23
Dear Colleagues, We are pleased to announce the eighth annual CCP4 crystallographic summer school at Advanced Photon Source (APS), Argonne National Laboratory (ANL). All details can be found at http://www.ccp4.ac.uk/schools/APS-2015/index.phphttp://www.ccp4.ac.uk/schools/APS-2014/index.php Title: CCP4 crystallographic school: From data collection to structure refinement and beyond Dates: June 16 through 23 Site: Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois (Near Chicago), USA The school content: Data collection workshop the first three days: beamline training and data collection on GM/CA@APS beamlines 23ID-B and 23ID-D. For data collection, only the participants' crystals will be used. Software workshop: The rest of the time after data collection will feature many modern crystallographic software packages taught by authors and other experts. The daily schedule will be organized in three sections – lectures, tutorials and hands-on trouble-shooting. There will be model data sets available for tutorials but data, provided by participants, will have higher priority for the hands-on sessions. Applicants: Graduate students, postdoctoral researchers and young scientists at the assistant professor level are encouraged to apply. Only 20 applicants will be selected for participation. Participants of the workshop are strongly encouraged to bring their own problem data sets or crystals so the problems can be addressed during data collection and/or computation workshops. Application: Application deadline is April 16. The application form, the program, contact info and other details can be found at http://www.ccp4.ac.uk/schools/APS-2015/index.php Fees: There is no fee for the workshop. The students will be responsible for their transportation and lodging. The workshop organizers can assist in making the reservations at economical lodging at the Argonne Guest House. The workshop will cover the expenses for all meals and refreshments. We hope to see you at the school, Garib, Ronan and Nukri Ruslan Sanishvili (Nukri) Macromolecular Crystallographer GM/CA@APS X-ray Science Division, ANL 9700 S. Cass Ave. Lemont, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsanishv...@anl.gov
[ccp4bb] Ugly fonts in ccp4i under Linux...
Hi! I don't know if anyone else is having problems with ccp4i fonts looking very ugly under Linux, in particular recent versions of Ubuntu? I couldn't find anything about it online. Well, if you are, I have the solution. 1. Install at least the xfonts-75dpi or xfonts-100dpi packages 2. Create a .rootrc file in your home directory containing X11.UseXft: Yes The following commands should it for you. You'll have to enter your password after the first step: sudo apt-get install xfonts-100dpi echo X11.UseXft: Yes .rootrc Kevin -- EMAIL DISCLAIMER: http://www.york.ac.uk/docs/disclaimer/email.htm
[ccp4bb] Postdoctoral position available at UT Southwestern Medical Center at Dallas
A postdoctoral researcher position has just become available in Dr. Hong Zhang’s laboratory to study mammalian circadian clocks. The overall goal of the project is to understand how various multi-domain clock proteins interact with each other; and how these interactions are modulated to regulate the clock-mediated transcription activation. A number of multi-protein complexes have been over-expressed, reconstituted, and purified for crystallization experiments. We are looking for a highly motivated postdoctoral fellow with a Ph.D. degree in a relevant field. He or she should be proficient in molecular cloning, protein expression, purification, crystallization, and X-ray crystal structure determination. Additional experiences in insect cell protein expression systems and various biochemical and biophysical techniques to study protein-protein interactions are particularly helpful. If you are interested in this position, please email your CV and contact info of two or more referees to zh...@chop.swmed.edu. Happy New Year and all the Best! Hong Zhang, Ph.D. Associate Professor Department of Biophysics and Department of Biochemistry UT Southwestern Medical Center at Dallas 4323 Harry Hines Blvd. Dallas, Texas 75390-8816 Phone: 214-645-6372 Fax: 214-645-5948 http://profiles.utsouthwestern.edu/profile/23445/hong-zhang.html
[ccp4bb] Tenure-track faculty positions in Immunity and Inflammation
Employer Rutgers Biomedical and Health Sciences, New Jersey Medical School Location Newark, NJ Discipline Life Sciences, Immunology Position Type Full Time Job Type Faculty Salary Academic rank and salary will be commensurate with qualifications and experience The Center for Immunity and Inflammation (CII) at New Jersey Medical School, Rutgers Biomedical and Health Sciences, located in Newark, NJ, invites applications for full time, tenure-track appointments at the Associate or Assistant Professor level. Faculty candidates will be considered in all areas of immunology, with a special focus on host-microbe interactions, immunopathology, and global health. The positions will be supported by competitive start up packages with exceptional candidates being considered for further support as Chancellor Scholars. Candidate Requirements: Applicants must have a Ph.D., M.D., or equivalent degree, post-doctoral experience, excellent communication skills and a record of productivity in immunology. Candidates at the Assistant Professor level should have a substantial trajectory toward developing a rigorous, externally-funded immunology research program. Candidates at the Associate Professor level should have a national scientific reputation, current research funding and a history of mentorship and leadership. The Center for Immunity and Inflammation: The Center is an integral part of the newly established Institute for Infectious and Inflammatory Diseases (i3D) at RBHS. Research in Infection and Inflammation has been selected for strategic development at RBHS with a vision of transforming this already strong program into a center of excellence and international reputation. With the creation of RBHS in July 2013 Rutgers University has become one of the most comprehensive university-based centers for improving human health and health care. We seek candidates to join CII at a pivotal time of growth in research excellence. Core resources include flow cytometry and cell sorter capability for BSL-2 and BSL-3 infectious disease research, histology, confocal, live-cell imaging, animal facilities including a nationally-designated BL3 laboratory and animal housing facilities, and an applied genomics center. Application Process: Applicants should submit a: (1) cover letter, (2) summary of present and future research plans, (3) curriculum vitae, and (4) names/email addresses of three references to: jennifer.ya...@njms.rutgers.edu Rutgers, the State University of New Jersey, is an Equal Opportunity/Affirmative Action employer, and is compliant with the Americans with Disabilities Act (ADA). Women and minorities are encouraged to apply. For more information, please visit http://jobs.rutgers.edu/TheRUCommitment.htm.
[ccp4bb] Macromolecular Software Scientist
Dear Colleagues We are looking to recruit a Macromolecular Software Scientist to join the Biology and Soft Matter Division at Oak Ridge National Laboratory. Interested Parties can apply using the link below. For informal inquiries please contact Leighton Coates at coat...@ornl.gov https://recruiting.ornl.gov/sap/bc/webdynpro/sap/hrrcf_a_posting_apply?PARAM=cG9zdF9pbnN0X2d1aWQ9MDAxNTVEMEYzNDAxMUVENEE1RDRGREY0REU1N0Q0MTQmY2FuZF90eXBlPUVYVA%3d%3dsap-client=010sap-language=EN *Macromolecular Software Scientist-NB50468984* Purpose: The Biology and Soft Matter Division (BSMD) of the Neutron Scattering Sciences Directorate (NScD) seeks highly qualified applications for a Staff Scientist position with expertise in computational crystallography. The function of this position is to develop and lead a research program in the field of crystallographic methodology for TOF data analysis of macromolecular structures using neutron diffraction data: while also developing innovative concepts and tools expanding and optimizing the capabilities of neutron instrumentation in application to macromolecular materials. Major Duties/Responsibilities Work on time of flight macromolecular data reduction software development. Conduct and present high-quality, high-impact research in the field of macromolecular crystallography with focus on neutron diffraction techniques. Collaborate with structural biology community in support of its needs for macromolecular structure analysis using neutron and X-ray scattering data. Work closely with instrument scientists and other team members developing and advancing single event data analysis and processing methods for the center's neutron scattering instruments. - Provide feedback to the Neutron Data Analysis Visualization (NDAV) group, Data Acquisition System (DAS) group, Detector Group to improve applications and instrumentation produced by those groups. - Assist with instrument validation and commissioning. - Represent SNS at conferences and/or workshops presenting and promoting its capabilities for the structural biology community. - Train internal and external facility users on how to use software and systems produced. Qualifications Required Successful candidate must have PhD in crystallography, with an emphasis on computational methods, with at least five years of related experience and demonstrated accomplishments in the field. The applicant must have documented experience in developing computational methods and software for the analysis of macromolecular crystallographic data. Experience of modern programming languages such as C, C++ and Python is required. The applicant must have good organizational and management skills and have the ability to interact effectively with colleagues displaying a broad range of expertise and interests. Qualifications Desired: Candidates should be able to work effectively with colleagues in a collaborative research environment. Work Directions and Interfaces Position reports to the MaNDi Group Leader and works closely with the MaNDi instrument team. Works with members of Computing Group and interfaces with Users and instrument scientists within NScD. Will also interface with personnel from DAS Group, User Office, and NScD IT. Collaborates with software developers at other facilities and in the User community to develop software. Works well as a team member leading when necessary, in addition, performs work independently with little guidance. Measures of Effectiveness Produces user-friendly software. Distributed software is widely adopted by User community, as assessed by citations in the scientific literature. Instrument Scientists and Users are satisfied with application capabilities. Demonstrate leadership and skill for developing software – develops a good reputation within NSSD. Produces software related documentation. Works effectively in a team environment. Performs work independently. Promotes NSSD throughout the User community when participating in meetings, workshops, or conferences. If you have trouble applying for a position, please email ornlrecruit...@ornl.gov. ORNL is an equal opportunity employer. All qualified applicants, including individuals with disabilities and protected veterans, are encouraged to apply. UT-Battelle is an E-Verify Employer.
Re: [ccp4bb] CCP4 Release 6.5
OK I tried this on a 3rd machine (6.4 to 6.5 w/o uninstall of 6.4 before 6.5 install). Same result. Window attached. Somehow it seems the shortcut icon does not properly update. Its command becomes C:\CCP4\TclTk84\bin\wish.exe C:\CCP4\6.5\share\ccp4i\bin\ccp4i.tcl Changing the command to C:\CCP4\ccp4i.bat fixes the problem. Attached as ccp4i.fat (to fool the mail attachment police). Maybe the attached info helps. 3x seems to show a patternthe only constant is me so maybe my fault... Best, BR -- This e-mail and any attachments do not contain confidential, copyright and or privileged material. Everyone can read it and do with it whatsoever. If you are not the intended addressee or an authorised recipient of the addressee please do not waste any time notifying us of receipt by returning the e-mail because we do not care if you use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of the rest of the world (ROW). ROW Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. ROW Limited (company no. 42) is registered in the Universe with its registered office pretty much anywhere on the 3rd planet including but not limited to Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom. -Original Message- From: Marcin Wojdyr [mailto:marcin.woj...@diamond.ac.uk] Sent: Wednesday, January 07, 2015 10:07 AM To: b...@hofkristallamt.org Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] CCP4 Release 6.5 On Mon, Dec 22, 2014 at 10:43:27AM +0100, Bernhard Rupp wrote: Upon windows upgrade with default settings, the previous desktop icon 6.4 command line C:\CCP4\TclTk84\bin\wish.exe C:\CCP4\6.5\share\ccp4i\bin\ccp4i.tcl will not work anymore. I forgot to reply to this in December. I couldn't reproduce it. The icon was apparently updated (C:\CCP4\6.5\...) by the installer. The command is the same as in the previous versions, except for the path (6.5 instead of 6.4). Hard to tell what didn't work without more details. Sometimes changing environment variables in the registry has no effect until rebooting or logging out and in. Maybe this was the case. Marcin -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom ccp4i.fat Description: Binary data
[ccp4bb] PhD studentship opportunity in
Dear CCP4ers, Could you please pass on details of this studentship opportunity to any suitable candidates? Many thanks, Mike Fully-funded three year PhD Studentship: April 2015 Generating Structural Movies of Enzyme Catalysis Supervisor: Dr Mike Hough, University of Essex Project Overview X-ray crystal structures of enzymes are vital to our understanding of biology. Such structures, however, provide only discrete static steps of dynamic enzyme mechanisms. In this Leverhulme Trust-funded project you will use state of the art technology breakthroughs to overcome this limitation by creating ‘structural movies’ that fully reveal the catalytic functions of enzymes at atomic resolution. X-rays will be used to generate electrons within protein crystals. These electrons will migrate to redox centres and be used to initiate and drive enzyme catalytic cycles at will. Tools will be developed using emerging technologies, including ultrafast X-ray detectors allowing structures be measured in rapid succession,. Enzyme states generated in this way are representative of those in vivo, where the electrons that drive reactions would be provided by biological electron transfer. The successful applicant will develop skills in recombinant protein expression, protein crystallization, synchrotron X-ray crystallography, several single crystal spectroscopies and advanced data analysis. The PhD student will also have the exciting opportunity to work and conduct experiments at the Diamond Light Source UK (http://www.diamond.ac.uk/Home.html), the Swiss Light Source (http://www.psi.ch/sls/swiss-light-source) and the European Synchrotron Radiation Facility (http://www.esrf.eu/). A generous stipend is provided and Home/EU fees are fully covered. https://www.essex.ac.uk/pgapply/enter.aspx Requirements: A first or upper second class degree or MSc Merit/Distinction in a relevant subject. The successful candidate will have strong organizational skills, with good oral and written communication. The candidate will be self-motivated and a team player. Informal enquiries should be addressed to Dr Mike Hough maho...@essex.ac.uk Apply via: Deadline for applications: 31st January 2015
Re: [ccp4bb] Some advices on model modification
Hi Allen, MR with low homology search models is also sensitive to the quality of your dataset. Besides the other recommendations already offered make sure that your dataset is of high quality. I recommend collecting a couple of good natives and try them all in your search. Good luck Carsten From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of allen price Sent: Tuesday, January 06, 2015 7:06 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Some advices on model modification Dear all: I got a dataset at 2.8 angstron. I have tried several ways such as phaser, MRBUMP,BALBES,but still can't solve the data,which means I have to edit my model. Maybe I'd better cut it off or delete the water or loop. I really have no idea,as it is my first time to do such things, I alway used the whole model to mr. Could anyone give me some advice? what kind of software do you guys use? really need you help! Best regards, Allen
Re: [ccp4bb] sftools and batch mode
I agree with Eleanor. Sftools was designed for a different purpose. I does have a batch mode but I am not sure it will solve your problems completely and the little notice on top already indicates that this was never considered to be an ideal solution. Here is the MODE help page. You can give it a try but you may have to go back to good old CAD. Bart selected: MODE Notice: This option is will become obsolete in the next release. Try to avoid using it in scripts. OPTION: MODE BATCH | INTERACTIVE Bring the program in or out of Batch mode Use MODE BATCH when running SFTOOLS in batch This surpresses some questions by SFTOOLS, e.g. to hit return to see the next page in LIST REF Use MODE INTERACTIVE to return to interactive mode if that would ever be useful EXAMPLES: MODE BATCH MODE INTERACTIVE On Wed, Jan 7, 2015 at 2:57 AM, Eleanor Dodson eleanor.dod...@york.ac.uk wrote: Easier to use CAD for this! SFTOOLS is too clever.. Eleanor On 7 January 2015 at 03:45, Seth Harris set...@gmail.com wrote: Hi all, I have a heterogeneous collection of mtz files I'm trying to whip into some kind of standardized vocabulary shape, namely setting column names and types so that subsequent scripts can sensibly make maps and so forth. I have set up the ever-useful sftools to do most of this, but of course sftools scripts rely on one providing a series of answers to questions you think it is going to ask, and by its own admission it was designed to be used interactively and includes various protections which, also by its own admission, makes it harder to use it in batch mode... Because it finds files with interesting columns (e.g. only 1's and 0's) that prompt it to ask you unexpected questions (e.g. is this an X-plor Rfree column? despite the Rfree_flag title and the 5% population of 1's ; ). , for which your prescribed answers no longer apply (and my log files end up with inane computer v computer dialogues like You must answer Y or N! You must answer Y or N! You must answer...etc.) So, presumably the number of exceptional cases is finite (though tedious) and I can just carry on dealing with them one after the other and learn to be a better coder, but... My question: is there some way to turn off these protections (i.e. please just read in the file without question!), or some version of SFTOOLS that is more batch-friendly about which I'm not yet aware? It would be nice to have something that can more programmatically interrogate mtz column headers and respond sensibly rather than this kind of 20 questions you do when you have to read the header and then parse the names and then ask a series of is it Rfree? is it CV? is it bigger than a breadbox? type stuff. Again, I know the sftools documentation is clear that the design goal was for interactive use and humans have little trouble with such questions, but when there might be several thousand of them... Thanks for any pointers or alternatives! Seth -- Bart Hazes Associate Professor Dept. of Medical Microbiology Immunology University of Alberta
Re: [ccp4bb] CCP4 Release 6.5
On Mon, Dec 22, 2014 at 10:43:27AM +0100, Bernhard Rupp wrote: Upon windows upgrade with default settings, the previous desktop icon 6.4 command line C:\CCP4\TclTk84\bin\wish.exe C:\CCP4\6.5\share\ccp4i\bin\ccp4i.tcl will not work anymore. I forgot to reply to this in December. I couldn't reproduce it. The icon was apparently updated (C:\CCP4\6.5\...) by the installer. The command is the same as in the previous versions, except for the path (6.5 instead of 6.4). Hard to tell what didn't work without more details. Sometimes changing environment variables in the registry has no effect until rebooting or logging out and in. Maybe this was the case. Marcin -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom
[ccp4bb] CCP4 Study Weekend 2015 Advances in Experimental Phasing - Live Web Streaming
Dear All, The webcast for this year's CCP4 Study Weekend on Advances in Experimental Phasing taking place on the 8/9 of January will be available from the STFC Webinars page: http://www.stfc.ac.uk/webinars A programme for the meeting can be found here: http://www.ccp4.ac.uk/events/CCP4_2015/programme.html Best wishes, Ronan
Re: [ccp4bb] problems with wincoot 8.1 on windows 7 with multiple desktop
Dear Laurent, I run the same multiple desktops. The only convenient way I found to fix this is to show WinCoot on all desktops. Its due to the new graphics libraries which were updated and I didnt want to dive into this to fix it properly (I thought I would be the only one running this - obviously not). Anyway, not worth fixing it I decided. B Dear CCP4 users, I just installed the latest CCP4 / wincoot on my windows 7 machine. This machine runs also the dexpot software in order to have multiples desktop. Wincoot runs fine as long as I don't switch to an other desktop. If I do and come back to the desktop where wincoot is displayed, I get a blank wincoot windows : menus and buttons are still available, but the graphic window is grey... Wincoot appears however to still run normally (I can see that hitting the barspace changes to the next residue, as indicated by the text as the bottom of the windows) but the graphic remains blank... Things were fine with wincoot 0.7.2... any ideas ?? thanks laurent --- This email has been checked for viruses by Avast antivirus software. http://www.avast.com
