[ccp4bb] cryoprotectant for crystals in isopropanol
Dear all, The question is regarding the cryoprotectant.We have crystallized a protein in 20% PEG 500 with 10% isopropanol.What should be the cryo we should try for data collection.Also,what percentage of PEG 500 is sufficient enough as a cryo for data collection. We are also trying to crystallize it with higher PEG's also like 1K, 2K, 4K.Lets C.Since the condition is having isopropanol also and it is reported that mounting with isoprop is very difficult and it evaporates as soon as we open the slides. Thanx in advance... Shivesh Kumar
Re: [ccp4bb] Broken Masks
I think it is a version bug of some sort - when I ran the same mask creation run in CCP4i on my MacBook laptop (which has the most recent CCP4) it displays fine and also worked perfectly in dm averaging, turning a tangled mess into interpretable density. The mask generated by NCSMASK on my desktop Mac displayed weirdly in COOT on that machine, and crashed COOT on the laptop as soon as I treid to display it. Anyway the job is done - thanks for the advice. Laurence Daniel Anderson wrote: Could it be that NCSMASK folded the mask back into an asymmetric unit? My NCSMASK input file contains explicit xyzlim boundaries and notrim keyword. On Tue, 18 Mar 2008, Laurence Pearl wrote: I'm trying to generate a mask around a molecule using NCSMASK under the CCP4i interface, for ultimate use in NCS averaging and density modification in dm. Being a little old-fashioned I wanted to check that it covered the required molecule. However when displayed in COOT, there seem to be arbitary flat slabs running through the mask, with some sort of inversion or other transformation on the other side of the slab. The mask has a similar appearance in the CCP4mg. The flattenings are parallel to cell edges, and sometimes, but not always adjacent to cell faces. Is this a known problem ? is it NCSMASK ? or is it COOT and CCP4mg ? -- - Laurence H. Pearl PhD FMedSci Professor of Protein Crystallography and Section Chairman Section of Structural Biology, Institute of Cancer Research Chester Beatty Laboratories, 237 Fulham Road, London SW3 6JB Phone +44-(0)20 7153 5422 : Secretary 5443 : FAX 5457 - Live Simply and do Serious Things .. - Dorothy Crowfoot Hodgkin - The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.
[ccp4bb] The Lawnmower Man
Dear everyone, Has anybody tried to hook up a protein display/model building program/computer with 3D glasses of the type people are developing for games? The type of glasses where one obviates the use of large monitors altogether, that is the display sits on the glasses themselves. Thanks, Jordi Benach, PhD ALBA - Synchrotron Light Source Edifici Ciències Nord. Mòdul C-3 central. Universitat Autònoma de Barcelona 08193 Bellaterra, Barcelona SPAIN phone: +34 93 592 4333 fax : +34 93 592 4302 cell : +34 60 810 7080 http://www.i-glassesstore.com/ image001.jpg
Re: [ccp4bb] The Lawnmower Man
Wow, that is like, so last week(!). I'm using COOT though a wireless interface to a head-up-display mounted inside my contact lenses, controlled via a neural lace* embedded directly into my parietal lobe. I can refine and rebuild my structure whilst doing minipreps, having a coffee, in the shower, sitting in a seminar, anywhere. You're not seriously telling me you're still using a mouse, keyboard monitor, are you? CyberDave v3.0 *thanks to Ian M Banks for that one. On 19/03/2008, Jordi Benach [EMAIL PROTECTED] wrote: Dear everyone, Has anybody tried to hook up a protein display/model building program/computer with 3D glasses of the type people are developing for games? The type of glasses where one obviates the use of large monitors altogether, that is the display sits on the glasses themselves. Thanks, Jordi Benach, PhD ALBA - Synchrotron Light Source Edifici Ciències Nord. Mòdul C-3 central. Universitat Autònoma de Barcelona 08193 Bellaterra, Barcelona SPAIN phone: +34 93 592 4333 fax : +34 93 592 4302 cell : +34 60 810 7080 http://www.i-glassesstore.com/ -- David C. Briggs PhD Father Crystallographer http://www.dbriggs.talktalk.net AIM ID: dbassophile image001.jpg
[ccp4bb] Post-Doctoral position at the University of Dundee
UNIVERSITY OF DUNDEE COLLEGE OF LIFE SCIENCES DIVISION OF BIOLOGICAL CHEMISTRY AND DRUG DISCOVERY POSTDOCTORAL RESEARCH ASSISTANT GRADE 7 (£26,666 - £32,796) Enthusiastic, highly motivated individuals are sought to study key enzymes of microbial pathogens to advance fundamental understanding of the biosynthesis and inhibition of glycosylphosphatidylinositol anchor assembly in trypanosomatid parasites. The position are funded by a Wellcome Trust programme grant to Bill Hunter and to be held in a world-class interdisciplinary centre. Applicants are expected to have experience in protein crystallography or molecular biology, biochemistry or chemical crystallography. Experience in production of proteins in eukaryotic systems or in enzyme assay methods would be particularly welcome. The position is available for two years in the first instance. The level of appointment is flexible and will depend on experience and track record. Applicants are expected to have, or to obtain shortly, a PhD in a relevant subject. Training, as required will be provided in a supportive environment enabling researchers to extend their skills and expertise. Career progression is important and staff will be encouraged to participate in a wide range of research, and in this the ability to work well in a team will be critical. The successful candidate will benefit from access to cutting edge facilities in crystallography, biochemistry, cell biology, synthetic and medicinal chemistry, parasitology, drug discovery, proteomic and other core facilities. In addition to joining the Scottish Structural Proteomics Facility, a highly successful cooperative with The University of St. Andrews. Informal enquiries may be made to Prof Bill Hunter, tel: (01382) 385745 or e-mail: [EMAIL PROTECTED] (Please do not send applications to this email address). A few facts about The College of Life Sciences at Dundee: ● The College of Life Sciences has over 720 research and support staff from 54 countries and an annual research turnover in excess of £20 million. ● According to Thompson Scientific of Philadelphia, based on citations per paper over the last 10 years, Dundee is the top University in Europe in ‘Biology and Biochemistry’ and 2nd in Europe in ‘Molecular Biology and Genetics’. ● Dundee has twice been named ‘the best place to work in Europe’ in a poll of scientists conducted by The Scientist magazine. ● The College of Life Sciences has been consistently rated ‘5-star’ (the highest rating) by the UK national Research Assessment Exercise. In addition to an excellent scientific environment Tayside offers an affordable standard of living in an area of outstanding natural beauty situated beside the sea and the highlands of Scotland. Applications in the form of a CV and covering letter, including the names and addresses of 3 referees, should be sent to [EMAIL PROTECTED] quoting LS/2150. Alternatively, please send 2 copies of your CV and covering letter to Human Resources, College of Life Sciences, MSI/WTB/JBC Complex, University of Dundee, DD1 5EH. Applicants will only be contacted if invited for interview. Closing date: 18 April 2008 The University of Dundee is committed to equal opportunities and welcomes applications from all sections of the community. www.jobs.dundee.ac.uk Dr Paul K. Fyfe Division of Biological Chemistry and Drug Discovery College of Life Sciences MSI/WTB Complex University of Dundee Dow Street Dundee DD1 5EH
Re: [ccp4bb] cryoprotectant for crystals in isopropanol
Not that all proteins are created alike, but we had a protein crystallize in a similar situation (PEG/20%IPA). I don't remember the exact details, but we did have good luck using just glycerol as a cryoprotectant. That is, I made up the well buffer and added to that well buffer 20-25% glycerol (in addition to IPA/PEG), and moved the crystal into that. We had no issues with cracking or anything, and data collection went well. The first thing I tried worked, so I don't have a lot of trial information for you. You could probably reduce the glycerol a bit with no worries, but I don't know. Good luck Dave shivesh kumar wrote: Dear all, The question is regarding the cryoprotectant.We have crystallized a protein in 20% PEG 500 with 10% isopropanol.What should be the cryo we should try for data collection.Also,what percentage of PEG 500 is sufficient enough as a cryo for data collection. We are also trying to crystallize it with higher PEG's also like 1K, 2K, 4K.Lets C.Since the condition is having isopropanol also and it is reported that mounting with isoprop is very difficult and it evaporates as soon as we open the slides. Thanx in advance... Shivesh Kumar
[ccp4bb] PRODRG?
BSD Hi all, Does anybody know what happened to the PRODRG server web site? Thanks Harry - Harry M. Greenblatt Staff Scientist Dept of Structural Biology [EMAIL PROTECTED] Weizmann Institute of SciencePhone: 972-8-934-3625 Rehovot, 76100 Facsimile: 972-8-934-4159 Israel
[ccp4bb] Workshop on Raw Image Formats in Structural Biology
There will be a workshop on Raw Image Formats in Structural Biology to be held at Brookhaven National Laboratory on 22 May 2008. Over the past 2 years, imgCIF has seen increasing use, and the interactions among raw image formats for x-ray crystallography, neutron crystallography and microscopy have started to be addressed. This one-day meeting will be a follow-up to the 2006--2007 imgCIF workshops at the summer 2006 ACA meeting, at BNL in May 2007, and in summer 2007 in conjunction with BSR 2007 in Manchester and at the Diamond Light Source. We will have reviews of the current status of imgCIF, exploration of ways to move between imgCIF and NeXus using XML and HDF and ways to work with microscopy and tomography images. The morning will be used for presentations and the afternoon for discussions and plans for the future. There is no registration fee, but space is limited, so registration will be required. Lunch will be provided. If you are interested in participating, please email [EMAIL PROTECTED] no later than 15 April 2008. The new imgCIF workshop series has been funded in part by NSF, NIH and DOE. -- = Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 121 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 [EMAIL PROTECTED] =
[ccp4bb] Crystal scoring sheets for iPhones/Pocket-PCs
Hi, I could be wrong, but I’m not aware of any servers that have tray inspection web pages designed for iPhones and Pocket-PCs, so I thought I’d try and make a web page with simple scoring sheets for such devices. I don’t own an iPhone myself, but the following web page seems to work well on a phone I tried out at an O2 store. Hope it’s of use to people who don't have a computer by their microscope. http://www.pageforaday.com/xtalwizard/fixed_order-i.html In response to a request, I’ve also allowed an option to include your custom screens. I’ve designed it so that you don’t need an account. P.S: I’ve read that you can’t print directly from an iPhone (though I assume you can either e-mail the data URL, or plug the phone into a computer with a printer). I’ve not tried the page out on a Pocket-PC, but I expect it will display reasonably well on these screens too (with JavaScript enabled), and I believe many of the newer Pocket-PCs allow wireless printing. Maybe Apple will release an appropriate iPhone update soon. Thanks _ Climb to the top of the charts! Play the word scramble challenge with star power. http://club.live.com/star_shuffle.aspx?icid=starshuffle_wlmailtextlink_jan
Re: [ccp4bb] cryoprotectant for crystals in isopropanol
Another anecdote for you: I had crystals that grew in 15% PEG 2000 and 15% isopropanol. Cryos with glycerol melted the crystals. The best cryo I found was with 15% PEG 2000, 15% isopropanol, and 20% PEG 400. It's hard to predict how your crystals will behave with different cryoprotectants-- hopefully you have enough crystals to try several different conditions. Evette S. Radisky, Ph.D. Assistant Professor and Associate Consultant II Mayo Clinic Cancer Center Griffin Cancer Research Building, Rm 310 4500 San Pablo Road Jacksonville, FL 32224 (904) 953-6372 (office) (904) 953-0046 (lab) From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of shivesh kumar Sent: Wednesday, March 19, 2008 3:34 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] cryoprotectant for crystals in isopropanol Dear all, The question is regarding the cryoprotectant.We have crystallized a protein in 20% PEG 500 with 10% isopropanol.What should be the cryo we should try for data collection.Also,what percentage of PEG 500 is sufficient enough as a cryo for data collection. We are also trying to crystallize it with higher PEG's also like 1K, 2K, 4K.Lets C.Since the condition is having isopropanol also and it is reported that mounting with isoprop is very difficult and it evaporates as soon as we open the slides. Thanx in advance... Shivesh Kumar
[ccp4bb] Senior Scientist Position at Evotec
Apologies for the slightly off topic post but can I draw people's attention to the job advert below. Due to continued expansion Evotec has a post for a Senior Scientist to join the X-ray crystallography team based in Abingdon, UK. Working within a small multidisciplinary project team your task will be the determination of high-resolution, three-dimensional structures of pharmaceutically important proteins, including crystallisation and structure solution of de novo protein structures and protein-ligand complexes. Ideally you will be PhD qualified in Chemistry, Biochemistry, Molecular Biology or Biophysics, with a minimum of one year's post-doctoral experience in protein X-ray crystallography. Candidates will also be considered who have a Masters degree with extensive experience. Extensive experience of using state-of-the-art crystallographic methods is a must. Expertise in protein ligand complex crystallization problems would be an advantage, although not essential. You will have excellent written and verbal communication skills and will be a strong team player. Dynamic and innovative, you will be a self-starter with a flexible approach who enjoys a challenge. We offer attractive salaries plus extensive benefits including profit-related bonus, pension plan and private medical cover. Please see the Careers section of the Evotec web site for details of how to apply: www.evotec.com Evotec (UK) Ltd is a limited company registered in England and Wales. Registration number:2674265. Registered office: 114 Milton Park, Abingdon, Oxfordshire, OX14 4SA, United Kingdom.
Re: [ccp4bb] Crystal scoring sheets for iPhones/Pocket-PCs
Sounds great. You can jailbreak an iPhone/iPod touch and install a whole BSD subsystem on it. So printing should be possible at some point... This of course also suggests that iPod touch is a valid research expense ... William G. Scott Contact info: http://chemistry.ucsc.edu/~wgscott/ On Mar 19, 2008, at 8:59 AM, P Hubbard wrote: Hi, I could be wrong, but I’m not aware of any servers that have tray inspection web pages designed for iPhones and Pocket-PCs, so I thought I’d try and make a web page with simple scoring sheets for such devices. I don’t own an iPhone myself, but the following web page seems to work well on a phone I tried out at an O2 store. Hope it’s of use to people who don't have a computer by their microscope. http://www.pageforaday.com/xtalwizard/fixed_order-i.html In response to a request, I’ve also allowed an option to include your custom screens. I’ve designed it so that you don’t need an account. P.S: I’ve read that you can’t print directly from an iPhone (though I assume you can either e-mail the data URL, or plug the phone into a computer with a printer). I’ve not tried the page out on a Pocket- PC, but I expect it will display reasonably well on these screens too (with JavaScript enabled), and I believe many of the newer Pocket-PCs allow wireless printing. Maybe Apple will release an appropriate iPhone update soon. Thanks _ Climb to the top of the charts! Play the word scramble challenge with star power. http://club.live.com/star_shuffle.aspx?icid=starshuffle_wlmailtextlink_jan
[ccp4bb] Phased Anomalous Difference Map
Hi All, Can anyone tell me how I calculate a phased anomalous difference map? I want to confirm such as the presence of Cl or S ion in an unknown electron density. Rajan.
Re: [ccp4bb] Crystal scoring sheets for iPhones/Pocket-PCs
Toys for crystallography: Maybe this could be filed under the same category as Johnny Chung Lee's Wii Remote projects a number of people here have mentioned about (though this certainly isn’t as cool as his “Minority Report” gloves or fake 3D-glasses)! Still, if Apple has it's way, in a year or two the iPod Touch will be as common in the science lab as an iPod is now. I suspect that if someone hasn't already, a LIMS will be adapted for hand held computers. P.S: From the log file, I’ve noticed a number of people trying this out on non-iPhone browsers. If you’d like to try it out on a non-iPhone/Pocket-PC computer, I would recommend using the following URL as it’s got a few more features (and a larger screen layout): http://www.pageforaday.com/xtalwizard/fixed_order.php (sans -i) Cheers! Date: Wed, 19 Mar 2008 11:11:17 -0700 From: [EMAIL PROTECTED] Subject: Re: [ccp4bb] Crystal scoring sheets for iPhones/Pocket-PCs To: CCP4BB@JISCMAIL.AC.UK Sounds great. You can jailbreak an iPhone/iPod touch and install a whole BSD subsystem on it. So printing should be possible at some point... This of course also suggests that iPod touch is a valid research expense ... William G. Scott Contact info: http://chemistry.ucsc.edu/~wgscott/ On Mar 19, 2008, at 8:59 AM, P Hubbard wrote: Hi, I could be wrong, but I’m not aware of any servers that have tray inspection web pages designed for iPhones and Pocket-PCs, so I thought I’d try and make a web page with simple scoring sheets for such devices. I don’t own an iPhone myself, but the following web page seems to work well on a phone I tried out at an O2 store. Hope it’s of use to people who don't have a computer by their microscope. http://www.pageforaday.com/xtalwizard/fixed_order-i.html In response to a request, I’ve also allowed an option to include your custom screens. I’ve designed it so that you don’t need an account. P.S: I’ve read that you can’t print directly from an iPhone (though I assume you can either e-mail the data URL, or plug the phone into a computer with a printer). I’ve not tried the page out on a Pocket- PC, but I expect it will display reasonably well on these screens too (with JavaScript enabled), and I believe many of the newer Pocket-PCs allow wireless printing. Maybe Apple will release an appropriate iPhone update soon. Thanks _ Climb to the top of the charts! Play the word scramble challenge with star power. http://club.live.com/star_shuffle.aspx?icid=starshuffle_wlmailtextlink_jan _ Need to know the score, the latest news, or you need your Hotmail®-get your fix. http://www.msnmobilefix.com/Default.aspx
Re: [ccp4bb] PRODRG?
Yes, it is down at the moment, due to a hacking event apparently. Don't know any more. Martyn -Original Message- From: CCP4 bulletin board on behalf of Harry M. Greenblatt Sent: Wed 3/19/2008 1:28 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] PRODRG? BSD Hi all, Does anybody know what happened to the PRODRG server web site? Thanks Harry - Harry M. Greenblatt Staff Scientist Dept of Structural Biology [EMAIL PROTECTED] Weizmann Institute of SciencePhone: 972-8-934-3625 Rehovot, 76100 Facsimile: 972-8-934-4159 Israel
Re: [ccp4bb] The Lawnmower Man
Neural lace embedding is too barbaric. Has anyone written a coot driver for this non-invasive alternative: http://techreport.com/discussions.x/13928 ? The superiority of thought driven building over dragging a mouse + modifier keys might be reason enough to get me to switch from O. James On Mar 19, 2008, at 4:22 AM, David Briggs wrote: Wow, that is like, so last week(!). I'm using COOT though a wireless interface to a head-up-display mounted inside my contact lenses, controlled via a neural lace* embedded directly into my parietal lobe. I can refine and rebuild my structure whilst doing minipreps, having a coffee, in the shower, sitting in a seminar, anywhere. You're not seriously telling me you're still using a mouse, keyboard monitor, are you? CyberDave v3.0 *thanks to Ian M Banks for that one. On 19/03/2008, Jordi Benach [EMAIL PROTECTED] wrote: Dear everyone, Has anybody tried to hook up a protein display/model building program/computer with 3D glasses of the type people are developing for games? The type of glasses where one obviates the use of large monitors altogether, that is the display sits on the glasses themselves. Thanks, Jordi Benach, PhD ALBA - Synchrotron Light Source Edifici Ciències Nord. Mòdul C-3 central. Universitat Autònoma de Barcelona 08193 Bellaterra, Barcelona SPAIN phone: +34 93 592 4333 fax : +34 93 592 4302 cell : +34 60 810 7080 image001.jpg http://www.i-glassesstore.com/ -- David C. Briggs PhD Father Crystallographer http://www.dbriggs.talktalk.net AIM ID: dbassophile -- James Stroud UCLA-DOE Institute for Genomics and Proteomics 611 Charles E. Young Dr. S. Los Angeles, CA 90095 http://www.jamesstroud.com
[ccp4bb] Back-Fourier transforming an EM map with SFALL
Hello All, I'm trying to back-FT an EM map to produce Fs and phases to use in molecular replacement, but am having a problem with running SFALL. Here's the issue: When running the back-transform in SFALL (generating structure factors from a map), I get the following error: Incorrect sampling grid factors 255 255 255 The map parameters are given below. Does anyone have any idea of how to deal with this? Thanks, Larry Number of columns, rows, sections ... 256 256 256 Map mode 2 Start and stop points on columns, rows, sections -128 127 -128 127 -128 127 Grid sampling on x, y, z 255 255 255 Cell dimensions . 459.0 459.0 459.0 90.0 90.0 90.0 Fast, medium, slow axes .XYZ Minimum density .-1.24222 Maximum density . 2.25668 Mean density 0.06370 Rms deviation from mean density . 0.0 Space-group .1 Number of titles 3 -- Lawrence Shapiro, Ph.D. Associate Professor Dept. of Biochemistry and Molecular Biophysics Jules and Doris Stein Professor of Research to Prevent Blindness Edward S. Harkness Eye Institute Columbia University 701 West 168th Street, 7th Floor New York, NY 10032 Tel: (212)342-6029 Fax: (212)342-6026 e-mail: [EMAIL PROTECTED] [EMAIL PROTECTED] http://www.shapirolab.org
