Re: [ccp4bb] Off-topic - Crystallisation in anaerobic glove box
Do you have evidence that the oil blocks diffusion of O2? O2 is a nonpolar molecule, generally much more soluble in oils than in water. I'm not sure about silicone oils, but I would think they also dissolve O2 readily. eab On 03/18/2015 08:02 AM, Patrick Shaw Stewart wrote: Hi Steve I have one more comment for this thread. The microbatch-under-oil method is very handy for anaerobic work: 1. You can keep the microbatch stock solutions in normal microtitre plates (polypropylene is best to reduce evaporation) for months, which hugely reduces the amount of degassing that you need to do. You will only use say 0.5 ul of stock per drop. 2. The oil offers a surprising amount of protection from oxidation, which may be helpful eg in harvesting. 3. Microbatch can be automated - in parallel to vapor diffusion if desired It's amazing how often (aerobic) microbatch produces far superior crystals to V.D. for no obvious reason - it's well worth trying for both screening and optimization. Best wishes Patrick On 11 March 2015 at 10:17, Stephen Carr stephen.c...@rc-harwell.ac.uk mailto:stephen.c...@rc-harwell.ac.uk wrote: Dear CCP4BBer's Apologies for the off-topic post, but the CCP4BB seems to be the best place to ask about crystallisation. I am looking to set up crystallisation in an anaerobic glove box and wondered how other people did this, specifically the crystallisation stage. My initial thoughts were to place a small crystallisation incubator inside the box, however the smallest I have come across so far (~27L) is still rather large. Has anyone come across smaller incubators? Alternatively are incubators even neccessary if the glove box is placed in a room with good air conditioning and stable temperature control? Any recommendations would be very helpful. Thanks in advance, Steve Carr Dr Stephen Carr Research Complex at Harwell (RCaH) Rutherford Appleton Laboratory Harwell Oxford Didcot Oxon OX11 0FA United Kingdom Email stephen.c...@rc-harwell.ac.uk mailto:stephen.c...@rc-harwell.ac.uk tel 01235 567717 tel:01235%20567717 This email 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 authorized 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 this email. Any views or opinions presented are solely those of the author and do not necessarily represent those of the Research Complex at Harwell. There is no guarantee that this email 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. We use an electronic filing system. Please send electronic versions of documents, unless paper is specifically requested. This email may have a protective marking, for an explanation, please see: http://www.mrc.ac.uk/About/informationandstandards/documentmarking/index.htm. -- patr...@douglas.co.uk mailto:patr...@douglas.co.ukDouglas Instruments Ltd. Douglas House, East Garston, Hungerford, Berkshire, RG17 7HD, UK Directors: Peter Baldock, Patrick Shaw Stewart http://www.douglas.co.uk Tel: 44 (0) 148-864-9090US toll-free 1-877-225-2034 Regd. England 2177994, VAT Reg. GB 480 7371 36
Re: [ccp4bb] Off-topic - Crystallisation in anaerobic glove box
Hi Steve I have one more comment for this thread. The microbatch-under-oil method is very handy for anaerobic work: 1. You can keep the microbatch stock solutions in normal microtitre plates (polypropylene is best to reduce evaporation) for months, which hugely reduces the amount of degassing that you need to do. You will only use say 0.5 ul of stock per drop. 2. The oil offers a surprising amount of protection from oxidation, which may be helpful eg in harvesting. 3. Microbatch can be automated - in parallel to vapor diffusion if desired It's amazing how often (aerobic) microbatch produces far superior crystals to V.D. for no obvious reason - it's well worth trying for both screening and optimization. Best wishes Patrick On 11 March 2015 at 10:17, Stephen Carr stephen.c...@rc-harwell.ac.uk wrote: Dear CCP4BBer's Apologies for the off-topic post, but the CCP4BB seems to be the best place to ask about crystallisation. I am looking to set up crystallisation in an anaerobic glove box and wondered how other people did this, specifically the crystallisation stage. My initial thoughts were to place a small crystallisation incubator inside the box, however the smallest I have come across so far (~27L) is still rather large. Has anyone come across smaller incubators? Alternatively are incubators even neccessary if the glove box is placed in a room with good air conditioning and stable temperature control? Any recommendations would be very helpful. Thanks in advance, Steve Carr Dr Stephen Carr Research Complex at Harwell (RCaH) Rutherford Appleton Laboratory Harwell Oxford Didcot Oxon OX11 0FA United Kingdom Email stephen.c...@rc-harwell.ac.uk tel 01235 567717 This email 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 authorized 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 this email. Any views or opinions presented are solely those of the author and do not necessarily represent those of the Research Complex at Harwell. There is no guarantee that this email 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. We use an electronic filing system. Please send electronic versions of documents, unless paper is specifically requested. This email may have a protective marking, for an explanation, please see: http://www.mrc.ac.uk/About/informationandstandards/documentmarking/index.htm . -- patr...@douglas.co.ukDouglas Instruments Ltd. Douglas House, East Garston, Hungerford, Berkshire, RG17 7HD, UK Directors: Peter Baldock, Patrick Shaw Stewart http://www.douglas.co.uk Tel: 44 (0) 148-864-9090US toll-free 1-877-225-2034 Regd. England 2177994, VAT Reg. GB 480 7371 36
Re: [ccp4bb] OS X yosemite
Hi Mirek, I have to reinstall xquartz to get my ccp4 and coot working after upgrading to Yosemite from Mavericks. Xiao On Tue, Mar 17, 2015 at 4:30 PM, Cygler, Miroslaw miroslaw.cyg...@usask.ca wrote: Hi, I am thinking of upgrading the os on my mac to Yosemite. Are there any known issues for crystallographic software that I should pay attention to? Thanks, Mirek
[ccp4bb] PhD position in Durham
Project description Herbicide resistance of weeds is a major challenge for global food production. The situation becomes particularly severe when weeds become resistant to multiple modes of herbicide action (multiple herbicide resistance=MHR). This collaborative project between Durham University and Syngenta aims to unravel the molecular mechanisms of MHR in black grass, a major weed in cereal crops in the UK and beyond. In recent work we have demonstrated that MHR in black grass is associated with the up-regulation of one particular glutathione-S-transferase (GSTF1), and furthermore, that the observed resistance can be reversed by certain chemical compounds. However, the molecular basis for these observations remains to be established and represents the key goal of this project. The research will involve the characterization of GSTF1-ligand interactions using a combination of biophysical (including thermal shift assay, surface plasmon resonance, isothermal titration calorimetry) computational and crystallographic methods. The insight gained will then be used to elucidate how the enzyme achieves multiple herbicide resistance and to design and synthesize new herbicide synergists. Ultimately we seek to apply these finding to explore to orthologous enzymes identified in other important cereal weeds including rye grass and wild oat which also display an MHR phenotype. Funding and how to apply This project is fully funded CASE with Syngenta. Success will depend on the quality of applications received. If you are interested in applying, in the first instance contact Ehmke (ehmke.p...@durham.ac.uk), with a CV and covering letter, detailing your reasons for applying for the project.
Re: [ccp4bb] Graphics cards for Coot, Pymol, Chimera on MacBook Pro Laptop
Hi Marc, I have a Macbook pro Mid 2009 model (with integrated graphics card) and I can run coot and pymol without any problem ( I haven't tested on Chimera), I do not think a discrete graphics is needed. However, for pymol I can not use the stereo function. I do not know if the discrete graphic card is needed for this function. Xiao On Tue, Mar 17, 2015 at 1:12 PM, Marc Graille marc.grai...@polytechnique.edu wrote: Hello, I would like to buy a MacBook Pro laptop that will allow me among others to solve structures, build models and visualize electron density maps using Pymol, Coot or Chimera. I have the choice between between Intel Iris Pro (5200 series) and Intel Iris Pro + Nvidia GT 750M for the graphics cards but I don’t know which one is fine for the programs I want to run. Can some of you share advices/feedback with me? Thanks a lot for your answer. Best wishes, Marc Dr Marc GRAILLE Directeur de recherche CNRS Team: Translation and degradation of eukaryotic mRNAs Team supported by the ATIP-Avenir CNRS program Laboratoire de Biochimie ECOLE POLYTECHNIQUE - UMR7654 CNRS 91128 PALAISEAU CEDEX Phone : +33 (0)1 69 33 48 90 – Fax : +33 (0)1 69 33 49 09 Office 033012B Email: marc.grai...@polytechnique.edu http://bioc.polytechnique.fr/spip.php?rubrique117
Re: [ccp4bb] Off-topic - Crystallisation in anaerobic glove box
Hi, As far as I can tell oil does not block diffusion of O2 whatsoever. You can keep larger volumes (≥1 ml) of solutions anoxic in air for several hours with dithionite (≥0.5%) to scavenge oxygen and a redox indicator dye such as phenosafranin to monitor the state of the solution. Small drops (large surface/volume ratio) however oxidize within seconds, whether or not they are covered with oil. Of course this may simply be because the oxygen gets in before the drop is covered with oil, but either way I don't see how you could set up anaerobic drops in an aerobic environment. Best, Julia On 18/03/15 14:47, Edward A. Berry wrote: Do you have evidence that the oil blocks diffusion of O2? O2 is a nonpolar molecule, generally much more soluble in oils than in water. I'm not sure about silicone oils, but I would think they also dissolve O2 readily. eab On 03/18/2015 08:02 AM, Patrick Shaw Stewart wrote: Hi Steve I have one more comment for this thread. The microbatch-under-oil method is very handy for anaerobic work: 1. You can keep the microbatch stock solutions in normal microtitre plates (polypropylene is best to reduce evaporation) for months, which hugely reduces the amount of degassing that you need to do. You will only use say 0.5 ul of stock per drop. 2. The oil offers a surprising amount of protection from oxidation, which may be helpful eg in harvesting. 3. Microbatch can be automated - in parallel to vapor diffusion if desired It's amazing how often (aerobic) microbatch produces far superior crystals to V.D. for no obvious reason - it's well worth trying for both screening and optimization. Best wishes Patrick On 11 March 2015 at 10:17, Stephen Carr stephen.c...@rc-harwell.ac.uk mailto:stephen.c...@rc-harwell.ac.uk wrote: Dear CCP4BBer's Apologies for the off-topic post, but the CCP4BB seems to be the best place to ask about crystallisation. I am looking to set up crystallisation in an anaerobic glove box and wondered how other people did this, specifically the crystallisation stage. My initial thoughts were to place a small crystallisation incubator inside the box, however the smallest I have come across so far (~27L) is still rather large. Has anyone come across smaller incubators? Alternatively are incubators even neccessary if the glove box is placed in a room with good air conditioning and stable temperature control? Any recommendations would be very helpful. Thanks in advance, Steve Carr Dr Stephen Carr Research Complex at Harwell (RCaH) Rutherford Appleton Laboratory Harwell Oxford Didcot Oxon OX11 0FA United Kingdom Email stephen.c...@rc-harwell.ac.uk mailto:stephen.c...@rc-harwell.ac.uk tel 01235 567717 tel:01235%20567717 This email 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 authorized 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 this email. Any views or opinions presented are solely those of the author and do not necessarily represent those of the Research Complex at Harwell. There is no guarantee that this email 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. We use an electronic filing system. Please send electronic versions of documents, unless paper is specifically requested. This email may have a protective marking, for an explanation, please see: http://www.mrc.ac.uk/About/informationandstandards/documentmarking/index.htm. -- patr...@douglas.co.uk mailto:patr...@douglas.co.uk Douglas Instruments Ltd. Douglas House, East Garston, Hungerford, Berkshire, RG17 7HD, UK Directors: Peter Baldock, Patrick Shaw Stewart http://www.douglas.co.uk Tel: 44 (0) 148-864-9090US toll-free 1-877-225-2034 Regd. England 2177994, VAT Reg. GB 480 7371 36 -- Dr. Julia Griese Postdoctoral Researcher Stockholm Center for Biomembrane Research Department of Biochemistry and Biophysics Stockholm University 106 91 Stockholm Sweden phone: +46-(0)8-162 778 email: gri...@dbb.su.se
[ccp4bb] Antw: Re: [ccp4bb] Offtopic: Software to closely visualize interacting partnets in protein complex
Hi, I just checked the PIC sever tim suggested. very nice indeed. If you only want to map different interfaces and the amino acids involved in, I suggest to run the pisa server, too. http://www.ebi.ac.uk/pdbe/pisa/ . I used it extensively to find out whether a certain set of crystal contacs leads to a certain crystal packing. best, matthias Tim tim.schu...@rub.de 11.03.15 18.25 Uhr Hi, Molprobity is also a nice software to do this kind of analysis - if you use it as implemented in phenix you also get good visualization in coot. I also asked the pymol community to create an implementation for pymol, but I did not follow if somebody took that up. Also this 'protein interactions calculation' server is very neat: http://pic.mbu.iisc.ernet.in/ /Tim On 10/03/15 11:25, Debasish Kumar Ghosh wrote: Dear All, Apologies for this little off-topic inquiry. I want to closely visualize the interacting residues in an multimeric protein complex to understand the nature of interactions. Is there any good software to give this information with good clarity. Any suggestion is highly appreciated. Thanks, Best !!! Debasish Kumar Ghosh CSIR- Junior Research Fellow (PhD Scholar) C/o: Dr. Akash Ranjan Computational and Functional Genomics Group Centre for DNA Fingerprinting and Diagnostics Hyderabad, INDIA Email(s): dkgh...@cdfd.org.in, dgho...@gmail.com Telephone: 0091-9088334375 (M), 0091-40-24749396 (Lab) Lab URL: http://www.cdfd.org.in/labpages/computational_functional_genomics.html
Re: [ccp4bb] Off-topic - Crystallisation in anaerobic glove box
I also wondered about the statement about oils blocking diffusion of O2. We had lots of trouble keeping things anaerobic in a glove box until we degassed the oils and waxes used to mount crystals in capillaries. We found that putting them under vacuum removed much of the dissolved oxygen. The waxes required cycling between heating and vacuum several times. Ron On Wed, 18 Mar 2015, Edward A. Berry wrote: Do you have evidence that the oil blocks diffusion of O2? O2 is a nonpolar molecule, generally much more soluble in oils than in water. I'm not sure about silicone oils, but I would think they also dissolve O2 readily. eab On 03/18/2015 08:02 AM, Patrick Shaw Stewart wrote: Hi Steve I have one more comment for this thread. The microbatch-under-oil method is very handy for anaerobic work: 1. You can keep the microbatch stock solutions in normal microtitre plates (polypropylene is best to reduce evaporation) for months, which hugely reduces the amount of degassing that you need to do. You will only use say 0.5 ul of stock per drop. 2. The oil offers a surprising amount of protection from oxidation, which may be helpful eg in harvesting. 3. Microbatch can be automated - in parallel to vapor diffusion if desired It's amazing how often (aerobic) microbatch produces far superior crystals to V.D. for no obvious reason - it's well worth trying for both screening and optimization. Best wishes Patrick On 11 March 2015 at 10:17, Stephen Carr stephen.c...@rc-harwell.ac.uk mailto:stephen.c...@rc-harwell.ac.uk wrote: Dear CCP4BBer's Apologies for the off-topic post, but the CCP4BB seems to be the best place to ask about crystallisation. I am looking to set up crystallisation in an anaerobic glove box and wondered how other people did this, specifically the crystallisation stage. My initial thoughts were to place a small crystallisation incubator inside the box, however the smallest I have come across so far (~27L) is still rather large. Has anyone come across smaller incubators? Alternatively are incubators even neccessary if the glove box is placed in a room with good air conditioning and stable temperature control? Any recommendations would be very helpful. Thanks in advance, Steve Carr Dr Stephen Carr Research Complex at Harwell (RCaH) Rutherford Appleton Laboratory Harwell Oxford Didcot Oxon OX11 0FA United Kingdom Email stephen.c...@rc-harwell.ac.uk mailto:stephen.c...@rc-harwell.ac.uk tel 01235 567717 tel:01235%20567717 This email 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 authorized 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 this email. Any views or opinions presented are solely those of the author and do not necessarily represent those of the Research Complex at Harwell. There is no guarantee that this email 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. We use an electronic filing system. Please send electronic versions of documents, unless paper is specifically requested. This email may have a protective marking, for an explanation, please see: http://www.mrc.ac.uk/About/informationandstandards/documentmarking/index.htm. -- patr...@douglas.co.uk mailto:patr...@douglas.co.ukDouglas Instruments Ltd. Douglas House, East Garston, Hungerford, Berkshire, RG17 7HD, UK Directors: Peter Baldock, Patrick Shaw Stewart http://www.douglas.co.uk Tel: 44 (0) 148-864-9090US toll-free 1-877-225-2034 Regd. England 2177994, VAT Reg. GB 480 7371 36
Re: [ccp4bb] Off-topic - Crystallisation in anaerobic glove box
It's a little complicated. It's true that oxygen is more soluble in most oils than in water - but in a high viscosity mineral oil the diffusion rate is orders of magnitude lower. So the combination of an oil overlay and a reducing agent in your buffer should protect your sample much longer than the reducing agent alone - as long as your oil was degassed to start with. Note that silicon oils are a bad choice for this - silicones have an enormous affinity for oxygen (so much so that they've been explored as artificial blood substitutes), and it diffuses through them very readily. Tristan Croll Lecturer Faculty of Health School of Biomedical Sciences Institute of Health and Biomedical Engineering Queensland University of Technology 60 Musk Ave Kelvin Grove QLD 4059 Australia +61 7 3138 6443 This email and its attachments (if any) contain confidential information intended for use by the addressee and may be privileged. We do not waive any confidentiality, privilege or copyright associated with the email or the attachments. If you are not the intended addressee, you must not use, transmit, disclose or copy the email or any attachments. If you receive this email by mistake, please notify the sender immediately and delete the original email. On 18 Mar 2015, at 11:49 pm, Edward A. Berry ber...@upstate.edu wrote: Do you have evidence that the oil blocks diffusion of O2? O2 is a nonpolar molecule, generally much more soluble in oils than in water. I'm not sure about silicone oils, but I would think they also dissolve O2 readily. eab On 03/18/2015 08:02 AM, Patrick Shaw Stewart wrote: Hi Steve I have one more comment for this thread. The microbatch-under-oil method is very handy for anaerobic work: 1. You can keep the microbatch stock solutions in normal microtitre plates (polypropylene is best to reduce evaporation) for months, which hugely reduces the amount of degassing that you need to do. You will only use say 0.5 ul of stock per drop. 2. The oil offers a surprising amount of protection from oxidation, which may be helpful eg in harvesting. 3. Microbatch can be automated - in parallel to vapor diffusion if desired It's amazing how often (aerobic) microbatch produces far superior crystals to V.D. for no obvious reason - it's well worth trying for both screening and optimization. Best wishes Patrick On 11 March 2015 at 10:17, Stephen Carr stephen.c...@rc-harwell.ac.uk mailto:stephen.c...@rc-harwell.ac.uk wrote: Dear CCP4BBer's Apologies for the off-topic post, but the CCP4BB seems to be the best place to ask about crystallisation. I am looking to set up crystallisation in an anaerobic glove box and wondered how other people did this, specifically the crystallisation stage. My initial thoughts were to place a small crystallisation incubator inside the box, however the smallest I have come across so far (~27L) is still rather large. Has anyone come across smaller incubators? Alternatively are incubators even neccessary if the glove box is placed in a room with good air conditioning and stable temperature control? Any recommendations would be very helpful. Thanks in advance, Steve Carr Dr Stephen Carr Research Complex at Harwell (RCaH) Rutherford Appleton Laboratory Harwell Oxford Didcot Oxon OX11 0FA United Kingdom Email stephen.c...@rc-harwell.ac.uk mailto:stephen.c...@rc-harwell.ac.uk tel 01235 567717 tel:01235%20567717 This email 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 authorized 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 this email. Any views or opinions presented are solely those of the author and do not necessarily represent those of the Research Complex at Harwell. There is no guarantee that this email 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. We use an electronic filing system. Please send electronic versions of documents, unless paper is specifically requested. This email may have a protective marking, for an explanation, please see: http://www.mrc.ac.uk/About/informationandstandards/documentmarking/index.htm. -- patr...@douglas.co.uk mailto:patr...@douglas.co.ukDouglas Instruments Ltd. Douglas House, East Garston, Hungerford, Berkshire, RG17 7HD, UK Directors: Peter Baldock, Patrick Shaw Stewart http://www.douglas.co.uk Tel: 44 (0) 148-864-9090US toll-free 1-877-225-2034 Regd. England 2177994, VAT Reg. GB 480 7371 36
[ccp4bb] Group Leader position in Helsinki, Finland
(Reposting this position as it didnt go to the jobs list..:) On behalf of the search committee (see links below): -- The Institute of Biotechnology is a leading European research institute within the University of Helsinki with a mission to increase knowledge in cross‐disciplinary biology and biotechnology. The Institute has state‐ofthe‐art facilities in imaging, model organisms, proteomics, genomics, crystallography and NMR. We seek outstanding candidates for GROUP LEADER positions in the areas of Molecular Cell Biology, Genomics and Quantitative Biology, Plant Biology, Developmental Biology, or Structural Biology and Biophysics. Applicants from different levels of the career path are welcomed. Successful candidates have a suitable strong track record including a PhD or an equivalent and postdoctoral experience in an international setting and are expected to develop an independent externally funded line of research. Appointments are based on BI tenuring system with external evaluations every four years. A globally competitive remuneration package and 3‐year startup funds are negotiable. Applications should include a presentation of past achievements (1 page) and research interests (max. 3 pages), curriculum vitae, list of publications (with citation numbers), and three letters of reference. Applications and letters of reference are to be submitted at www.biocenter.helsinki.fi/bi/recruit no later than on Tuesday March 31, 2015. For further information and detailed contacts, please visit www.biocenter.helsinki.fi/bi/recruit or contact bi‐direc...@helsinki.fi. www.biocenter.helsinki.fi/bi Tommi Kajander, Ph.D. Team Leader Structural Biology and Biophysics Institute of Biotechnology University of Helsinki Viikinkaari 1 (P.O. Box 65) 00014 Helsinki Finland p. +358-50-4480991 tommi.kajan...@helsinki.fi http://www.biocenter.helsinki.fi/bi/kajander/
[ccp4bb] Mosquito Tips (4.5mm / 9.0mm)
Hello CCP4, Sorry for the labware related post, but I think this is the right audience. I have 4 new reels of mosquito tips with 4.5mm pitch (for 384 well setups, TTP labtech part number 4150-03010). I only use 96well format, thus am looking to swap these for 9mm pitch (part number 4150-03020). Anyone out there in the reverse situation or sitting on a surplus of 9mm tips? Thanks, --Paul -- Nothing can be more incorrect than the assumption one sometimes meets with, that physics has one method, chemistry another, and biology a third. --Thomas Huxley + Dr. Paul Smith Assistant Professor Department of Chemistry Fordham University 441 E. Fordham Road Bronx, NY 10458 phone: 718-817-4461 fax: 718-817-4432 email: psmit...@fordham.edu office: JMH 638 http://www.fordham.edu/academics/programs_at_fordham_/chemistry/index.asp http://www.fordham.edu/academics/sciences_at_fordham/
Re: [ccp4bb] Off-topic - Crystallisation in anaerobic glove box
Actually I may have misunderstood the original post. Patrick never said oils block O2 diffusion: On 03/18/2015 09:47 AM, Edward A. Berry wrote: The microbatch-under-oil method is very handy for anaerobic work: (In a glove box, of course) 1. You can keep the microbatch stock solutions in normal microtitre plates (polypropylene is best to reduce evaporation) for months, which hugely reduces the amount of degassing that you need to do. You will only use say 0.5 ul of stock per drop. (reagents including oils stored in a tray in the glove box to reduce degassing time) 2. The oil offers a surprising amount of protection from oxidation, which may be helpful eg in harvesting. Perhaps by the O2-buffering effect of anoxic oil that Tristan mentioned, and by preventing an air/water interface where a skin forms and interferes with harvesting. 3. Microbatch can be automated - in parallel to vapor diffusion if desired And now as an aside, the advantages of oil for aerobic (oxic) work: It's amazing how often (aerobic) microbatch produces far superior crystals to V.D. for no obvious reason - it's well worth trying for both screening and optimization. If that was what was meant I apologize, but at least this will prevent someone else from getting the wrong Idea as I did. eab
Re: [ccp4bb] Graphics cards for Coot, Pymol, Chimera on MacBook Pro Laptop
Hello Marc, obvious differences between card are memory bandwidth, intel 13 GB/sec vs. nvidia 29 GB/s, the texture rate, 2 GTexel/s vs. 31 GTexel/s, and pixel rate, 0.5 GPix/s vs. 15.5 GPix/s. Some of these values result because of graphics memory differences. There is no difference in energy consumption. Question is indeed, what do you need for doing crystallography. If you look at the performance in popular games, the difference is much less than you would expect looking only at the naked values. The intel is merely 20% slower than the nvidia in most reference games So, not worth spending the extra money I would say as the actual graphics performance between cards is similar. However, if you plan to process a lot of graphical data (video editing, etc), the nvidia will by far out-perform the intel. Otherwise, the Intel Iris Pro model is more than fine and you better invest your money by getting more memory. Best wishes Jeroen On 17 Mar 2015, at 16:12, Marc Graille marc.grai...@polytechnique.edu mailto:marc.grai...@polytechnique.edu wrote: Hello, I would like to buy a MacBook Pro laptop that will allow me among others to solve structures, build models and visualize electron density maps using Pymol, Coot or Chimera. I have the choice between between Intel Iris Pro (5200 series) and Intel Iris Pro + Nvidia GT 750M for the graphics cards but I don’t know which one is fine for the programs I want to run. Can some of you share advices/feedback with me? Thanks a lot for your answer. Best wishes, Marc -- Dr.math. et dis. nat. Jeroen R. Mesters Deputy, Senior Researcher Lecturer Coordinator master's program Infection Biology Institute of Biochemistry, University of Lübeck Ratzeburger Allee 160, 23538 Lübeck, Germany phone: +49-451-5004065 (secretariate -5004061) fax: +49-451-5004068 http://www.biochem.uni-luebeck.de Http://www.biochem.uni-luebeck.de http://www.uni-luebeck.de/studium/studiengaenge/infection-biology http://www.iobcr.org Http://www.iobcr.org -- If you can look into the seeds of time and tell which grain will grow and which will not, speak then to me who neither beg nor fear (Shakespeare's Macbeth, Act I, Scene 3) -- Disclaimer * This message contains confidential information and is intended only for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail by mistake and delete this e-mail from your system. * E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission. If verification is required please request a hard-copy version. Please send us by fax any message containing deadlines as incoming e-mails are not screened for response deadlines. * Employees of the Institute are expressly required not to make defamatory statements and not to infringe or authorize any infringement of copyright or any other legal right by email communications. Any such communication is contrary to Institute policy and outside the scope of the employment of the individual concerned. The Institute will not accept any liability in respect of such communication, and the employee responsible will be personally liable for any damages or other liability arising. Employees who receive such an email must notify their supervisor immediately. --
