Re: [ccp4bb] Mac mini advice
Dmitry... everyone is of course entitled to their opinion - but as one of the brain-washed masses I feel I need to at least reply (!). Sorry Cara... I am not happy with the direction OS X is going. Too much emphasis on eye candy and not enough on underlying technology. Fair enough, but it does seem to be the way that most of the UIs/OSes are going. Erm, Windows 8, Unity... Also Apple are *constantly* innovating under the hood - albeit mainly hardware - Lightning connectors, Fusion hard-drives etc... so they are one of the few computer manufacturers actually innovating at all(!) ZFS (long ago), Xgrid and X11 have been ditched, which I find disturbing. I don't see Apple investing in computers given current revenue from that sector. I sort of agree with you here - but on the other hand at least it is still a Unix variant underneath and we still have Xquartz. X11/X window is itself becoming quite an old beast and I'm pretty sure there's ever going to be an X12. Hence the probable rise and prevalence of Qt - so you can run any OS you like... Linux in a virtual machine of your choice might be a better bang for the buck. Or, Windows in a virtual machine on a Linux box for that matter. Or, ( controversially ) a Mac running Linux and Windows in virtual boxes !? Tony. Sent from my iPhone On 23 Jan 2013, at 03:03, Dmitry Rodionov d.rodio...@gmail.commailto:d.rodio...@gmail.com wrote: AFAIK there is no problem mixing and matching different timing RAM: system will run at the speed of the slowest module. I don't think anybody will notice the difference with CAS latency Coot'ing and Refmac'ing. I don't think there is much sense in having more than 4 GB of RAM per physical core on a Mac. Majority of the Mac flock does not really care for where the RAM modules come from. As for Mac Pro's- they use ECC RAM with proprietary heat sensors, so that's a completely different story. You can still use generic ECC RAM in a MAC PRO at the cost of the fan being stuck in hurricane mode. The bottleneck of pretty much any modern system is the HDD. Apple-branded HDDs were known to have somewhat modified firmware, causing problems at times (mostly with AppleRAID, if not using an Apple-branded HDD) An end user most definitely will notice an SSD VS HDD, which brings up TRIM support on OS X, which is limited to controllers sold by Apple. Upgradeability-wise Apple is not the way to go in any case. DISCLAIMER: The rest may be much more inflammatory. Personally, I am not convinced OS X and Apple is the way to go log term (having been surrounded by MACs for the past 4-5 years) I am not happy with the direction OS X is going. Too much emphasis on eye candy and not enough on underlying technology. ZFS (long ago), Xgrid and X11 have been ditched, which I find disturbing. I don't see Apple investing in computers given current revenue from that sector. Linux in a virtual machine of your choice might be a better bang for the buck. Or, Windows in a virtual machine on a Linux box for that matter. Don't kick me, DIR On 2013-01-22, at 7:22 PM, Bryan Lepore bryanlep...@gmail.commailto:bryanlep...@gmail.com wrote: On Tue, Jan 22, 2013 at 1:40 PM, Phil Jeffrey pjeff...@princeton.edumailto:pjeff...@princeton.edu wrote: I don't think that anybody has shown a significant performance difference on Apple memory vs a reasonable 3rd party supplier. Apple may potentially have better quality controls but places like Crucial essentially have lifetime warranties on their memory. I use Crucial at home and at work. [...] sure, I agree with all this the only other point I really wanted to make is to be cautious when configuring a computer on the Apple website, where they might say for memory DDR3 ECC SDRAM (checked this for a Mac Pro just now) but that is a non-obvious way of, from what I can tell, selling only high end memory when e.g. different CAS latency is available elsewhere - again, not obvious what their CL is (perhaps it is listed somewhere). and maybe other specs apply.
Re: [ccp4bb] Off-topic: ITC - what to buy?
Hi Those are the only two brands out there that I know of too. Depending on what sort of experiments you will be doing (high, medium or low troughput ? Full characterisation ?), one model might be better suited than the other. I would consider TTP labtech ChipCAL too. Not wanting to introduce any biased review here, what I have seen is that labs go for the GE Healthcare ITC, the ITC 200. So far I have not met a research group using TA instruments, or anyone appraising them. TA instruments do make some comparisons between their calorimeter and GE Healthcare's. Would be good if someone who is using TA instruments could join in this thread and share his/her oppinions on it. Leo On 22 January 2013 15:41, Wulf Blankenfeldt wulf.blankenfe...@uni-bayreuth.de wrote: Dear all: we are looking into buying an isothermal titration calorimeter, but are only aware of two manufacturers: TA Instruments and MicroCal (GE Healthcare). Are there any more? Do you have any recommendations (brand, model etc.) for us? Thanks in advance, Wulf -- Prof. Dr. Wulf Blankenfeldt NW-I, 2.0.U1.09Universitaet Bayreuth fon:+49-(0)921-55-2427 Lehrstuhl fuer Biochemie fax:+49-(0)921-55-2432 Universitaetsstrasse 30 e-mail: wulf.blankenfeldt [at] uni-bayreuth.de95447 Bayreuth web:www.biochemie.uni-bayreuth.deGermany
[ccp4bb] Hi clashscore
Hi I am refining my 2 angstrom strucutre using phenix windows based software. After many refinements my clashscore is not at all reducing and showing a value of 12. Can anybody suggest how to reduce the clashscore. Is there any technique to do it. Or i have to deal with each individual clashes mentioned in the list manually ? Supratim
Re: [ccp4bb] Mac mini advice
On Jan 22, 2013, at 11:20 PM, Nat Echols wrote: The real difficulty is integrating Macs into a Linux-centric environment, for example configuring NFS, NIS, etc. That's because NFS and NIS are antiquities left over from the days of mainframes. Distributed file systems and user information databases are designed for an environment of many workers and few machines, when the typical graphics workstation cost $50,000. These days, we argue whether to spend an extra $200 on a $500 computer. We have moved to a new paradigm: many workers with many more machines, with each machine having essentially mainframe levels of storage and computing power. In other words, instead of NFS, you should run git. James
Re: [ccp4bb] protein solubility predictions
Hi Careina, If your protein is expressed in E. coli, you can have a prediction of its solubility on this website: http://biotech.ou.edu Hope it helps! Alberto Manfrin From: Careina Edgooms careinaedgo...@yahoo.com Reply-To: Careina Edgooms careinaedgo...@yahoo.com Date: Tue, 22 Jan 2013 04:22:44 -0800 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] protein solubility predictions Dear ccp4 Apologies for the off topic question. I was wondering whether anyone could suggest a good tool or methodology to use to predict protein solubility and ability to fold from the sequence? I am working with a large protein of multiple domains. I would like to work with as close to the full length protein as possible without affecting its solubility and ability to fold correctly. I know there are web based tools where you can upload a sequence and see the predicted solubility but I wonder if there is any good strategy to use to determine how best to construct the truncated protein? ie which parts of the sequence to keep and which to remove so as to maximise solubility. Also I have an eye to crystallising this protein in the future and I wonder if there are any specific things I should look out for with that in mind? I'm sure minimising flexible loops is one such thing. All help appreciated Best Careina
Re: [ccp4bb] Hi clashscore
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Supratim, I am afraid so, yes, you'll have to do it manually. Model building is the other half of creating a model, and time-wise surely the more time consuming one. On the other hand it is also the more scientific one where you feel less reduced to somebody just pushing buttons, so enjoy! You might try arp/warp. At 2A it should produce a pretty good result. Regards, Tim On 01/23/2013 09:47 AM, supratim dey wrote: Hi I am refining my 2 angstrom strucutre using phenix windows based software. After many refinements my clashscore is not at all reducing and showing a value of 12. Can anybody suggest how to reduce the clashscore. Is there any technique to do it. Or i have to deal with each individual clashes mentioned in the list manually ? Supratim - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFQ/6w+UxlJ7aRr7hoRAsP3AJ9U41iQhk75SWGX+GbH1T4NtaTwowCeMwGo qPH1SJgumSHytCtF5j9Vn0c= =xKve -END PGP SIGNATURE-
Re: [ccp4bb] Hi clashscore
Hi Supratim, The clashscore gives the relative number of clashes, not their severity. This makes it difficult to see what your specific problem is. Sever clashes (with large overlaps) are usually the result of errors in your model and need individual attention. Light bumps can usually be solved by optimizing the refinement parameters. Overrestraining bonds and angles can cause a lot of clashes. Cheers, Robbie -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of supratim dey Sent: Wednesday, January 23, 2013 09:47 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Hi clashscore Hi I am refining my 2 angstrom strucutre using phenix windows based software. After many refinements my clashscore is not at all reducing and showing a value of 12. Can anybody suggest how to reduce the clashscore. Is there any technique to do it. Or i have to deal with each individual clashes mentioned in the list manually ? Supratim
Re: [ccp4bb] Mac mini advice
I am of the opinion that the truth lies somewhere in between ... Here are my two cents based on personal experience ... For example, I am happy myself using a MacBook Pro, which is sufficient for all my activities, and has all software and data that I need. Thus, I am myself on the 'new' paradigm side, having a machine with mainframe levels of storage and computing power (I do not run git, but time machine in a mac has the bits I need from the git idea - as far as I know git that is). In the department, we have about 20-25 scientists. These people need to ''maintain and be proficient in many software suites, many more than a traditional crystallographer (like me in my PhD time for example) would need: vector design software for cloning, databases for keeping track of clones, sequencing viewing software for their clones, interfaces for crystallisation and biophysical equipment, analysis suites like Graphpad/Prism, Origin, Kintek (etc etc) for biophysical experiments ... and lets not forget SAXS software ... Our experience, is that most of these people like to use a Windows workstation for these (the choice is free), others prefer a Mac, thats not my point here. Many of that software also needs to maintained by these people... Also, for a variety of reasons which have to do with IT support restrictions, the Windows machines we have for them are miss-configured with ancient versions of the windows operating system, but still Ok for many things, but not for really straightforward use of CCP4/Phenix ... My point here is, that these people are less likely to be keen of the idea to also install and run ccp4/coot/phenix/buster in their machines (they use pymol/yassara/chimera though locally since they can copy/paste to their presentations and papers then). So, we find it useful to keep an old fashioned setup running in parallel. Linux boxes, hooked to Zalmans or really big or double LCDs, in a specific room ... People like these for data processing, all data of many years back are online, incremental backup is running etc. For historical reasons we even run NFS/NIS there (I agree its not a great choice if one would start now). My conclusion and advice for labs or departments that have more than 5-6 people, and are doing crystallography but not as their full-time business is that besides personal PC/Mac, a common room with a few relatively powerful machines with nice, big, double, screens, likely also Stereo, is useful for a few reasons: 1. Easier to make sure everybody is using the same software more or less 2. Same machine to everybody - not the situation that a new student gets a new machine at year 0, which is redundant by graduation time at +3 years (...or +5,6,7...) 3. Mixing of people in the room and ability for people to look over the shoulder of others, the point that my colleague Titia Sixma always favours, which has indeed proved great for teaching others and learning from others. 4. Centralised real backup, availability of diffraction data on-line with less mounts... For these machines, centralised user account information and 'home' sharing is in my view essential, as it allows to blindly choose any of the machines that is available at a time ... and, being a Mac fun, I think Linmux is better suited for that purpose, financially and practically... These said, it reminds me that we need to update the OS, buy a few new machines, new LCDs ... argh. Sorry of this lecture was outside the scope of the original thread. Tassos On 23 Jan 2013, at 9:54, James Stroud wrote: On Jan 22, 2013, at 11:20 PM, Nat Echols wrote: The real difficulty is integrating Macs into a Linux-centric environment, for example configuring NFS, NIS, etc. That's because NFS and NIS are antiquities left over from the days of mainframes. Distributed file systems and user information databases are designed for an environment of many workers and few machines, when the typical graphics workstation cost $50,000. These days, we argue whether to spend an extra $200 on a $500 computer. We have moved to a new paradigm: many workers with many more machines, with each machine having essentiallymainframe levels of storage and computing power. In other words, instead of NFS, you should run git. James
Re: [ccp4bb] protein solubility predictions
Indeed there are many web tools predicting solubility. My personal bias is that your brain is the best tool for ideas on how to design expression constructs. (since one question in a multi-domain protein, is which bit is interesting ...!) Many brains are better than one (talk to your colleagues - even to your supervisor ! - for ideas). A tool we like (since we developed it ...) helps to combine information from many other tools and help us make decisions (and order pcr primers to implement our decisions) is available at: http://xtal.nki.nl/ccd Another advice is whatever constructs you try, try them in many vectors - I could give another self-plugin here but I will not. There are many good systems allowing to put the same PCR product to many vectors for expression. A. From: Careina Edgooms careinaedgo...@yahoo.com Reply-To: Careina Edgooms careinaedgo...@yahoo.com Date: Tue, 22 Jan 2013 04:22:44 -0800 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] protein solubility predictions Dear ccp4 Apologies for the off topic question. I was wondering whether anyone could suggest a good tool or methodology to use to predict protein solubility and ability to fold from the sequence? I am working with a large protein of multiple domains. I would like to work with as close to the full length protein as possible without affecting its solubility and ability to fold correctly. I know there are web based tools where you can upload a sequence and see the predicted solubility but I wonder if there is any good strategy to use to determine how best to construct the truncated protein? ie which parts of the sequence to keep and which to remove so as to maximise solubility. Also I have an eye to crystallising this protein in the future and I wonder if there are any specific things I should look out for with that in mind? I'm sure minimising flexible loops is one such thing. All help appreciated Best Careina
Re: [ccp4bb] Mac mini advice
Cara you have re-ignited the perennial Mac v PC debate!!! You'll be asking about depositing raw diffraction data next ;) Cheers Ashley Sent from my iPhone On 23/01/2013, at 10:29 PM, Anastassis Perrakis a.perra...@nki.nl wrote: I am of the opinion that the truth lies somewhere in between ... Here are my two cents based on personal experience ... For example, I am happy myself using a MacBook Pro, which is sufficient for all my activities, and has all software and data that I need. Thus, I am myself on the 'new' paradigm side, having a machine with mainframe levels of storage and computing power (I do not run git, but time machine in a mac has the bits I need from the git idea - as far as I know git that is). In the department, we have about 20-25 scientists. These people need to ''maintain and be proficient in many software suites, many more than a traditional crystallographer (like me in my PhD time for example) would need: vector design software for cloning, databases for keeping track of clones, sequencing viewing software for their clones, interfaces for crystallisation and biophysical equipment, analysis suites like Graphpad/Prism, Origin, Kintek (etc etc) for biophysical experiments ... and lets not forget SAXS software ... Our experience, is that most of these people like to use a Windows workstation for these (the choice is free), others prefer a Mac, thats not my point here. Many of that software also needs to maintained by these people... Also, for a variety of reasons which have to do with IT support restrictions, the Windows machines we have for them are miss-configured with ancient versions of the windows operating system, but still Ok for many things, but not for really straightforward use of CCP4/Phenix ... My point here is, that these people are less likely to be keen of the idea to also install and run ccp4/coot/phenix/buster in their machines (they use pymol/yassara/chimera though locally since they can copy/paste to their presentations and papers then). So, we find it useful to keep an old fashioned setup running in parallel. Linux boxes, hooked to Zalmans or really big or double LCDs, in a specific room ... People like these for data processing, all data of many years back are online, incremental backup is running etc. For historical reasons we even run NFS/NIS there (I agree its not a great choice if one would start now). My conclusion and advice for labs or departments that have more than 5-6 people, and are doing crystallography but not as their full-time business is that besides personal PC/Mac, a common room with a few relatively powerful machines with nice, big, double, screens, likely also Stereo, is useful for a few reasons: 1. Easier to make sure everybody is using the same software more or less 2. Same machine to everybody - not the situation that a new student gets a new machine at year 0, which is redundant by graduation time at +3 years (...or +5,6,7...) 3. Mixing of people in the room and ability for people to look over the shoulder of others, the point that my colleague Titia Sixma always favours, which has indeed proved great for teaching others and learning from others. 4. Centralised real backup, availability of diffraction data on-line with less mounts... For these machines, centralised user account information and 'home' sharing is in my view essential, as it allows to blindly choose any of the machines that is available at a time ... and, being a Mac fun, I think Linmux is better suited for that purpose, financially and practically... These said, it reminds me that we need to update the OS, buy a few new machines, new LCDs ... argh. Sorry of this lecture was outside the scope of the original thread. Tassos On 23 Jan 2013, at 9:54, James Stroud wrote: On Jan 22, 2013, at 11:20 PM, Nat Echols wrote: The real difficulty is integrating Macs into a Linux-centric environment, for example configuring NFS, NIS, etc. That's because NFS and NIS are antiquities left over from the days of mainframes. Distributed file systems and user information databases are designed for an environment of many workers and few machines, when the typical graphics workstation cost $50,000. These days, we argue whether to spend an extra $200 on a $500 computer. We have moved to a new paradigm: many workers with many more machines, with each machine having essentiallymainframe levels of storage and computing power. In other words, instead of NFS, you should run git. James
Re: [ccp4bb] Mac mini advice (rapidly veering off topic)
In the great internet tradition I'll chip in with my opinion even though it doesn't differ substantially from those already stated earlier in the thread. I'm responsible for a mixed bag of Windows, Linux and Mac boxen used for crystallography and structural electron microscopy. In terms of setting up the infrastructure and getting things working, Linux wins by a mile. It's easy to buy cheap, powerful machines as desktops or servers. There's a wealth of resources to help the sysadmin. The ubiquity of Linux means that if you're trying to do something, there's almost always someone who has done it already and posted about it on a forum or blog. In terms of getting people to use the machines, OS X wins hands down. Putting people in front of linux machines requires more hand-holding on my part, especially for people who are inexperienced or even afraid of computers. This is becoming more of an issue: gone are the days when most crystallographers had a favourite shell and were happy editing scripts. Linux has come on in leaps and bounds but it's still not quite user-friendly enough; even something as simple as copying and pasting still doesn't have a uniform implementation. People familiar with commercial software struggle with the open source equivalents. I won't cover Windows as I have an irrational hatred of it. Having said all that, I too am worried about the way Apple is going. They haven't released a proper Mac Pro upgrade in ages, and seem to be concentrating on making iMacs as wafer thing as possible at the expense of other practical considerations. Their move to using the App Store for everything has concentrated on individual users and hasn't included support for corporate IT. Support for NFS and other UNIXy under-the-hood features is changed or dropped seemingly on a whim with no real documentation. Their habit of making every change or new release a big surprise makes it difficult to plan for the future. I'm glad I've got that off my chest. Now I can do something productive. Chris -- Dr Chris Richardson :: Sysadmin, structural biology, icr.ac.uk 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.
Re: [ccp4bb] Mac mini advice
On Wed, 2013-01-23 at 01:54 -0700, James Stroud wrote: On Jan 22, 2013, at 11:20 PM, Nat Echols wrote: The real difficulty is integrating Macs into a Linux-centric environment, for example configuring NFS, NIS, etc. That's because NFS and NIS are antiquities left over from the days of mainframes. Distributed file systems and user information databases are designed for an environment of many workers and few machines, when the typical graphics workstation cost $50,000. These days, we argue whether to spend an extra $200 on a $500 computer. We have moved to a new paradigm: many workers with many more machines, with each machine having essentially mainframe levels of storage and computing power. Technically there is something in what you say as a pattern for day-to-day work (for some people, although not all), but I think that describing the debate in terms of modern vs. antiquated is missing the point completely. The real difference between local vs. centralised storage is to do with responsibility for the hardware and the data that it contains. Local workstation storage is OK for the following kinds of cases: (i) the data that are stored locally have no value, so it doesn't matter if they are lost (either through hardware failure, misbehaving software or accidental deletion). (ii) the user has the expertise and the time to set up and maintain a strategy for recovering data that are lost from local disks (iii) the institution that the user works for allows the user to include data on local workstation disks in the institution's regular backup operations When none of these apply, there is a real, contemporary case for using something like NFS, where the storage is centrally maintained and backed up. The cost of storage has fallen of course, but what that means is that the real questions now are about the value of the data. In some fields, you could store your entire career's data on a few USB memory sticks, but I doubt that many people would want to do that without having made other copies somewhere else, and the same applies to local workstation storage too :-). There are other considerations in favour of connecting a workstation to networked services: if you use more than one machine it can be an incredible pain to be constantly moving data around from one to the other, and to keep track of what the authoritative versions are. Having independent, local user id's and passwords on every workstation can also cause difficulties. I could go on In other words, instead of NFS, you should run git. This is simply not an option for many crystallographers, who do not have a background in software development or data management. Advocating and supporting git (or indeed any content/version management system) for those kind of users is a losing battle: they see it as an unnecessary complication to their daily work, and will avoid using it as far as they can. 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
[ccp4bb] ATP binding
Dear All , Could anybody suggest the best possible manner to measure the halflife time of a protein-ATP complex? Our protein binds to ATP and we would like to measure its half life time after it is bound to radiolabelled ATP. Looking forward for your valuable suggestions. Best wishes, Jan
[ccp4bb] Two PhD Positions in Structural Biology, Research Centre Juelich Germany
At the Structural Biochemistry Institute (ICS-6, Forschungszentrum Juelich, Germany), we are looking for two highly motivated PhD students interested in biochemical and structural studies on photosignaling proteins and enzymes. The positions can be filled starting from March 2013. The project is part of a strategic research initiative Next generation of biotechnological methods- Biotechnology 2020+, funded by Federal Ministry of Education and Research, where several research groups from Research Centre Juelich (FZJ) and Heinrich-Heine-Universität Düsseldorf will combine their efforts to develop novel opto-sensors and photoregulatory proteins for the light-mediated analysis and control of molecular systems. FZJ is one of the largest interdisciplinary German research centers in Europe, located close to Cologne, Netherlands and Belgium that offers excellent opportunities for research in an international environment. Salaries are competitive (TvöD + allowance depending on the candidate's profile) and dissertations are usually completed within three years. Equal opportunities are a cornerstone of our staff policy for which we have received the TOTAL E-QUALITY award. Project details: Blue-light photoreceptors containing light-oxygen-voltage (LOV) domains regulate a myriad of different physiological responses in both eukaryotes and prokaryotes. Due to their intrinsic photochemical /photophysical properties, LOV proteins have proven as novel fluorescent reporters and blue-light sensitive photoswitches. Biotechnological applications include their use as real-time oxygen independent flavin-based fluorescent reporter proteins (FbFPs), as biological trap to produce flavin mononucleotide (FMN), as well as in development of LOV-based optogenetic tools. In ICS-6, our group utilizes structure-based techniques. Specifically, protein expression, purification, crystallization, spectroscopy, X-ray crystallography and comparative modeling will be employed to design and characterize the photophysical properties of various FbFPs. The selected PhD students will also collaborate with partners from the network for the use of other molecular biology and fluorescence techniques. More details about the actual research projects are available from the contact persons listed below. PD Dr. Renu Batra-Safferling (Email: r.batra-safferl...@fz-juelich.demailto:r.batra-safferl...@fz-juelich.de) PD Dr. Joachim Granzin (Email: j.gran...@fz-juelich.demailto:j.gran...@fz-juelich.de) Requirements: Candidates should have a recent MSc or equivalent degree in Biochemistry, Biophysics, Chemistry or a related discipline. Skills in either protein chemistry purification, or protein crystallography would be an asset. Application: Please send your application to above listed contact persons via e-mail, including the following documents: - Cover letter explaining the motivation for the position - A complete CV - Copy of exam certificate - Names of two Referees (with phone no., email, and relation to the applicant) Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt
Re: [ccp4bb] Mac mini advice
I assume nobody of you is running an actual Osx server ? I mean the upgrade to a full server version of the commonly distributed normal Osx releases ? I have not done it yet but I do think many of the issues mentioned regarding NFS/NIS could be addressed there. Regarding the missing macpro upgrades I expect to see new machines with thunderbolt connectivity in the next 4 months. And I will buy my third macpro then to run it as a true server. Jürgen Sent from my iPad On Jan 23, 2013, at 5:21, Peter Keller pkel...@globalphasing.com wrote: On Wed, 2013-01-23 at 01:54 -0700, James Stroud wrote: On Jan 22, 2013, at 11:20 PM, Nat Echols wrote: The real difficulty is integrating Macs into a Linux-centric environment, for example configuring NFS, NIS, etc. That's because NFS and NIS are antiquities left over from the days of mainframes. Distributed file systems and user information databases are designed for an environment of many workers and few machines, when the typical graphics workstation cost $50,000. These days, we argue whether to spend an extra $200 on a $500 computer. We have moved to a new paradigm: many workers with many more machines, with each machine having essentially mainframe levels of storage and computing power. Technically there is something in what you say as a pattern for day-to-day work (for some people, although not all), but I think that describing the debate in terms of modern vs. antiquated is missing the point completely. The real difference between local vs. centralised storage is to do with responsibility for the hardware and the data that it contains. Local workstation storage is OK for the following kinds of cases: (i) the data that are stored locally have no value, so it doesn't matter if they are lost (either through hardware failure, misbehaving software or accidental deletion). (ii) the user has the expertise and the time to set up and maintain a strategy for recovering data that are lost from local disks (iii) the institution that the user works for allows the user to include data on local workstation disks in the institution's regular backup operations When none of these apply, there is a real, contemporary case for using something like NFS, where the storage is centrally maintained and backed up. The cost of storage has fallen of course, but what that means is that the real questions now are about the value of the data. In some fields, you could store your entire career's data on a few USB memory sticks, but I doubt that many people would want to do that without having made other copies somewhere else, and the same applies to local workstation storage too :-). There are other considerations in favour of connecting a workstation to networked services: if you use more than one machine it can be an incredible pain to be constantly moving data around from one to the other, and to keep track of what the authoritative versions are. Having independent, local user id's and passwords on every workstation can also cause difficulties. I could go on In other words, instead of NFS, you should run git. This is simply not an option for many crystallographers, who do not have a background in software development or data management. Advocating and supporting git (or indeed any content/version management system) for those kind of users is a losing battle: they see it as an unnecessary complication to their daily work, and will avoid using it as far as they can. 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] Mac mini advice
We did work with a full blown OSX Server in 2004 - indeed many issues on NFS were Ok, but NIS was a problem - or we could not figure it out. We used it as server for developers, running X-grid, SVN, WebObjects servers for a couple of EC networks, but never deployed it fully as a departmental-level server, due to the NIS issues. For a while it also hosted the protein-ccd server. We wanted to move to Kerberos if I recall correctly, but since my colleague Serge Cohen moved out and our IT are mac-o-phobic I opted to continue with Linux. The Server was decommissioned a few weeks ago, and will likely get a second life in Soleil/Ipanema, but I think as an electric heat generator - almost as good on it as my old 8-proc Alpha (2000) ;-) A. On 23 Jan 2013, at 15:05, Bosch, Juergen wrote: I assume nobody of you is running an actual Osx server ? I mean the upgrade to a full server version of the commonly distributed normal Osx releases ? I have not done it yet but I do think many of the issues mentioned regarding NFS/NIS could be addressed there. Regarding the missing macpro upgrades I expect to see new machines with thunderbolt connectivity in the next 4 months. And I will buy my third macpro then to run it as a true server. Jürgen Sent from my iPad On Jan 23, 2013, at 5:21, Peter Keller pkel...@globalphasing.com wrote: On Wed, 2013-01-23 at 01:54 -0700, James Stroud wrote: On Jan 22, 2013, at 11:20 PM, Nat Echols wrote: The real difficulty is integrating Macs into a Linux-centric environment, for example configuring NFS, NIS, etc. That's because NFS and NIS are antiquities left over from the days of mainframes. Distributed file systems and user information databases are designed for an environment of many workers and few machines, when the typical graphics workstation cost $50,000. These days, we argue whether to spend an extra $200 on a $500 computer. We have moved to a new paradigm: many workers with many more machines, with each machine having essentially mainframe levels of storage and computing power. Technically there is something in what you say as a pattern for day-to-day work (for some people, although not all), but I think that describing the debate in terms of modern vs. antiquated is missing the point completely. The real difference between local vs. centralised storage is to do with responsibility for the hardware and the data that it contains. Local workstation storage is OK for the following kinds of cases: (i) the data that are stored locally have no value, so it doesn't matter if they are lost (either through hardware failure, misbehaving software or accidental deletion). (ii) the user has the expertise and the time to set up and maintain a strategy for recovering data that are lost from local disks (iii) the institution that the user works for allows the user to include data on local workstation disks in the institution's regular backup operations When none of these apply, there is a real, contemporary case for using something like NFS, where the storage is centrally maintained and backed up. The cost of storage has fallen of course, but what that means is that the real questions now are about the value of the data. In some fields, you could store your entire career's data on a few USB memory sticks, but I doubt that many people would want to do that without having made other copies somewhere else, and the same applies to local workstation storage too :-). There are other considerations in favour of connecting a workstation to networked services: if you use more than one machine it can be an incredible pain to be constantly moving data around from one to the other, and to keep track of what the authoritative versions are. Having independent, local user id's and passwords on every workstation can also cause difficulties. I could go on In other words, instead of NFS, you should run git. This is simply not an option for many crystallographers, who do not have a background in software development or data management. Advocating and supporting git (or indeed any content/version management system) for those kind of users is a losing battle: they see it as an unnecessary complication to their daily work, and will avoid using it as far as they can. 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] Mac mini advice
We have 10.510.6 servers and briefly tested 10.7 server. Last time I tried, Ubuntu 12.04 box would not authenticate users registered on the OS X Open Directory server. Before that, 10.04 clients would cause random user lockouts. NFS GUI is gone as of 10.7 Regards, Dmitry On 2013-01-23, at 9:05 AM, Bosch, Juergen wrote: I assume nobody of you is running an actual Osx server ? I mean the upgrade to a full server version of the commonly distributed normal Osx releases ? I have not done it yet but I do think many of the issues mentioned regarding NFS/NIS could be addressed there. Regarding the missing macpro upgrades I expect to see new machines with thunderbolt connectivity in the next 4 months. And I will buy my third macpro then to run it as a true server. Jürgen Sent from my iPad On Jan 23, 2013, at 5:21, Peter Keller pkel...@globalphasing.com wrote: On Wed, 2013-01-23 at 01:54 -0700, James Stroud wrote: On Jan 22, 2013, at 11:20 PM, Nat Echols wrote: The real difficulty is integrating Macs into a Linux-centric environment, for example configuring NFS, NIS, etc. That's because NFS and NIS are antiquities left over from the days of mainframes. Distributed file systems and user information databases are designed for an environment of many workers and few machines, when the typical graphics workstation cost $50,000. These days, we argue whether to spend an extra $200 on a $500 computer. We have moved to a new paradigm: many workers with many more machines, with each machine having essentially mainframe levels of storage and computing power. Technically there is something in what you say as a pattern for day-to-day work (for some people, although not all), but I think that describing the debate in terms of modern vs. antiquated is missing the point completely. The real difference between local vs. centralised storage is to do with responsibility for the hardware and the data that it contains. Local workstation storage is OK for the following kinds of cases: (i) the data that are stored locally have no value, so it doesn't matter if they are lost (either through hardware failure, misbehaving software or accidental deletion). (ii) the user has the expertise and the time to set up and maintain a strategy for recovering data that are lost from local disks (iii) the institution that the user works for allows the user to include data on local workstation disks in the institution's regular backup operations When none of these apply, there is a real, contemporary case for using something like NFS, where the storage is centrally maintained and backed up. The cost of storage has fallen of course, but what that means is that the real questions now are about the value of the data. In some fields, you could store your entire career's data on a few USB memory sticks, but I doubt that many people would want to do that without having made other copies somewhere else, and the same applies to local workstation storage too :-). There are other considerations in favour of connecting a workstation to networked services: if you use more than one machine it can be an incredible pain to be constantly moving data around from one to the other, and to keep track of what the authoritative versions are. Having independent, local user id's and passwords on every workstation can also cause difficulties. I could go on In other words, instead of NFS, you should run git. This is simply not an option for many crystallographers, who do not have a background in software development or data management. Advocating and supporting git (or indeed any content/version management system) for those kind of users is a losing battle: they see it as an unnecessary complication to their daily work, and will avoid using it as far as they can. 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] Mac mini advice
Hi, I'm running a mac mini server. The file sharing seems to work fine - I'm not running NIS. There is a lag in software starting up - up to 20-30 s but once the software is loaded, it runs fine. We did some benchmarking with phaser last week there was no perceivable difference in running it of the server or locally (on a Mac Pro) Software may require fiddling with to ensure that paths point to where the software is mounted. This may be referred to as 'hacking' … so I wouldn't do it :-) Sid Dr K S Sidhu Department of Biochemistry 1/61 Henry Wellcome Building Lancaster Road Leicester LE1 9HN Tel: 0116 229 7237 On 23 Jan 2013, at 14:05, Bosch, Juergen jubo...@jhsph.edumailto:jubo...@jhsph.edu wrote: I assume nobody of you is running an actual Osx server ? I mean the upgrade to a full server version of the commonly distributed normal Osx releases ? I have not done it yet but I do think many of the issues mentioned regarding NFS/NIS could be addressed there. Regarding the missing macpro upgrades I expect to see new machines with thunderbolt connectivity in the next 4 months. And I will buy my third macpro then to run it as a true server. Jürgen Sent from my iPad On Jan 23, 2013, at 5:21, Peter Keller pkel...@globalphasing.commailto:pkel...@globalphasing.com wrote: On Wed, 2013-01-23 at 01:54 -0700, James Stroud wrote: On Jan 22, 2013, at 11:20 PM, Nat Echols wrote: The real difficulty is integrating Macs into a Linux-centric environment, for example configuring NFS, NIS, etc. That's because NFS and NIS are antiquities left over from the days of mainframes. Distributed file systems and user information databases are designed for an environment of many workers and few machines, when the typical graphics workstation cost $50,000. These days, we argue whether to spend an extra $200 on a $500 computer. We have moved to a new paradigm: many workers with many more machines, with each machine having essentially mainframe levels of storage and computing power. Technically there is something in what you say as a pattern for day-to-day work (for some people, although not all), but I think that describing the debate in terms of modern vs. antiquated is missing the point completely. The real difference between local vs. centralised storage is to do with responsibility for the hardware and the data that it contains. Local workstation storage is OK for the following kinds of cases: (i) the data that are stored locally have no value, so it doesn't matter if they are lost (either through hardware failure, misbehaving software or accidental deletion). (ii) the user has the expertise and the time to set up and maintain a strategy for recovering data that are lost from local disks (iii) the institution that the user works for allows the user to include data on local workstation disks in the institution's regular backup operations When none of these apply, there is a real, contemporary case for using something like NFS, where the storage is centrally maintained and backed up. The cost of storage has fallen of course, but what that means is that the real questions now are about the value of the data. In some fields, you could store your entire career's data on a few USB memory sticks, but I doubt that many people would want to do that without having made other copies somewhere else, and the same applies to local workstation storage too :-). There are other considerations in favour of connecting a workstation to networked services: if you use more than one machine it can be an incredible pain to be constantly moving data around from one to the other, and to keep track of what the authoritative versions are. Having independent, local user id's and passwords on every workstation can also cause difficulties. I could go on In other words, instead of NFS, you should run git. This is simply not an option for many crystallographers, who do not have a background in software development or data management. Advocating and supporting git (or indeed any content/version management system) for those kind of users is a losing battle: they see it as an unnecessary complication to their daily work, and will avoid using it as far as they can. 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
[ccp4bb] Crystallography Near Absolute Zero?
Is anyone aware of any datasets taken at near absolute zero? I was wondering what would happen... Jacob -- *** Jacob Pearson Keller, PhD Postdoctoral Associate HHMI Janelia Farms Research Campus email: j-kell...@northwestern.edu ***
Re: [ccp4bb] Crystallography Near Absolute Zero?
On 01/23/13 10:11, Jacob Keller wrote: Is anyone aware of any datasets taken at near absolute zero? I was wondering what would happen... http://www.ncbi.nlm.nih.gov/pubmed/12718921 New techniques in macromolecular cryocrystallography: macromolecular crystal annealing and cryogenic helium. Hanson BL http://www.ncbi.nlm.nih.gov/pubmed?term=Hanson%20BL%5BAuthor%5Dcauthor=truecauthor_uid=12718921, Schall CA http://www.ncbi.nlm.nih.gov/pubmed?term=Schall%20CA%5BAuthor%5Dcauthor=truecauthor_uid=12718921, Bunick GJ http://www.ncbi.nlm.nih.gov/pubmed?term=Bunick%20GJ%5BAuthor%5Dcauthor=truecauthor_uid=12718921. J Struct Biol. http://www.ncbi.nlm.nih.gov/pubmed/12718921# 2003 Apr;142(1):77-87. -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
Re: [ccp4bb] Mac mini advice
On 23 Jan 2013, at 14:05, Bosch, Juergen wrote: I assume nobody of you is running an actual Osx server ? I mean the upgrade to a full server version of the commonly distributed normal Osx releases ? At the moment we have two OS X servers. One runs open directory for user authentication. The other is an AFP server for network home directories. They are elderly Xeon-based XServes and will be retired as soon as possible. We're getting rid of the authentication server because of unrelated changes to the way user authentication will be handled. We're getting rid of the file server because it's old and needs replacing. It will, however, be replaced by a Linux server. In my opinion, Apple's abandonment of its rack-mountable server line shows a lack of commitment to servers. The Promise RAID storage they resell is considerably more expensive than the equivalent from our Windows/Linux supplier. Finally, the other Mac admins in my organisation haven't been saying nice things about mountain lion server. If you look at forums like AFP548.com it's apparent that many other people are moving away from OS X server. Moving to OS X servers does simplify some aspects of administration. In the past, there was the added bonus that it was easy to get Linux and Windows machines to talk to a Mac server. Creeping changes made by Apple since OS X server 10.4 mean that this is less true. In particular, the horrible way Apple sets up SMB make its use a nightmare with other modern operating systems. Chris -- Dr Chris Richardson :: Sysadmin, structural biology, icr.ac.uk 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] 2013 ACA meeting - speakers for undergraduate research session
CCP4BB members, I am writing to recruit protein crystallographers who work with undergraduate students to consider submitting an abstract to present a short talk at the 2013 American Crystallographic Association Meeting (July 20-24, Honolulu, HI) in our session, (13.08) Building Protein and Small Molecule Research Capacity at an Undergraduate Institution. We are particularly interested in talks that address curriculum development, best practices for integrating protein X-ray crystallography into undergraduate teaching and research, acquisition of relevant research equipment, and strategies for faculty research success and productivity at an undergraduate institution. In addition to sharing your expertise and networking with crystallography folks in the undergraduate teaching and research community, you can loll in the tropical sun as well. (For those of us in the northern U.S., this is quite appealing at this particular moment.) If you are interested in presenting in our session at the ACA meeting, please submit an abstract ( http://www.amercrystalassn.org/2013-abstracts , *deadline March 31, 2013*) or contact me for more information. The session is being organized by Kraig Wheeler (Eastern Illinois University) and me. We would like to have a similar session every year, and build a strong community at the ACA to promote undergraduate involvement in protein and small molecule crystallography. Last year's inaugural session was well-attended, and we hope to build on that effort in 2013. Thanks for reading, ___ Roger S. Rowlett Gordon Dorothy Kline Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu
Re: [ccp4bb] Crystallography Near Absolute Zero?
Coming next : Negative Absolute Temperature for Motional Degrees of Freedom http://m.sciencemag.org/content/339/6115/52
[ccp4bb] scala, cad, free flag
Hello all, please consider the following scenario of converting XDS data to MTZ, preserving the rfree flag from an older MTZ file. 1. POINTLESS with input XDS_ASCII.HKL 2. CCP4I-scaling: scala with 'Copy FreeR from another MTZ' option, implicitly using CAD, cad log attached. I would expect my output cell dimensions to match exactly those in XDS_ASCII.HKL. Should I not? The output cell dimensions, however, match exactly those of the MTZ file that supplied the free flag. In this case, the difference is just a couple 1/100 Angstroms, but could it happen in cases of more severe deviations from isomorphism? Did anyone else come across this behavior? Could it be intended? Best regards, Wolfram Tempel cad.20130123.log Description: Binary data
[ccp4bb] GPCR DOCK 2013 announcement
Since there may some on this bb who have modelers as colleagues... On behalf of the PSI GPCR Network group: -- Dear GPCR modeling and docking researcher, We are writing to announce the 3rd round of the GPCR Docking and Modeling Assessment, GPCR Dock 2013, and to invite you to submit your predictions of GPCR-ligand structures for comparison prior to publication of the results. The first two GPCR Dock assessments were conducted in 2008 and 2010 and were based on the structures of A2A adenosine receptor (GPCR Dock 2008; NRDD 2009), dopamine D3 receptor and chemokine receptor CXCR4 (GPCR Dock 2010; Structure 2011). As before, the results from GPCR Dock 2013 will be published once an analysis is complete. The present round of the assessment will be focused on four target complexes. Participants can choose to predict any one, two, three, or all four targets. Predicting all four targets is strongly encouraged. Registered participants will receive receptor and ligand information at midnight (Pacific standard time) on Feb 1st, and will have until midnight (PST) March 3rd (30 days) to deposit models. Further information about the assessment and registration forms to participate can be found at http://gpcr.scripps.edu/GPCRDock2013 If you have any questions, please email (gpcrd...@scripps.edu) we will try to get back to you quickly and will also post any general comments to all registered participants. GPCR Network Ray Stevens Ruben Abagyan Irina Kufareva Angela Walker Seva Katritch Margaret J. Gabanyi, Ph.D. Asst. Research Professor, Department of Chemistry and Chemical Biology Sr. Outreach Coordinator, PSI Structural Biology Knowledgebase Rutgers, The State University of New Jersey 174 Frelinghuysen Rd Piscataway, NJ 08854-8076 phone: 848-445-4932 gaba...@rcsb.rutgers.edu Discover more at http://sbkb.org --
[ccp4bb] off topic - legacy hardware help needed
Hi all, By the way, thanks for all the suggestions on the linux versions. I went against my better judgement and just stuck with Fedora, mainly because I'm familiar with it. I have to admit, I kind of like it. I was able to get it up and running, run nfs to mount local drives, and install all the necessary crystallography software with no hitch - quick. It's kind of nice. And it set up my wireless printer automatically - so all is great. Anyway, we have an old Indigo SGI that runs our NMR. It's a console only system, and we access it via the network from another old SGI (toaster model - blue). The console does not have a video card (nor space for one), so I can't plug in to it and see what's happening. Anyway, our network was recently updated, and in doing so it has made access to our console system unavailable. We can't get there because the IP's that used to be needed are no more. So, I can get the disk out, and I have a variety of unix/linux systems that I could plug it in to. But, alas, I have no motherboards or systems that take SCSI (that I have a sled for or a way to put it in). I need to be able to mount the drive on some sort of system, edit a few config files to fix the network, then plug it all back in. All without messing up boot tables and such (not a big deal, just thought I'd throw that out there). Is there a cable that simply allows me to plug in the back of a SCSI drive then connect to an IDE port on a newer motherboard (or better yet, an external USB port)? Just curious - that would be worth it to me. Any thoughts? Thanks Dave
Re: [ccp4bb] off topic - legacy hardware help needed
On 23 Jan 2013, at 16:07, Dave Roberts drobe...@depauw.edu wrote: Anyway, we have an old Indigo SGI that runs our NMR. It's a console only system, and we access it via the network from another old SGI (toaster model - blue). The console does not have a video card (nor space for one), so I can't plug in to it and see what's happening. Anyway, our network was recently updated, and in doing so it has made access to our console system unavailable. We can't get there because the IP's that used to be needed are no more. I'm not familiar with the Indigo, but I presume it has a serial port over which you could log in to the machine. Connect the Indigo to an accessible machine with a serial cable (you can even get serial/USB adapters that sort-of work, too) and run something like minicom or screen. // Cheers; Johan Postdoctoral Fellow @ Physical Biosciences Division ___ Lawrence Berkeley National Laboratory * 1 Cyclotron Rd. Mail Stop 64R0121 * Berkeley, CA 94720-8118 * +1 (510) 495-8055
