Re: [ccp4bb] project and literature organization software (laboratory information management software)
Hi Tobias, We use LabTrove: http://www.labtrove.org/ Pros: Relatively easy local install Revision control Ability to attach any file Cons: clumsy blog formatting does not lay eggs. Regards, Dmitry It is a bit clumsy being based on a blog engine and does not lay eggs… But it works fine for an electronic lab book and On 2014-04-29, at 7:21 AM, Tobias Beck tobiasb...@gmail.com wrote: Dear all, I am looking for a software solution to organize many pieces of information 1.) Results from (bio)chemical experiments, such as spectral data, pictures. 2.) Project ideas, milestones, etc. 3.) Literature, including tags, short comments, etc. For example, for a certain project I would like to collect information about experiments conducted, then link this to literature/literature experiments and to project outlines. All this should be accessible for multiple users on different OS. I have briefly looked into PiMS (too much crystallography oriented), Contor ELN (only on Safari on Mac?), Labguru (nice, but not too flexible and mostly for biosciences) and Confluence (nice wiki, but so far no real literature plugin). I know that this sounds maybe a little bit like something called in German a 'eierlegende Wollmilchsau' http://en.wiktionary.org/wiki/eierlegende_Wollmilchsau But I would be happy to hear about what software people (and labs) have tried, liked/disliked and ideally the reasons. (I am aware that there was a similar query https://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg24657.html, but this was more than 2 years ago) Thanks a lot! Best wishes, Tobias. -- ___ Dr. Tobias Beck ETH Zurich Laboratory of Organic Chemistry Vladimir-Prelog-Weg 3, HCI F 322 8093 Zurich, Switzerland phone: +41 44 632 68 65 fax:+41 44 632 14 86 web: http://www.protein.ethz.ch/people/tobias ___
Re: [ccp4bb] PyMol and Schrodinger
Hi Mirek, If you happen to be using OS X, Fink makes it very easy to install recent open-source pymol. Best regards, Dmitry On 2014-04-23, at 11:43 AM, Cygler, Miroslaw miroslaw.cyg...@usask.ca wrote: Hi, I have inquired at Schrodinger about the licensing for PyMol. I was surprised by their answer. The access to PyMol is only through a yearly licence. They do not offer the option of purchasing the software and using the obtained version without time limitation. This policy is very different from many other software packages, which one can use without continuing licensing fees and additional fees are only when an upgrade is needed. At least I believe that Office, EndNote, Photoshop and others are distributed this way. I also remember very vividly the Warren’s reason for developing PyMol, and that was the free access to the source code. He later implemented fees for downloading binary code specific for one’s operating system but there were no time restrictions on its use. As far as I recollect, Schrodinger took over PyMol distribution and development promising to continue in the same spirit. Please correct me if I am wrong. I find the constant yearly licensing policy disturbing and will be looking for alternatives. I would like to hear if you have had the same experience and what you think about the Schrodinger policy. Best wishes, Mirek
Re: [ccp4bb] Protein concentration form chromatograms
If using Unicorn, 1)Open your chromatogram in Evaluation window. 2)Go to Operations- Pool 3)Choose which baseline estimation suits you, define the pools (numbered rulers that appear under the chromatogram) 4)type in the path length (2 or 10 mm for UV-900 and 2 mm for UPC-900) 5)type in the mass extinction coefficient (Molar extinction coefficient/Mw in daltons) 6) get your answer from the table at the bottom of the screen The reading will make sense for pure protein. Also note that for the most accurate result you need to know the exact path length which varies a little bit from cell to cell (or so they say). Regards, Dmitry On 2014-01-15, at 10:09 AM, Karel Chaz wrote: Dear all, A question for the biochemistry-inclined folks in the bb; how do I calculate protein concentration of chromatography fractions, starting from Abs280 from the UV monitor? I know I could figure it out myself if I really tried, but why bother when I have access to so many brilliant minds Thanks to all, K smime.p7s Description: S/MIME cryptographic signature
Re: [ccp4bb] AW: [ccp4bb] Dealnig with O-linked mannose
Thanks, Herman. Zhijie, what is the difference between LINK and LINKR? Maybe this will help somebody (though phenix-related): phenix.link_edits parses the pdb for LINK records and outputs the pdb.edits file. Alternatively, phenix.ligand_linking can guess what should be bonded in the absence of LINK records and produce apply_link.def Best rgards, Dmitry On 2013-11-22, at 3:18 AM, herman.schreu...@sanofi.com wrote: Using your favorite editor, you can copy the LINK record from the pdb file generated by Coot and paste it into the pdb file produced by Phenix. You can also make a script to do this. This is what I did during the time LINK records were not properly handled by coot, refmac and buster. Best regards, Herman -Ursprüngliche Nachricht- Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Dmitry Rodionov Gesendet: Donnerstag, 21. November 2013 22:09 An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] Dealnig with O-linked mannose Thank you all for helpful suggestions. My question was how to properly connect a mannose to a serine and real-space refine the result. My apologies for not being clear enough. Coot can't find MAN-SER or SER-MAN in it's library (Coot 0.7.1, mon_lib 5.41) It does not automatically make the bond between MAN C1 and OG of SER either. Here is the way I finally made the connection followed by refinement it in Coot: 1) Get monomer... MAN 2) real-space refine MAN into reasonable position 3) Delete hydrogens and reducing hydroxyl Bond is not detected 4) Extensions-Modelling ...-make Link (Click 2 atoms) ... Click on C1 of MAN and OG of SER dashed bond appears 5) Sphere refine A whole different issue that was touched in the replies is how this model will be handled by refinement programs. For the sake of a record, I am using Phenix and it seems to not respect the described link without massaging by means of either pdb.edits or apply_link.def. Also, phenix.refine does not produce LINK records in the output PDB, so step 4 might have to be repeated. Best regards, Dmitry smime.p7s Description: S/MIME cryptographic signature
Re: [ccp4bb] Dealnig with O-linked mannose
Thank you all for helpful suggestions. My question was how to properly connect a mannose to a serine and real-space refine the result. My apologies for not being clear enough. Coot can't find MAN-SER or SER-MAN in it's library (Coot 0.7.1, mon_lib 5.41) It does not automatically make the bond between MAN C1 and OG of SER either. Here is the way I finally made the connection followed by refinement it in Coot: 1) Get monomer... MAN 2) real-space refine MAN into reasonable position 3) Delete hydrogens and reducing hydroxyl Bond is not detected 4) Extensions-Modelling ...-make Link (Click 2 atoms) ... Click on C1 of MAN and OG of SER dashed bond appears 5) Sphere refine A whole different issue that was touched in the replies is how this model will be handled by refinement programs. For the sake of a record, I am using Phenix and it seems to not respect the described link without massaging by means of either pdb.edits or apply_link.def. Also, phenix.refine does not produce LINK records in the output PDB, so step 4 might have to be repeated. Best regards, Dmitry smime.p7s Description: S/MIME cryptographic signature
[ccp4bb] Dealnig with O-linked mannose
Good day! I am refining what appears to be O-mannosylated protein structure. In my hands Coot (0.7.1) does not form the SER-MAN bond automatically. I made a SER-MAN.cif with jLigand, which takes care of the glycosidic bond. However, now the peptide bonds are not made to this custom residue (same chain, consecutive numbering). Am I doing something wrong? How can I fix this? Many thanks, Dmitry smime.p7s Description: S/MIME cryptographic signature
[ccp4bb] Conflicting Qt on OS X 10.6
Good day! I'm having problems with qtrview (on OS X 10.6): it crashes or hangs after spitting out a screenful of messages like objc[2975]: Class QCocoaMenu is implemented in both /Applications/ccp4-6.4.0/bin/../Frameworks/QtGui.framework/Versions/4/QtGui and /Library/Frameworks/QtGui.framework/Versions/4/QtGui. One of the two will be used. Which one is undefined. Just like the message says, I have Qt 4 installed in the standard location. It seems like the global Qt it is being used instead of the one supplied with CCP4 6.4 since moving /Library/Frameworks/Qt* elsewhere fixes the problem. Oddly enough, qtrview of CCP4 6.3 worked fine under the same conditions. Is there a way to make qtrview use CCP4's Qt and ignore other versions? Thanks! Best regards, Dmitry smime.p7s Description: S/MIME cryptographic signature
Re: [ccp4bb] Conflicting Qt on OS X 10.6
Thanks for the suggestions! I just opened a new terminal window, and it appears that problem had disappeared (by itself?). Sorry for the false alarm- I'll go see a mental health professional. Best regards, Dmitry On 2013-10-28, at 12:49 PM, William Scott wrote: It looks like it should be doing the right thing, i.e., zsh-% otool -L qtrview qtrview: @executable_path/../Frameworks/QtWebKit.framework/Versions/4/QtWebKit (compatibility version 4.9.0, current version 4.9.3) @executable_path/../Frameworks/QtXmlPatterns.framework/Versions/4/QtXmlPatterns (compatibility version 4.8.0, current version 4.8.4) @executable_path/../Frameworks/QtGui.framework/Versions/4/QtGui (compatibility version 4.8.0, current version 4.8.4) @executable_path/../Frameworks/QtXml.framework/Versions/4/QtXml (compatibility version 4.8.0, current version 4.8.4) @executable_path/../Frameworks/QtNetwork.framework/Versions/4/QtNetwork (compatibility version 4.8.0, current version 4.8.4) @executable_path/../Frameworks/QtCore.framework/Versions/4/QtCore (compatibility version 4.8.0, current version 4.8.4) If you have $DYLID_LIBRARY_PATH set, try unsetting it. On Oct 28, 2013, at 9:00 AM, Dmitry Rodionov d.rodio...@gmail.com wrote: Good day! I'm having problems with qtrview (on OS X 10.6): it crashes or hangs after spitting out a screenful of messages like objc[2975]: Class QCocoaMenu is implemented in both /Applications/ccp4-6.4.0/bin/../Frameworks/QtGui.framework/Versions/4/QtGui and /Library/Frameworks/QtGui.framework/Versions/4/QtGui. One of the two will be used. Which one is undefined. Just like the message says, I have Qt 4 installed in the standard location. It seems like the global Qt it is being used instead of the one supplied with CCP4 6.4 since moving /Library/Frameworks/Qt* elsewhere fixes the problem. Oddly enough, qtrview of CCP4 6.3 worked fine under the same conditions. Is there a way to make qtrview use CCP4's Qt and ignore other versions? Thanks! Best regards, Dmitry smime.p7s Description: S/MIME cryptographic signature
Re: [ccp4bb] Advise on setting up/ maintaining a Ubuntu cluster
We don't have any performance/ reliability issues with our cheapskate setup either. Make sure the network is wired with Cat5e or Cat6 cables, especially if distances are 8m+ Dmitry On 2013-07-31, at 7:36 AM, Kay Diederichs wrote: I have a very different experience with NFS: we are using Gigabit Ethernet, and a 64bit RHEL6 clone with ECC memory as a file server; it has RAID1 ext4 home directories and RAID6 ext4 for synchrotron data. We have had zero performance or reliability problems with this in a computer lab with ~ 10 workstations, and I have seen 115 MB/sec file transfers via NFS, at peak times. Just make sure to export using the async option. HTH, Kay On Wed, 31 Jul 2013 09:21:48 +0900, Francois Berenger beren...@riken.jp wrote: Be careful that running data intensive jobs over NFS is super slow (at least an order of magnitude compared to writing things on a local disk). Not only the computation is slow, but you may be slowing down all other users of the cluster too... F. smime.p7s Description: S/MIME cryptographic signature
Re: [ccp4bb] Advice on setting up / maintaining a Ubuntu cluster
Dear Sergei, IMO, the easiest way to achieve your goals is good old NIS and NFS with a centralized server on wired gigabit network. You could go with LDAP instead of NIS, but it is considerably more difficult to set up. One computer would act as a server, containing the user database, homes and programs. Hardware RAID is not worth it. You are better off getting a Linux-supported SAS/SATA HBA (e.g. Dell SAS 6/iR) and making a software RAID 5 with mdadm out of a bunch of inexpensive consumer-grade SATA disks. You need a minimum of 4 drives for RAID5. An external HDD enclosure might be necessary depending on server's chassis and the desired number of drives. We built our server from an old P4 workstation with a couple gigs of RAM (8 clients). Having two or more cores is a benefit. If I am not mistaken, software RAID 5 is not bootable, so you would need an extra drive (can be very small) for the core part of the OS. Export /home and /usr/local with NFS, mount them from client machines, hook the clients up to NIS and you are done. Some programs might not reside in /usr/local in which case you would have to export and mount more directories. Ubuntu community has pretty good and easy to follow guides for NIS, NFS and mdadm. Bets regards, Dmitry On 2013-07-29, at 6:22 AM, Sergei Strelkov wrote: Dear all, In old times I, just like about any protein crystallographer, used to work on a cluster of SGI/IRIX workstations with complete NFS-based cross-mounting of hard disks. A typical operation included: 1. A single home directory location for every user: if my home directory was on workstation X, I would by default use it after logging on any of the workstations in the cluster. 2. A single location for all software for general use. (And, obviously, 3. The ability to log on any node from any terminal; today this is done via the 'ssh -X' command). I wondered if someone could give us an advice on a painless setup enabling 1. and 2., for a small cluster of Ubuntu computers. We (will) have about five similar Dell computers in a local (192.168.*.*) network (wired/wireless). Any tips on the hardware (especially the LAN and network disks) are also welcome. Many thanks, Sergei -- Prof. Sergei V. Strelkov Laboratory for Biocrystallography Dept of Pharmaceutical and Pharmacological Sciences, KU Leuven Herestraat 49 bus 822, 3000 Leuven, Belgium Work phone: +32 16 330845 Mobile: +32 486 294132 Lab pages: http://pharm.kuleuven.be/anafar smime.p7s Description: S/MIME cryptographic signature
Re: [ccp4bb] Off-topic: Fungal growth in robot trays
8. Empty the carboy and fill the supply lines and wash stations with 20% ethanol at the end of the day. (Requires decontamination in this case) Best regards, Dmitry On 2013-03-13, at 10:04 PM, Viswanathan Chandrasekaran v...@biochem.utah.edu wrote: Dear All: Thank you for your responses. Here is a summary of suggested fixes: 1. Cleaning the supply carboy and lines with bleach and flushing thoroughly with DD water afterwards 2. Adding 0.02% sodium azide to the protein 3. Adding 0.02% azide to commercial screens 4. Adding 0.02% azide to the water used for washing 5. Using fresh screens and storing them at low temperatures (4 or 12 degree C) 6. Manually dispensing the reservoir solution using a multi-channel pipette 7. Using a Mosquito robot (it uses fresh needles each time) Best, Vish From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Viswanathan Chandrasekaran Sent: Friday, March 08, 2013 4:24 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Off-topic: Fungal growth in robot trays Dear All: I would like some advice on getting rid of persistent fungal growth in 96-well sitting drop crystal plates that were set up using a Phoenix robot. 24-well sitting drop trays prepared by hand don’t have this problem. Washing the robot with 0.5% bleach followed by plenty of water had no effect. Is adding sodium azide directly to commercial screen hotels (or the protein sample) a good idea? If so, how much should I add? Other suggestions are welcome. I will post a summary of all replies. Thank you. Best, Vish
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
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.com wrote: On Tue, Jan 22, 2013 at 1:40 PM, Phil Jeffrey 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] Convert cbf to png/tiff?
I think ADXV will do the trick. Regards, Dmitry On 2013-01-10, at 3:36 PM, Frank von Delft wrote: Hello all - anybody know an easy way to convert CBF images (Pilatus) into something lossless like tiff or png? Ideally *easy* as in r e a l l y e a s y and not requiring extensive installation of dependencies and stuff. Because then I might as well write my own stuff using cbflib and PIL in python. Thanks! phx
Re: [ccp4bb] hkl2000 install
I believe cr_info should go in /usr/local/hklint along with site files. It does not have to be executable but must be readable by all. (chmod a+r cr_info) Regards, Dmitry Rodionov On 2012-11-13, at 12:33 AM, 王瑞 wrote: Dear everyone: I have got the returned cr_info.dat to /usr/local/lib and /usr/local/hklint,when I typing HKL2000,it still display: dell@ubuntu:~$ HKL2000 ERROR: Not a valid HKL-2000 license: Licence info file (cr_info) not found Error code: -1 So could anyone can help me ? 2012/11/9 王瑞 wangrui...@gmail.com: Dear everyone: I'm sorry for a little off-topic! I want to install HKL2000 on ubuntu11.10 32bits, but it produces a file named info not cr_info after run the access_prod program.And when I put info to /usr/local/lib directory and typingHKL2000 in terminal, it display: root@ubuntu:/usr/local/bin# HKL2000 ERROR: Not a valid HKL-2000 license: Licence info file (cr_info) not found Error code: -1 So could anyone tell me how to do it ? Rui Wang
Re: [ccp4bb] hkl2000 install
Rui, I just noticed in your email you wrote cr_info.dat That is the cause of your problem If you actually added .dat extension. We have always kept ours in /usr/local/hklint Which is funny because it is not one of the folders suggested by HKL people. Thierry and Felix are right about other locations. Dmitry On 2012-11-13, at 11:26 AM, Felix Frolow wrote: cr_info can be in several places ~/ (user home directory) working directory /usr/local/lib ( This is the place where I keep it as it is a consensus location for cr_info) about /usr/local/hklint I am not sure, but if you say so, you probably know :-) FF Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Nov 13, 2012, at 18:12 , Dmitry Rodionov d.rodio...@gmail.com wrote: I believe cr_info should go in /usr/local/hklint along with site files. It does not have to be executable but must be readable by all. (chmod a+r cr_info) Regards, Dmitry Rodionov On 2012-11-13, at 12:33 AM, 王瑞 wrote: Dear everyone: I have got the returned cr_info.dat to /usr/local/lib and /usr/local/hklint,when I typing HKL2000,it still display: dell@ubuntu:~$ HKL2000 ERROR: Not a valid HKL-2000 license: Licence info file (cr_info) not found Error code: -1 So could anyone can help me ? 2012/11/9 王瑞 wangrui...@gmail.com: Dear everyone: I'm sorry for a little off-topic! I want to install HKL2000 on ubuntu11.10 32bits, but it produces a file named info not cr_info after run the access_prod program.And when I put info to /usr/local/lib directory and typingHKL2000 in terminal, it display: root@ubuntu:/usr/local/bin# HKL2000 ERROR: Not a valid HKL-2000 license: Licence info file (cr_info) not found Error code: -1 So could anyone tell me how to do it ? Rui Wang
Re: [ccp4bb] Stabilization of crystals and ligand exchange
Hi Sabine, Glutaraldehyde crosslinking worked pretty good for various soaks in my experience. J. Appl. Cryst. (1999). 32, 106-112[ doi:10.1107/S002188989801053X ] A gentle vapor-diffusion technique for cross-linking of protein crystals for cryocrystallography C. J. Lusty Best regards, Dmitry On 2012-10-17, at 12:26 PM, Sabine Schneider wrote: Hi everyone, I am trying to get the structure of a protein-ligand complex were I need to exchange the ligand which it co-crystallises nicely with. Problem: either they crack, disolve, turn brown,... OR they still look very nice, well shaped but do not show a single reflection at the synchrotron!!! Here is what I tried so far: 1) initially stabilising with higher precipitant (here PEG1500) before slowly transferring (*) it to the ligand-removal solution (= artifical mother liquor with higher PEG, ethylen glycol or glucose, but without initial ligand) (*) by slow exchange I mean : initially mixing drop solution with stabilising/ligand-removal solution and adding it back to the drop stepwise before fully transferring it. Or calculation wise I have fully exchange the solution to the new solution 2) here I let them ist over night (if they did not disolve, crack or whatever) 3) slow exchange transfer to the artificial ML with the new ligand (10mM), left them over night and directly froze them 'Best' so far (crystals still looking nice but no reflection...) was slow exchange into higher PEG, than to higher PEG with ethylenglycol (30% and also adding ethylenglycol to the reservoir), let them sit for over night, before again slow exchange to the solution with the new ligand in higher PEG and 30% ethylen glycol. As I said here the crystals keep shape, but don't diffract at all anymore. Just freezing them with 30% ethylen glycol they diffract nicely to 2.5A on a home source. But already after step one they are sometimes not happy anymore. Co-crystallisation failed since when I add the ligand, which is not that soluble to the purified protein, everything crashed out of solution. I am thinking about to test adding the ligand to the diluted protein and concentrate it together. But I don't have that much ligand, since the synthesis is quite tedious The ligand can be dissolved in 30% ethylenglycol to ~50mM Thus I was wondering if someone has done successfully ligand exchange with glutaraldehyd stabilised xtals? Or any ideas how to stabilise them? I appreciate any ideas or comments! Sorry for the lengthy email! Best, Sabine
Re: [ccp4bb] CCP4 update 6.3.0 006
Hi Ben, Applications launched from Finder and Spotlight get environment variables from ~/.MacOSX/environment.plist (before 10.8) their own Info.plist (10.8) and launchd (system-wide) and not .tcshrc etc. Sounds like to get the updater to work from Finder for all users you have to set your $CCP4 in launchd.conf Not sure if it's worth the effort. The environment is probably set correctly (somewhere) on the machine that was used to install CCP4... http://apple.stackexchange.com/questions/57385/where-are-system-environment-variables-set-in-mountain-lion http://www.dowdandassociates.com/content/howto-set-environment-variable-mac-os-x-etclaunchdconf Dmitry On 2012-10-12, at 3:46 PM, Ben Eisenbraun wrote: On Mon, Oct 08, 2012 at 06:20:59PM +, Ronan Keegan wrote: Dear CCP4 Users, A CCP4 update has just been released, consisting of the following changes: Hi Ronan et al, The update client on OS X doesn't seem to like our installation and dies with: Can't make class cfol of alias programs:i386-mac:ccp4:6.3.0:lib_exec:Update.app: into type Unicode text But I found an odd workaround. If I double-click the Update.app in Finder, I get the administrator password prompt, enter the credentials, and then the updater tells me that $CCP4 is unset, etc. I can then run 'open Update.app' from the shell, and it inherits $CCP4 and runs correctly. Any ideas? The workaround works, but since I don't really know why, I don't feel particularly good about it. Also, my installation is on NFS and is not owned by root, so it doesn't require administrator privileges to update. It would be nice if the application checked for write privileges before assuming it needs to be run with escalated privileges. -ben -- | Ben Eisenbraun | SBGrid Consortium | http://sbgrid.org | | Harvard Medical School | http://hms.harvard.edu |
