[ccp4bb] Incubator for crystallization
Hi everybody, I want to buy a smaller incubator for protein crystallization (30-50 l). Do you have any recommendations ? Do you prefer specialized incubator models with low vibration or are you just using standard incubators ? Best wishes, Ulrike
Re: [ccp4bb] Incubator for crystallization
Dear Ulrike, Molecular dimensions incubator model MD5-601 works pretty good in our lab. -Peltier type -low vibration -fully programmable up to 99 days -temperature up to 4C -accommodate low space -with RS232 Check the following links | From archives related to your question posted previously. DT2-MP-38: DigiTherm(R) 38-liter Heating/Cooling Incubator - Tritech Research, Inc. DT2-MP-38: DigiTherm(R) 38-liter Heating/Cooling Incu... View on www.tritechresearch... Preview by Yahoo EchoTherm™ IN30, IN35, IN40, IN45, IN50 and IN55 Bench Top Incubators | Torrey Pines Scientific EchoTherm™ IN30, IN35, IN40, IN45, IN50 and IN55 B... EchoTherm™ IN30, IN40 and IN50 Series Bench Top, Chilling/Heating Incubators with Fully Programmable or Non-programmable Controls Chill or heat... View on www.torreypinesscien... Preview by Yahoo Cheers Dr.S.M.Jaimohan On Tuesday, 11 November 2014 4:01 PM, Ulrike Demmer ulrike.dem...@biophys.mpg.de wrote: Hi everybody, I want to buy a smaller incubator for protein crystallization (30-50 l). Do you have any recommendations ? Do you prefer specialized incubator models with low vibration or are you just using standard incubators ? Best wishes, Ulrike 00,
[ccp4bb] Amino acid side chains without density
Dear CCP4bb, Sorry for asking a naive question. I am trying to deposit a structure in PDB. I would like to know whether we have to delete the side chains of amino acids for which we are not finding density or people prefer keeping the side chains occupancy zero? Is there any other way to do this?
Re: [ccp4bb] Amino acid side chains without density
I think you'll find that this is not a naive question.. I doubt there is a consensus for this. Neither option is ideal, mainly because of possible confusion generated for non-crystallographers. My preference is to include the side chain but set the atoms i do not see to zero occupancy. The PDB does not like this however Others will probably chime in here; in any case i think this has been discussed before, so digging in the archives might help as well. Bert From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Sasha Pausch [sashapau...@gmail.com] Sent: Tuesday, November 11, 2014 1:14 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Amino acid side chains without density Dear CCP4bb, Sorry for asking a naive question. I am trying to deposit a structure in PDB. I would like to know whether we have to delete the side chains of amino acids for which we are not finding density or people prefer keeping the side chains occupancy zero? Is there any other way to do this?
Re: [ccp4bb] Amino acid side chains without density
Dear Sasha, There was a survey done by Ed Pozharski back in 2011 The results of the online survey on what to do with disordered side chains (from total of 240 responses): Delete the atoms 43% Let refinement take care of it by inflating B-factors41% Set occupancy to zero12% Other 4% Reference: https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1103L=CCP4BBD=0P=321265 So, the other way (appart from what you mention) is to keep the atoms and let the B-factors refine to relatively large values. Best regards, Folmer 2014-11-11 14:14 GMT+01:00 Sasha Pausch sashapau...@gmail.com: Dear CCP4bb, Sorry for asking a naive question. I am trying to deposit a structure in PDB. I would like to know whether we have to delete the side chains of amino acids for which we are not finding density or people prefer keeping the side chains occupancy zero? Is there any other way to do this? -- Folmer Fredslund
[ccp4bb] workstation crystallography
Dear ccp4 bb members, I need to buy a desktop workstation for the purpose of running crystallography related applications. I have short-listed HP's Z420 and Dell's T7600, I chose this because their configuration description looks impressive (8 cores, 16 threads, 3.6 GHz processor etc.). However, I have no practical idea about their performance. Can anyone , who has experience with these workstations comment on performance ? And whether these workstations are optimal/suboptimal for the desired purpose ? what other options do I have apart from dell and hp ? Please suggest. *Is desktop iMac a good option for this purpose ?* many thanx in advance abhishek
Re: [ccp4bb] Amino acid side chains without density
Dear Sasha, you should bear in mind that the major part of users of your deposited structure will not be crystallographers, and they probably don't know what e.g. a B-value is. So also may no use Coot to visualise the structure hence may not be pointed at graphically that occupancies are set to zero. E.g. I have the impression that sometimes people running molecular dynamics simulations take a PDB file for granted and as absolute truth, even irrespective of the resolution and other quality indicators. Therefore you are on the safe side to delete side chains for which you don't see density. When you place them, you decide for a position without experimental evidence. You can run two tests: 1) remove the side chain and refine. Does the difference map indicate where the side chain should be? Put it back, otherwise leave it out The difference density is a little more sensitive than the direct map. 2) place the side chain a little bit, e.g. select a different rotamer in Coot that does not clash. Then refine. Does the side chain go back to where you initially placed it? Then there may be some signal in the data supporting that position. Otherwise, leave it out. Best, Tim On 11/11/2014 02:14 PM, Sasha Pausch wrote: Dear CCP4bb, Sorry for asking a naive question. I am trying to deposit a structure in PDB. I would like to know whether we have to delete the side chains of amino acids for which we are not finding density or people prefer keeping the side chains occupancy zero? Is there any other way to do this? -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A signature.asc Description: OpenPGP digital signature
Re: [ccp4bb] workstation crystallography
I'm running home-built Ubuntu boxes with old, plain-vanilla CPUs (e.g., Q9300 or core i3/i5/i7) and 6-8Gbyte of RAM, and a cheap Nvidia video card (e.g. GT 9xxx or GT 620).This is more than sufficient to do routine structure solution. Any contemporary desktop or laptop computer should be sufficient, although if running Linux I have not had good luck with integrated Intel graphics. (If you want stereo display, you have to choose a compatible graphics card and video monitor.) It's not like the old days, where you needed special, dedicated hardware (remember Silicon Graphics?) to get the graphics and computing performance required. Current technology is more than sufficient for routine work. ___ 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 On 11/11/2014 8:27 AM, abhishek jamwal wrote: Dear ccp4 bb members, I need to buy a desktop workstation for the purpose of running crystallography related applications. I have short-listed HP's Z420 and Dell's T7600, I chose this because their configuration description looks impressive (8 cores, 16 threads, 3.6 GHz processor etc.). However, I have no practical idea about their performance. Can anyone , who has experience with these workstations comment on performance ? And whether these workstations are optimal/suboptimal for the desired purpose ? what other options do I have apart from dell and hp ? Please suggest. *Is desktop iMac a good option for this purpose ?* many thanx in advance abhishek
Re: [ccp4bb] workstation crystallography
I will comment on specific features you might look for in a crystallographic workstation, rather than brand names. I usually build from parts rather than buy intact machines. CPU: 3+ GHz per compute core is good these days. For a standard single user desktop, 4 CPU cores is fine. More cores will allow you to run multiple independent jobs, but will not speed up a single job. Server chips may have 6 or 8 cores (or maybe even more, but then they start cutting the clock speed). It's up to you to decide what kind of workload this machine is likely to experience. (Those server CPUs will lack on-chip graphics, but see the next point) Graphics: 1) First question: do you want stereo 3D? If so, that places restrictions on which graphics cards and which monitors are supported. 2) If the answer to 1 is no, then you have more freedom. I would not recommend on-CPU graphics for a couple reasons. a) Better graphics performance with separate graphics cards. Any mid-range or better card should do. b) An add-in graphics card will allow the CPU to run faster. This is because the turbo feature built into modern CPU/GPU chips will slow down the compute cores based on the total thermal load of all CPU/GPU cores. Monitor: Get one with LED backlighting. Lasts longer and is more efficient. RAM: More RAM is good, and it is relatively cheap at present. 8 GB minimum, recommended 16 GB. Storage (disk is now an anachronism): I strongly recommend a quality SSD, at least for the OS. It makes a noticable difference in speed. 120 GB or more for the OS. If you need multi-terabytes of storage space for data (and who doesn't?), get hard drives for that. Ports: Gigabit (at least) ethernet to get on the network. USB3.0 for connecting peripherals like portable drives. By next year I will be recommending USB3.1, which will have higher data throughput, higher power throughput and convenient symmetrical connectors. Cheers, On 11/11/14 08:27, abhishek jamwal wrote: Dear ccp4 bb members, I need to buy a desktop workstation for the purpose of running crystallography related applications. I have short-listed HP's Z420 and Dell's T7600, I chose this because their configuration description looks impressive (8 cores, 16 threads, 3.6 GHz processor etc.). However, I have no practical idea about their performance. Can anyone , who has experience with these workstations comment on performance ? And whether these workstations are optimal/suboptimal for the desired purpose ? what other options do I have apart from dell and hp ? Please suggest. *Is desktop iMac a good option for this purpose ?* many thanx in advance abhishek -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
[ccp4bb] To scale or not to scale: XDS_ASCII.HKL input to POINTLESS/AIMLESS
Hello all, in a discussion https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1307L=CCP4BBH=1P=186901 on this board, Kay Diederichs questioned the effect of scaling data in AIMLESS after prior scaling in XDS (CORRECT). I understand that the available alternatives in this work flow are to specify the AIMLESS ‘onlymerge’ command, or not. Are there any arguments for the preference of one alternative over the other? Thank you for your insights, Wolfram Tempel
Re: [ccp4bb] To scale or not to scale: XDS_ASCII.HKL input to POINTLESS/AIMLESS
Hi, I actually choose the option 'constant' further down in the aimless gui but I guess the effect is similar to 'onlymege'. Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of wtempel [wtem...@gmail.com] Sent: Tuesday, November 11, 2014 9:50 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] To scale or not to scale: XDS_ASCII.HKL input to POINTLESS/AIMLESS Hello all, in a discussion on this board, Kay Diederichs questioned the effect of scaling data in AIMLESS after prior scaling in XDS (CORRECT). I understand that the available alternatives in this work flow are to specify the AIMLESS ‘onlymerge’ command, or not. Are there any arguments for the preference of one alternative over the other? Thank you for your insights, Wolfram Tempel
Re: [ccp4bb] To scale or not to scale: XDS_ASCII.HKL input to POINTLESS/AIMLESS
Thank you Boaz. So if CORRECT can do a fully corrected scaling, are there no corrections that XSCALE might apply to XDS_ASCII.HKL data that are beyond CORRECT's capabilities? Wolfram On Tue, Nov 11, 2014 at 3:05 PM, Boaz Shaanan bshaa...@bgu.ac.il wrote: Hi, I actually choose the option 'constant' further down in the aimless gui but I guess the effect is similar to 'onlymege'. Boaz *Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il bshaa...@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710* -- *From:* CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of wtempel [ wtem...@gmail.com] *Sent:* Tuesday, November 11, 2014 9:50 PM *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* [ccp4bb] To scale or not to scale: XDS_ASCII.HKL input to POINTLESS/AIMLESS Hello all, in a discussion https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1307L=CCP4BBH=1P=186901 on this board, Kay Diederichs questioned the effect of scaling data in AIMLESS after prior scaling in XDS (CORRECT). I understand that the available alternatives in this work flow are to specify the AIMLESS ‘onlymerge’ command, or not. Are there any arguments for the preference of one alternative over the other? Thank you for your insights, Wolfram Tempel
Re: [ccp4bb] To scale or not to scale: XDS_ASCII.HKL input to POINTLESS/AIMLESS
http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Xscale XSCALE http://www.mpimf-heidelberg.mpg.de/%7Ekabsch/xds/html_doc/xscale_parameters.html is the scaling program of the XDS suite. It scales reflection files (typically called XDS_ASCII.HKL) produced by XDS. Since the CORRECT step of XDS already scales an individual dataset, XSCALE is only /needed/ if several datasets should be scaled relative to another. However, it does not deterioriate a dataset if it is scaled again in XSCALE, since the supporting points of the scalefactors are at the same positions in detector and batch space. The advantage of using XSCALE for a single dataset is that the user can specify the limits of the resolution shells. _Scaling with scala/aimless_ http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Scaling_with_SCALA_%28or_better:_aimless%29 -Sudhir *** Sudhir Babu Pothineni GM/CA @ APS 436D Argonne National Laboratory 9700 S Cass Ave Argonne IL 60439 Ph : 630 252 0672 On 11/11/14 14:42, wtempel wrote: Thank you Boaz. So if CORRECT can do a fully corrected scaling, are there no corrections that XSCALE might apply to XDS_ASCII.HKL data that are beyond CORRECT's capabilities? Wolfram On Tue, Nov 11, 2014 at 3:05 PM, Boaz Shaanan bshaa...@bgu.ac.il mailto:bshaa...@bgu.ac.il wrote: Hi, I actually choose the option 'constant' further down in the aimless gui but I guess the effect is similar to 'onlymege'. Boaz /Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il mailto:bshaa...@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 / // // / / *From:* CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK mailto:CCP4BB@JISCMAIL.AC.UK] on behalf of wtempel [wtem...@gmail.com mailto:wtem...@gmail.com] *Sent:* Tuesday, November 11, 2014 9:50 PM *To:* CCP4BB@JISCMAIL.AC.UK mailto:CCP4BB@JISCMAIL.AC.UK *Subject:* [ccp4bb] To scale or not to scale: XDS_ASCII.HKL input to POINTLESS/AIMLESS Hello all, in a discussion https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1307L=CCP4BBH=1P=186901 on this board, Kay Diederichs questioned the effect of scaling data in AIMLESS after prior scaling in XDS (CORRECT). I understand that the available alternatives in this work flow are to specify the AIMLESS ‘onlymerge’ command, or not. Are there any arguments for the preference of one alternative over the other? Thank you for your insights, Wolfram Tempel
[ccp4bb] CCPBioSim one day training workshop on free energy calculations
Dear all, CCPBioSim are running a free one-day training course on performing free energy calculations in protein systems. The particular focus will be on estimating protein-ligand binding affinities, but the role of solvation in mediating protein-ligand interactions will also be explored. Date: Tuesday 25th November, 2014 Location: University of Southampton, Highfield Campus, Building 36, Room 2065 Instructors: Dr Julien Michel (Edinburgh), Dr Sam Genheden (Southampton), Dr Richard Bradshaw (Southampton), Dr Greg Ross (Southampton), Ana Cabedo Martinez (Southampton) Further details are available at http://www.ccpbiosim.ac.uk/workshops/2ndFreeEnergy and registration is open at https://eventbooking.stfc.ac.uk/news-events/ccpbiosim-free-energy-methods-for-modelling-of-protein-ligand-interactions-250 Cheers Martyn on behalf of Professor Jonathan W. Essex (Southampton) * * Dr. Martyn Winn * STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. * Tel: +44 1925 603455 (DL) or +44 1235 567865 (RcaH) * E-mail: martyn.w...@stfc.ac.uk Skype: martyn.winn * -- Scanned by iCritical.
Re: [ccp4bb] To scale or not to scale: XDS_ASCII.HKL input to POINTLESS/AIMLESS
You can take XDS data into Pointless Aimless (the CCP4 Data Reduction task) either from the unscaled INTEGRATE.HKL or the scaled XDS_ASCII.HKL file (or files). In the case of a single XDS_ASCII.HKL you don't need to rescale it in Aimless, though you can if you want. Aimless uses a similar but not identical scaling model to XDS, which may be better or worse (and how do you judge?). Phil On 11 Nov 2014, at 19:50, wtempel wtem...@gmail.com wrote: Hello all, in a discussion on this board, Kay Diederichs questioned the effect of scaling data in AIMLESS after prior scaling in XDS (CORRECT). I understand that the available alternatives in this work flow are to specify the AIMLESS ‘onlymerge’ command, or not. Are there any arguments for the preference of one alternative over the other? Thank you for your insights, Wolfram Tempel
[ccp4bb] Structural biology faculty search at UC-Davis
Dear Colleagues, The Molecular Cellular Biology department at the University of California, Davis is searching for two tenure track faculty at the assistant professor level in many areas, including structural biology. The UC-Davis College of Biological Sciences is an excellent environment for Molecular Cell biology, Chromosome biology, Molecular Genetics and Plant biology. There is a strong interest in increasing the faculty ranks in modern structural biology. The molecular Cellular Biology department houses modern state-of-the-art setups for biochemistry, x-ray crystallography and cryo-electron microscopy. Details can be found at: https://www.mcb.ucdavis.edu/ and https://www.mcb.ucdavis.edu/jobs/faculty.cfm Jawdat Al-Bassam Ph.D. Molecular Cellular Biology University of California Davis
Re: [ccp4bb] workstation crystallography
The more recent integrated graphics chips, starting from the Intel HD3000, have adequate performance for crystallography. Really, most crystallography applications are less computationally demanding than video games now. I think the most important issue is to make sure your hardware plays nicely with your favorite linux distribution. Aloha, Ho Ho Leung Ng University of Hawaii at Manoa Assistant Professor, Department of Chemistry h...@hawaii.edu
Re: [ccp4bb] Incubator for crystallization
We use wine refrigerators. Peltier cooling, no compressor, no vibrations, cheap. They look nice too. But they can't cool to 4C. Aloha, Ho Ho Leung Ng University of Hawaii at Manoa Assistant Professor, Department of Chemistry h...@hawaii.edu
