Re: [ccp4bb] crystals that dont diffract :( :(
Hi Careina, if you don't have grey hair (available in the lab), you can still mount crystals at room temperature. With a MiTeGen RT kit, very little skill is required to test crystal diffraction or even collect entire data sets at room temperature. https://www.mitegen.com/product/micrort-room-temperature-starter-kits/ All best. Andreas On Tue, Aug 14, 2018 at 12:48 PM, Harry Powell < 193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote: > Hi > > One other thing to try that someone with grey hair in your lab might know > about - mount a "crystal" in a capillary and see if it diffracts at room > temp. As long as you have a source and detector in your home lab, there's > no need to go to a synchrotron and use their in situ facilities. > > There are those of us who would contend that if your sample doesn't > diffract, then it isn't a crystal, no matter how nice it looks (though it > might have been one once...)! > > Harry > -- > Dr Harry Powell > Chairman of European Crystallographic Association SIG9 (Crystallographic > Computing) > > > > > On 14 Aug 2018, at 11:14, Elspeth Garman wrote: > > Yes, essential to test at room temperature without changing their buffer > medium before getting worried! > If they don’t diffract at RT, they are very very unlikely to diffract at > cryotemperatures, whatever you do to them before hand! > Best wishes > Elspeth > > *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of > *Hughes, > Jon > *Sent:* 14 August 2018 11:11 > *To:* CCP4BB@JISCMAIL.AC.UK > *Subject:* [ccp4bb] AW: [ccp4bb] crystals that dont diffract :( :( > > maybe it's the cryobuffer that's the problem (you didn't mention it). you > could try to fish the crystals with minimal liquid attached by mounting > them in oil rather than a cryobuffer. or you could test the native > diffraction "in situ" (at room temperature in the drop): quite a few > beamlines offer this possibility these days. > best > jon > > *Von:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK > ] *Im Auftrag von *Careina Edgooms > *Gesendet:* Dienstag, 14. August 2018 11:59 > *An:* CCP4BB@JISCMAIL.AC.UK > *Betreff:* [ccp4bb] crystals that dont diffract :( :( > > I got the most beautiful crystals I have ever seen and they don't diffract > at all. Not poor diffraction, NO diffraction. Anyone know why this could be > and how I can go about fixing it? I had three beautiful crystals and not > one diffracted. I did leave them in the drop for about 3 weeks before > harvesting and in liquid nitrogen for about a month before diffracting. > Could that be a factor? If I regrew more beautiful crystals and diffracted > straight away could that help? > Careina > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > > > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
Re: [ccp4bb] Might be of interest to this group
Wouldn’t that be something for the PyMOL mailing list? All best - Andreas On Fri, 9 Feb 2018 at 20:38, David Schuller wrote: > http://www.cell.com/current-biology/fulltext/S0960-9822(18)30014-9 > A Novel Form of Stereo Vision in the Praying Mantis > Vivek Nityananda ,Ghaith Tarawneh, Sid > Henriksen,Diana Umeton,Adam Simmons, Jenny C.A. Read > > DOI: https://doi.org/10.1016/j.cub.2018.01.012 > > Current Biology > > -- > === > All Things Serve the Beam > === >David J. Schuller >modern man in a post-modern world >MacCHESS, Cornell University >schul...@cornell.edu > >
Re: [ccp4bb] NMR or Homology Model as a MR model
Dear Nishant, Rosetta is a good suggestion. You can also use an ensemble of several related (superposed) structures as your search model. This will improve your chances of success. All best. Andreas On Tue, Aug 29, 2017 at 12:50 PM, Nishant Varshney wrote: > Dear Crystallographers, > > I am working to solve an human protein structure which has a domain > sequence identity of 24% with domain of another protein. As Phaser as well > as Molrep failed to give any definite solution (TFZ=3.7 from MR), I want to > ask, if solution structure of another protein having domain sequence > similarity of 25% or a homology model can be used as a template for MR? > Many thanks and Regards > Nishant > > -- > Dr. Nishant Kumar Varshney, > Research Associate, > C/O Dr. Sameena Khan, > Drug Discovery Research Center, > Translational Health Science and Technology Institute (THSTI) > NCR Biotech Science Cluster, > 3rd Milestone, Faridabad – Gurgaon Expressway, > Faridabad – 121001 (HARYANA), India > Ph: +91- 0129-2876477 <+91%20129%20287%206477> > Mob: 8390564690 >
Re: [ccp4bb] Stable Refinement as Low(ish) resolution
Dear Rhys, I second Roger on the use of jelly-body refinement. In addition, give Buster a try. It sometimes does magic at lowish resolution. All best. Andreas On Thu, Jul 13, 2017 at 1:17 AM, Rhys Grinter wrote: > Dear All, > > I'm currently in the process of refining a low(ish) resolution structure > at 3.2 Ang, with a fair level of anisotropy. I processed the data through > the anisotropy server (https://services.mbi.ucla.edu/anisoscale/), which > elliptically truncated the data to 4.0, 3.8 and 3.2 Ang. This really > improved the maps and allowed me to trace the majority of the chain and > build most side chains. > > The R-factors are reasonable (0.29 work and 0.35 free respectively). but > I'm having trouble with over fitting in refinement as I continue to refine. > What parameters/restraints would the community generally use when refining > this kind of structure? Additionally Refmac doesn't seem to read the > structure factors from the anisotropy server output file properly, giving > vastly inflated R values and strange looking maps. > > Cheers, > > Rhys > > -- > Dr Rhys Grinter > Sir Henry Wellcome Fellow > Monash University > +61 (0)3 9902 9213 <+61%203%209902%209213> > +61 (0)403 896 767 <+61%20403%20896%20767> >
Re: [ccp4bb] looking for paper describing optimisation of crystals using a screen kit as additive
Hi Sebastian, you're thinking about local sparse matrix screening. I've done this at a 90:10 ratio. Majeed, S., Ofek, G., Belachew, A., Huang, C.C., Zhou, T., and Kwong, P.D. Enhancing protein crystallization through precipitant synergy. Structure. 2003; 11: 1061–1070 All best. Andreas On Mon, May 8, 2017 at 3:18 PM, Sebastiano Pasqualato < sebastiano.pasqual...@gmail.com> wrote: > > Dear all, > I recall a paper (or was is a talk at a conference?) describing the > optimisation of initial hits of crystallisation by using a standard screen > kit as additive. > Something like setting the tray using the initial crystallisation hit > condition in the reservoir and mixing 75% of the hit condition with 25% of > a commercial sparse matrix screen kit with the protein in the drop. > I can’t find the reference, can anybody help me? > Thanks a lot, > ciao, > Sebastiano > > > -- > *Sebastiano Pasqualato, PhD* > Crystallography Unit > Department of Experimental Oncology > European Institute of Oncology > IFOM-IEO Campus > via Adamello, 16 > 20139 - Milano > Italy > > tel +39 02 9437 5167 <+39%2002%209437%205167> > fax +39 02 9437 5990 <+39%2002%209437%205990> > web http://is.gd/IEOXtalUnit > >
Re: [ccp4bb] Crystallization Screens
Hi FBDD Evangelist, Emerald Bio is now Rigaku Reagents. https://www.rigakureagents.com/ They don't seem to sell the pHAT screen on their website, but they might be able to provide you with a PDF of the compositions. All best. Andreas On Mon, Mar 6, 2017 at 10:56 AM, Hernani Silvestre wrote: > Dear community, > > Quite likely you have been in this situation, you come across a screen > where you have hits but the screen has been discontinued. I am looking for > the following screen: > Emerald Biosystems pHAT buffer screen. > > I did find a pdf with some of the buffers described (but , as usual, the > well composition I am interested I cant see it there..the pdf is incomplete. > Does anyone know the 96-well composition of this buffer screen? > Not sure what happened to Emerald Bio, they are no longer active (oh > dear...) > > Many thanks > FBDD Evangelist >
Re: [ccp4bb] Choosing test set for twin refinement, with multiple operators
Dear Andre, I agree with Jacob that P 42 21 2 might be the right space group, and that and R free of 33% isn't so bad. If your electron density is poor, that might just reflect the low resolution. Have you tried refinement with Buster? It has a way with low-resolution data. All best. Andreas On Tue, Dec 6, 2016 at 3:25 PM, Keller, Jacob wrote: > What were the twinning tests like in p42212? I suspect that it is really > that spacegroup, the low Rfree is artificial (33% is not too bad at 3.9 > Ang) and the electron density is bias. > > > > JPK > > > > *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of > *Andre > Luis Berteli Ambrosio > *Sent:* Tuesday, December 06, 2016 9:17 AM > *To:* CCP4BB@JISCMAIL.AC.UK > *Subject:* [ccp4bb] Choosing test set for twin refinement, with multiple > operators > > > > Dear all, > > We are currently refining a low resolution model (3.9 A max), obtained by > MR. Dataset was collected from a single crystal with one long cell axis > (~620 A) and high solvent content (74%). > > Best refinement results (by far!) are obtained in Refmac, by imposing P21 > sg (20 multidomain monomers/AU) and allowing for amplitude-based twin > refinement. > > Accordingly, Refmac identifies four twin operators, which I understand > have considerable fractions, as follows: > > > > Twin operators with estimated twin fractions > > > > Twin operator: H, K, L: Fraction = 0.249; Equivalent operators: -H, K, > -L > > Twin operator: -H, -K, L: Fraction = 0.260; Equivalent operators: H, -K, > -L > > Twin operator: -K, -H, -L: Fraction = 0.235; Equivalent operators: K, > -H, L > > Twin operator: K, H, -L: Fraction = 0.257; Equivalent operators: -K, > H, L > > > > I suspect that the low Rfree (~25%) may be artificial and results from an > inappropriate selection of the test due to the multiple operators. > > However, I cannot figure out how to properly select the test set when such > a high number of operators must be considered. > > FYI, space group P42212 resulted in the best processing statistics (5 > monomers/AU); however, model never improved from an Rfree of 33%, with the > quality of the electron density distribution for some of the domains being > heavily compromised. > > I honestly apologize if I am missing some obvious points here and will be > happy to provide more info, including statistics on data processing. > > Since is a multidomain protein, is it also appropriate to include TLS > refinement at this low resolution? > > I thank you all in advance. > > Best, > > Andre. > > > > > > > > >
Re: [ccp4bb] XDS questions
Dear Wei, if you process your data with XDS, the best is probably to do the scaling in XDS (CORRECT) and be done with it. If you want to use Aimless for merging, you can turn off scaling with the ONLYMERGE keyword or use SCALES CONSTANT. All best. Andreas On Thu, Nov 17, 2016 at 9:40 PM, Wei Wang wrote: > Hi, > > Is there a way to let xds_par use less than all processors/threads on the > machine? Sometimes I would like to process something else while XDS is > running. > > Another question is related to the scaling procedure. My understanding is > that the XDS already does the scaling during correction. So if I follow the > XDS-Aimless route, then probably I should let Aimless do "skip scaling and > only merge"? Please elucidate me on this issue. > > Regards, > > Wei >
Re: [ccp4bb] Problem regarding output in ccp4i 6.5
Dear Deepa, there was a time when spaces in the names of foldera and files was a big nono in ccp4. Maybe it still is. Try changing New Folder to New_Folder or something else without a space. Best Andreas On Wed, Jun 3, 2015 at 6:09 AM, Deepa Raju wrote: > Dear all, > I have installed ccp4i 6.5 version, I need to find out the contacts > between the atoms of SAM and amino acid residues of the protein. But I'm > not getting the output. Output is showing like this > > #CCP4I VERSION CCP4Interface 6.5.0 > #CCP4I SCRIPT LOG contact > #CCP4I DATE 02 Jun 2015 17:33:09 > #CCP4I USER 'UNKNOWN' > #CCP4I PROJECT deepasam > #CCP4I JOB_ID 64 > #CCP4I SCRATCH C:/ccp4temp/ > #CCP4I HOSTNAME DEEPA-PC > #CCP4I PID 7176 > > *** > * Information from CCP4Interface script > *** > The program run with command: contact XYZIN "D:/sum_proj/New > Folder/structure analysis/5.6.2014/1XDS_chain_A.pdb" > has failed with error message > couldn't execute "contact": invalid argument > *** > > > #CCP4I TERMINATION STATUS 0 "couldn't execute "contact": invalid argument" > #CCP4I TERMINATION TIME 02 Jun 2015 17:33:09 > #CCP4I MESSAGE Task failed > > > please suggest the solution for this problem. > > Thank you in advance > With Regards, > Deepa >
Re: [ccp4bb] Low Phaser RFZ
Hi Eric, What does your map look like? Do you see features that don't come from the search model? That's the key. That said, with a TFZ of above 10, I'd be rather positive about my prospects. Andreas On Tue, May 19, 2015 at 2:36 AM, Eric Karg < 052044071b36-dmarc-requ...@jiscmail.ac.uk> wrote: > Hi all, > > Running Phaser using the apo protein as search model on a ~2.5 A dataset > of a protein-DNA complex, I get a single solution but with low RFZ. The map > looks reasonable but I was wondering why the RFZ is so low. Would this > solution be acceptable? > >SOLU SET RFZ=3.2 TFZ=8.4 PAK=0 LLG=66 TFZ==10.6 RFZ=2.9 TFZ=13.7 PAK=0 > LLG=203 > TFZ==14.0 LLG=1440 TFZ==34.2 >SOLU SPAC P 62 2 2 >SOLU 6DIM ENSE ensemble1 EULER 181.8 55.7 74.8 FRAC 0.27 0.26 -0.40 > BFAC -7.38 >SOLU 6DIM ENSE ensemble1 EULER 4.5 120.2 7.9 FRAC -0.31 0.20 -0.09 BFAC > 12.61 >Ensemble ensemble1 RMS variance(s): 0.87 > > Thank you for your help! >
Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures....
Hey Tommi, I am under the impression that Zbyszek Otwinowski has looked in depth at all of the structures that have now been retracted and has prepared a long manuscript detailing the evidence for fabrication and falsification. As far as I know, this manuscript hasn't been published yet (shame!), but it's bound to come out soon. Keep you patience just a little longer. Andreas On Fri, Dec 11, 2009 at 9:19 AM, Tommi Kajander wrote: > Would the exact analysis of how each of these things were wrong and > fabricated be somewhere > available Would be fair (apart from the known case of C3b) to have the > whole analysis available > instead of just this kind of news feed. I suspect its not obvious by five > minute check in all cases. > > Perhaps there needs to be ways within PDB in form of automated tools that > would raise those red > flags in suspicious cases (e.g. some data analysis --such as the > contribution by solvent etc now that data beyond 8Å > is by default used in refinement) - as it appears peer review/editing by > journals isn't/cant always be(?) stringent enough. > > In any case, some type of automated analysis of the whole data base might > be a good idea, as there can be > other cases (with another couple of thousand papers citing them..). > > tommi > > On Dec 10, 2009, at 4:16 PM, Ibrahim Moustafa wrote: > >> "After a thorough examination of the available data, which included a >> re-analysis of each structure alleged to have been fabricated, the >> committee >> found a preponderance of evidence that structures 1BEF, 1CMW, 1DF9/2QID, >> 1G40, 1G44, 1L6L, 2OU1, 1RID, 1Y8E, 2A01, and 2HR0 were more likely than >> not >> falsified and/or fabricated and recommended that they be removed from the >> public record," the university said in its statement this week." >
[ccp4bb] ctruncate error (kind of)
Dear all, I'm converting intensities from scala to amplitudes with ctruncate like so: ctruncate -mtzin scala_protein_3_001_180.mtz -colin "/*/*/[IMEAN,SIGIMEAN]" The data are native. An mtz file is generated, and it looks ok, but ctruncate doesn't terminate properly. Instead, after Anisotropy analysis, the following error is reported: >> CCP4 library signal mtz:No architecture information in file. (Warning) raised in MtzGet << >> CCP4 library signal mtz:File not identified as MTZ (Error) raised in MtzGet << Segmentation fault This happens with ctruncate in ccp4 6.1.0 and with ctruncate downloaded from ftp://ftp.ccp4.ac.uk/nds/bin/ctruncate, both on RHEL 5.4. Should I be concerned? Andreas === Andreas Förster Macromolecular Structure and Function Imperial College London
Re: [ccp4bb] Computer hardware and OS "survey"
As Warren pointed out, dual-boot is so 20th century it's surprising people still bother with it. For me, dual boot (never mind it was on a fantastic Thinkpad) was the major reason to go for OSX. I was simply too sick of it.. It might sound like heresy to true Macolytes but I feel I have now the advantages of Linux (shell, fink, scientific programs) and XP (commercial programs) in one box, and I can't see why anyone would prefer to do science any other way. Andreas On Fri, May 1, 2009 at 9:02 PM, Christopher Bahl wrote: > I'm surprised that dual booting hasn't been brought up yet. A dual boot > machine has two (or more if you like) operating systems installed to > different hard drive partitions, and switching between them is as simple as > restarting. All major distributions of linux nowadays come with the option > to set up dual boot during installation, so it's very easy to get going. > This way you are able to get the graphical benefits of a host platform over > a virtual machine without the necessity of a dedicated computer for each > operating system. > > -Chris > > > > Warren DeLano wrote: > >> My advice: >> Embrace virtualization for all tasks except interactive 3D visualization. >> >> If you're not yet familiar with VMware, Parallels, or open-source >> work-alikes, then it is high time you joined the revolution --- the rest of >> us have been running Mac OS X, Linux, and Windows on the same hardware >> *simultaneously* for years now. >> So long as you can dedicate at least 1-2 GB of RAM per running OS, it >> works great, and you get many other benefits from breaking the link between >> OS and hardware (e.g. easy backup & restore, better security, snapshots, >> test before you upgrade, trivial migration to new hardware, never reinstall, >> never have to buy new software, etc). >> >> Unfortunately, however, for interactive 3D visualization, you must still >> choose the host OS platform which runs your favorite visualization tools >> best, since effective virtualization of OpenGL remains an elusive goal. >> >> Personally, I prefer Mac hardware and typically use Mac OS X as the host >> operating system. But, as I write this, I am also simultaneously running >> Windows for Excel & PowerPoint and GNU/Linux for open-source software >> development. >> >> Of course, there are good reasons for running other host OS platform >> instead, such as to obtain native 3D graphics support under Linux or ActiveX >> Controls under Windows. >> The point is, you don't have to choose just one OS anymore. This survey >> seems to suffer from an outdated assumption. >> Cheers, >> Warren >> >> From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of >> Roger Rowlett >> Sent: Friday, May 01, 2009 8:04 AM >> To: CCP4BB@JISCMAIL.AC.UK >> Subject: Re: [ccp4bb] Computer hardware and OS "survey" >> >> Well, Coot, O, Pymol, CNS, and CCP4i, as well as Open-EPMR all have >> Windows versions. The main issues with a Windows workflow are (1) jobs will >> run significantly slower than in Linux, and (2) the DOS command shell is not >> as powerful as Linux, although it can be extended by installing DOS versions >> of Linux commands and utilities. You will also lose access to a number of >> Linux(Unix)-only XRD tools, but those are getting fewer each year. It's also >> easier, more stable, and more secure to set up a laboratory data server in >> Linux than in Windows. You will also find that you can get excellent >> computing performance out of fairly modest hardware in Linux compared to >> Windows. >> >> I'm not sure there is much "institutional support" required for Linux if >> you know how to install your own OS and software. All I need from my >> networking people is a hole in the firewall for my MAC address and SSH port. >> After that, there is not much for IT to do for me other than stay out of the >> way. Ubuntu has made it a lot easier than it has been to maintain your own >> Linux systems, but I'm still currently wedded to Fedora. The main Linux >> headache is hardware support, especially printers and graphics drivers for >> Nvidia cards, but even that is relatively painless now. >> >> Cheers, >> >> Roger S. Rowlett >> Professor >> Colgate University Presidential Scholar >> 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...@mail.colgate.edu >> >> Link,Todd M wrote: My home institution, in effort to cut costs, is making >> an effort to push those of us on Macs onto PCs. Up till now they have been >> very generous via a lease program for computer hardware, but that is >> changing given the current economics. The institution currently does not >> support Linux so we are limited to Mac and Windows OS. >> We certainly make use of William Scotts crystallography on OS X (thanks >> so much!) so our main argum
Re: [ccp4bb] Fwd: [ccp4bb] crystallisation robot
Depends on your robot, obviously. On Mon, Apr 14, 2008 at 10:32 PM, William Scott <[EMAIL PROTECTED]> wrote: > Does this include the customary grieving period? > > > > On Apr 14, 2008, at 2:10 PM, JOE CRYSTAL wrote: > > Hi, > > > > > > Does anyone have information about how long it takes to set up a 96-well > > tray for the crystallization robots available? Besides cost per tray > > and > > maintenance cost, another important feature we consider is the time for > > setting up a 96-well tray. It is an important factor since we are > > talking > > about sub-microliter drops. > > > > > > Best, > > > > > > Joe > > > > On Fri, Jan 18, 2008 at 12:28 PM, Lisa A Nagy <[EMAIL PROTECTED]> wrote: > > > > Al's Oil on the plates: > > > What a nightmare!!! > > > The oil creeps up the plate and over the sides. It dissolves > > > adhesives. > > > It makes me say bad words in multiple languages. > > > Bigger drops + no oil = fewer bad words. > > > > > > Lisa > > > -- > > > Lisa A. Nagy, Ph.D. > > > University of Alabama-Birmingham > > > [EMAIL PROTECTED] > > > > > > -Original Message- > > > From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of > > > Patrick Shaw Stewart > > > Sent: Friday, January 18, 2008 2:20 AM > > > To: CCP4BB@JISCMAIL.AC.UK > > > Subject: [ccp4bb] Fwd: [ccp4bb] crystallisation robot > > > > > > One thing that people often overlook is that quite a lot of protein > > > can be lost by denaturation on the surface of the drop. This is more > > > significant for smaller drops. Two suggestions: (1) increase the > > > proportion of protein in the - technical term - teeny drop to say two > > > thirds and (2) cover the drops with oil eg Al's oils > > > (silicone/paraffin). You still get vapor diffusion though the oil , > > > and you'd like to slow up equilibration. of course (2) slows up the > > > robotics a little, but both should be trivial to set up.. > > > > > >
Re: [ccp4bb] xtalview and mifit
Hey Ethan, all, On Feb 6, 2008 1:02 AM, Ethan Merritt <[EMAIL PROTECTED]> wrote: > The problem is that both Fedora and Suse 10.3 currently ship with a > broken xorg library. This is a known problem (Google for details), > but I do not know if there is a fixed version available for download. Now, could this broken xorg library be the reason that on my Fedora 7 system (kernel 2.6.23.14-64, xorg 7.1) with ATI FireGL T2 128 graphics card, the latest ATI driver I can get from livna (catalyst 7.12 - version 443) installs just fine and gives ripping performance (40% faster than earlier versions), but some applications don't like it at all? For example, the pymol display window remains forever useless. See a screenshot at http://www.flickr.com/photos/b5foan/2245587039/sizes/l/ Same stunning effect with glxgears or fgl_glxgears, except is also moves. Note that the problem only relates to 3D performance. VLC plays videos just fine. The graphics card itself is recognized just fine (lower right of screenshot). Can anyone suggest a solution? Or do I just patiently wait for updates while my MacBook Pro goes on solving structures for me? Thanks Andreas
Re: [ccp4bb] the worst molecular replacment probes
To avoid excessive excitement potentially caused by such a list, people should also indicate the time spent with a model just good enough to initially justify the eventually futile effort. Andreas On 9/21/07, Bryan W. Lepore <[EMAIL PROTECTED]> wrote: > > would anyone be willing to share stories of the worst molecular > replacement search probes they used to get the correct solution purely > with MR? > > perhaps in terms of %-scattering, RMSD, Z-score, LLG, or other possibly > specific scoring values. > > -bryan >
Re: [ccp4bb] post-doc possibility in newcastle
You'd need quite a large French press or meat grinder to crack the cells and get the protein. William Scott wrote: On Thu, 20 Sep 2007 17:23:05 +0100 "R. J. Lewis" <[EMAIL PROTECTED]> wrote: a large signalling complex called the 'stressosome' from B. subtilis. - If you decide to go for the human form of this signalling complex, I am an over-producing strain. -- >> Andreas Förster << Imperial College London https://wasatch.biochem.utah.edu/~andreas
Re: [ccp4bb] public forums
Before going into an ethics class, I think this material needs to go into a crystallography class. Every crystallographer (and maybe even every structural biologist) should know why the structure is fishy, how fishiness can be detected, how one can make sure one's own structure is legit, etc. Analysis of others' structures and validation of your own, basically going back to how Eleanor started this thread. These past two days have proven infinitely insightful and inspiring to me. Andreas On 8/17/07, Hurley, Thomas D. <[EMAIL PROTECTED]> wrote: > > Just to be clear on my previous email, I encourage all evidence to be > gathered, posted and accumulated for proper evaluation of this case. It > will prove incredibly useful for all involved as this case moves forward. > > > > It is also proving useful for course development – frankly, I am > accumulating files, commentaries, responses and arguments (with appropriate > acknowledgments for their efforts at data analysis in this situation) for > use in our research ethics course – hope no one minds. If anyone does, > please let me know and I'll remove that content, and any reference to that > content in this case study. > > > > My email was just to be wary of what one says in a publicly posted forum. > > > > Tom Hurley > > > > >
Re: [ccp4bb] Stereo grpahics and Virtual Reality
For the benefit of overworked and stressed-out graduate students and post-docs, funding agencies need to be convinced that the remotes cannot be bought without the console. Andreas Stephen Graham wrote: Full VR systems with motion tracking and are now affordable to most labs (~$2500 for all the peripherals). Nintendo Wii remotes are about £25 and they do 3-dimensional motion tracking. Perhaps we should by trying to use them for refinement instead? They communicate via the Bluetooth protocol (http://www.wiili.org/Wiimote) and have already been used for controlling industrial robots (http://www.youtube.com/watch?v=0qEotHQgUsg). Stephen -- Dr Stephen Graham Nuffield Medical Fellow Division of Structural Biology Wellcome Trust Centre for Human Genetics Roosevelt Drive Oxford OX3 7BN United Kingdom Phone: +44 1865 287 549 -- >>> Andreas Förster <<< 8 rue Doudart de Lagrée, F-38000 Grenoble +33.438.866201docandreas.blogspot.com https://wasatch.biochem.utah.edu/~andreas
Re: [ccp4bb] libstdc++.so.5: cannot open shared object file: No such file or directory
This is an old version of the c++ libraries. You get it by installing compat-libstdc++-33 Andreas Paul Kraft wrote: Hiys, I've got an hp pavillion dv2000 with a 64x2 processor and I loaded the redhat version of CCP4-6.0.2. I tried loading it manually but there was no configure or make files, so I went for the ./install.sh and ran the run-all on the /examples/ and got the error "libstdc++.so.5: cannot open shared object file: No such file or directory" for pretty much all of the progrrams. I know this is a library problem I've seen before but can't remember how to fix it. Your help would be appreciated. Thanks, Paul Dr. Paul Kraft -- >>> Andreas Förster <<< 8 rue Doudart de Lagrée, F-38000 Grenoble +33.438.866201docandreas.blogspot.com https://wasatch.biochem.utah.edu/~andreas
Re: [ccp4bb] Fwd: [ccp4bb] Swiss humour - no laughing matter? (Re: [ccp4bb] process SeMet labelled data)
Hello Klaus, I think you should give Gerard some "Hofnarrenfreiheit". (That's a fine German word for you to figure out, Gerard.) He is certainly not an evil racist at heart. Andreas Klaus Piontek wrote: Greetings (or in "correct" Swiss German "Grüezi wohl", with Umlaut=vowel mutation) to all CCP4BB subscribers, being a CCP4BB reader (and sometimes writer) since something like 15 years, I realized today that the comment of Gerard was the first one I read since then containing a side-swipe regarding the nationality or the national character of authors. I think, within a multinational scientific community with a very long lasting tradition of internationalism such comments should be beyond this forum. On the other hand Gerard's comment contains a somewhat humorous (Swiss, Swedish, German, Dutch, ... kind of?) aspect, since it refers partly to Switzerland, a country where* many* foreigners live and work, including Germans like Dirk. I would guess a situation similar like in Sweden or The Netherlands, isn't it? Sorry being German too I could not resist making such a moralizing comment. snip -- >>> Andreas Förster <<< 8 rue Doudart de Lagrée, F-38000 Grenoble +33.438.866201docandreas.blogspot.com https://wasatch.biochem.utah.edu/~andreas
[ccp4bb] [summary] grids and detergent
Dear all, two days ago I asked the ccp4 and 3DEM lists how one could prevent carbon films from being destroyed by detergent. At least that's what I meant to ask. Thanks for the many responses I got in no time (summarized below). Thanks to all who responded and apologies to those I don't mention. All suggestions have been relayed to our EM wizard. Most asked what I meant by 'eats the carbon grid' and guessed correctly that the carbon film explodes into little pieces when sample is applied between mica and film. The film suffers the same sad fate when it is adhered to the copper grid first. - Deposit thicker carbon films (Mark Rosenberg, Ricardo Bernal). Didn't help us. - Use glue (e.g., strip from clear tape with chloroform) to hold the carbon film to the copper mesh (Richard Easingwood, Guy Schoehn). Be careful not to fill the holes in the grid. - Use 1000 mesh grids or holeyfilms so small areas stay intact (Rachel Scherer). - Work with a different detergent. DDM and digitonin are good (Bettina Boettcher, John Rubinstein). - Put a plastic film between the copper grid and the carbon film (Bettina Boettcher, Ed Gogol). - Instead of applying the sample between mica and carbon film and then adhering the carbon film to the grid, adhere the carbon to the grid first, dry well and apply sample (Daphna Frenkiel-Krispin). Didn't help us. - Be very diligent when you prepare the carbon films (Reinhard Rachel, Guy Schoehn). - Make carbon film hydrophilic by glow-discharging grids (Ching-Ju Tsai). - Dilute protein solution (and thus detergent) right before applying to grid. Might work if protein doesn't aggregate immediately (Matt L.Walker). - Good luck (all who responded). Thanks. A special Methods issue on EM is forthcoming that will contain a review on EM of membrane proteins by John Rubinstein. Andreas
Re: [ccp4bb] dmmulti NCS mask
Hey all, this is wildly off-topic, but since we were even talking about NMR the other day, I was thinking why not EM? I'm trying to get negative stain images of a membrane protein. Problem is that the detergent (similar to triton) that best stabilizes the protein eats the carbon grid, even at concentrations of 0.1x CMC. Has anyone encountered a similar problem and found a solution around it? Are there different types of carbon grids? Thanks. Andreas
Re: [ccp4bb] off-topic Apple computer question
Steve, Steve Lane wrote: Given the current situation at Apple, particularly their shift in focus and revenue percentage from "computers" to other types of devices, i.e. iPods, either/both of the above reasons for refusal to do the work are plausible. are you saying one shouldn't buy one's scientific computing equipment from a lifestyle company? Sorry, couldn't resist. Andreas -- >>> Andreas Förster <<< 8 rue Doudart de Lagrée, F-38000 Grenoble +33.438.866201docandreas.blogspot.com https://wasatch.biochem.utah.edu/~andreas
Re: [ccp4bb] problem with anisotropic refinement using refmac
Hey all, let me give this discussion a little kick and see if it spins into outer space. How many reflections do people use for cross-validation? Five per cent is a value that I read often in papers. Georg Zocher started with 5% but lowered that to 1.5% in the course of refinement. We've had problems with reviewers once complaining that the 0.3% of reflections we used were not enough. However, Axel Brünger's initial publication deems 1000 reflections sufficient, and that's exactly what 0.3% of reflections corresponded to in our data set. I would think the fewer observations are discarded, the better. Can one lower this number further by picking reflections smartly, eg. avoiding symmetry-related reflections as was discussed on the ccp4bb a little while back? Should one agonize at all, given that one should do a last run of refinement without any reflections excluded? Andreas On 1/31/07, Georg Zocher <[EMAIL PROTECTED]> wrote: First of all, I would like to thank you for your comments. After consideration of all your comments, I conclude that there are three possibilities. 1.) search for some particularly poorly-behaved regions using parvati-server a.) refining the occupancy of that atoms and/or b.) tightening the restraints Problems which have already been metioned: If I tighten the restraints, the anisotropic model may not be statistically justified, which seems to be the case. Using all reflections may not help that much, because I chose a set of 1.5% for Rfree (~1300 reflections) to get as much data as possible for the refinement. For my first tries of anisotropic refinement I used 5% of the reflections for Rfree but the same problem arose, so that I decided to cut the Rfree to 1.5%. 2.) Using shelxl 3.) TLS with multi-groups Should be the safe way!? I will try all the possiblities, but especially the tls refinement seems to be a good option to be worthy to try. Thanks for your helpful advices, georg
