Re: [ccp4bb] the structures of Nucleic acid
The phosphorus absorption edge is about 5.8Å. I've had much better luck with 5-Br-U for anomalous phasing. Molecular replacement with sub-structural fragments can also work: <https://scottlab.ucsc.edu/scottlab/reprints/2010_Scott_Methods.pdf> Yours sincerely, William G. Scott Professor, Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA University of California at Santa Cruz Santa Cruz, California 95064 USA > On Sep 18, 2023, at 2:43 AM, Eleanor Dodson > <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote: > > I am afraid most scientists will use the most straightforward technique! > If SAD is available the PHOSPHATE backbone of DNA will provide sufficient > signal to allow SAD to work, and you get an unambiguous answer to whether it > is A-DNA or B or Z... > MR will usually work of course as well > Eleanor > > > On Mon, 18 Sept 2023 at 09:18, Natesh Ramanathan > wrote: > Dear Fu Xingke, > > Depends on what Nucleic Acid you are talking of. If it is RNA, you > can expect some sequence to tertiary structure correspondence so you might be > able to try more MR as compared to DNA. DNA may have double helical > architecture but less sequence to tertiary structure correspondence, and > hence DNA is less likely to have a 3D structure like RNA specific structure > for a sequence. > > SAD has become a straight forward method to avoid all these problems > to get ab-initio structure. So many go for it directly. > > Hope that helps. > Best wishes, > Natesh > > On Mon, 18 Sept 2023 at 13:36, fuxingke wrote: > Dear Colleagues, > > Reacently, I find the structures of Nucleic acid are solved by > single-wavelength anomalous diffraction(SAD). So, why molecular replacement > (MR) not? > > Regards > > > > Best wishes, > > Fu Xingke > > Institute of Physics CAS > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > > > > -- > -- > "Live Simply and do Serious Things .. " > - Dorothy Mary Crowfoot Hodgkin OM, FRS > > "In Science truth always wins" > - Max Ferdinand Perutz OM FRS > -- > Dr. Ramanathan Natesh > Associate Professor, > School of Biology and Center for High-Performance Computing (CHPC), > Founding and Current President of Cryo Electron Microscopy and 3 Dimensional > Image Processing Society of India (CEM3DIPSI), > Indian Institute of Science Education and Research Thiruvananthapuram > (IISER-TVM), > Maruthamala P.O., Vithura, > Thiruvananthapuram, 695551, Kerala, India > > nat...@iisertvm.ac.in > http://faculty.iisertvm.ac.in/natesh > > Researcher ID: http://www.researcherid.com/rid/C-4488-2008 > ORCID: http://orcid.org/-0002-1145-5962 > Vidwan-ID : 94134: http://iisertvm.irins.org/profile/94134 > PUBLONS: https://publons.com/author/1520837/ramanathan-natesh#profile > > Office Ph. 0091- 471-2778087 > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] Coot installation issue
homebrew heavy-handedly wiped out coocanvas v. 2 when upgrading. I made a temp fix with a sym link as follows: ln -s /usr/local/Cellar/goocanvas/3.0.0/lib/libgoocanvas-3.0.9.dylib /usr/local/lib/libgoocanvas-2.0.9.dylib your path prefix will be different, but you get the idea. > On Sep 30, 2022, at 7:38 AM, tim smith wrote: > > Hi All, > > I am having an issue with installing coot. Here is the outcome when I type > coot in command line. I am using M1 mac pro. Thank you. > > Best regards > Tim > > > CSI363227 ~ % coot > dyld[11265]: Library not loaded: > '/opt/homebrew/opt/goocanvas/lib/libgoocanvas-2.0.9.dylib' > Referenced from: '/opt/homebrew/Cellar/coot/HEAD-4c7971f/libexec/coot-bin' > Reason: tried: '/opt/homebrew/opt/goocanvas/lib/libgoocanvas-2.0.9.dylib' > (no such file), > '/opt/homebrew/Cellar/coot/HEAD-4c7971f/lib/libgoocanvas-2.0.9.dylib' (no > such file), > '/opt/homebrew/Cellar/goocanvas/3.0.0/lib/libgoocanvas-2.0.9.dylib' (no such > file), '/opt/homebrew/Cellar/coot/HEAD-4c7971f/lib/libgoocanvas-2.0.9.dylib' > (no such file) > /opt/homebrew/bin/coot: line 211: 11265 Abort trap: 6 $coot_bin "$@" > Coot crashed. > > > > CSI363227 ~ % coot --version > dyld[11238]: Library not loaded: > '/opt/homebrew/opt/goocanvas/lib/libgoocanvas-2.0.9.dylib' > Referenced from: '/opt/homebrew/Cellar/coot/HEAD-4c7971f/libexec/coot-bin' > Reason: tried: '/opt/homebrew/opt/goocanvas/lib/libgoocanvas-2.0.9.dylib' > (no such file), > '/opt/homebrew/Cellar/coot/HEAD-4c7971f/lib/libgoocanvas-2.0.9.dylib' (no > such file), > '/opt/homebrew/Cellar/goocanvas/3.0.0/lib/libgoocanvas-2.0.9.dylib' (no such > file), '/opt/homebrew/Cellar/coot/HEAD-4c7971f/lib/libgoocanvas-2.0.9.dylib' > (no such file) > /opt/homebrew/bin/coot: line 211: 11238 Abort trap: 6 $coot_bin "$@" > Coot crashed. > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] Phasing a difficult RNA heteroduplex structure
Dear Charlie, Eleanor et al:
"Hate" might be a wee bit extreme, but I fully appreciate that RNA certainly
can be rather frustrating.
(I used to say the only things that catalytic RNA degraded faster than itself
were my self-esteem and career prospects.)
I managed to crystallize the same RNA molecule in the same space group
(P3_{2}21) with the same cell dimensions in two
incommensurate crystal forms. One had two molecules in the asymmetric unit, the
other only one. The difference Patterson
maps were impossible to interpret until I finally figured out what was going
on. I wasted a lot of time falsely assuming I had
a hexagonal space group. (The best part is Max Perutz overheard me complaining
about isomorphous replacement, and gave
me that slight smile that said "go now and ponder".)
Based on this, and a number of equally traumatic experiences, I suggest trying
to solve it in the lowest symmetry space group
compatible with the indexing, whlle making no assumptions about the symmetry
(or lack thereof) within the molecule. Short
duplexes (and heteroduplexes) can behave rather differently from what we expect
when crystallized. You might get two
hairpins, or you might get one (or two) homo-duplexes with base mismatches.
Even if it forms the secondary structure you expect,
there are often (retrospectively-obvious) surprises.
One thing we stumbled upon during such trials and tribulations was that many
novel RNA crystal structures can in fact be solved
without resorting to isomorphous replacement, by simply using a small subset of
modeled duplexes for molecular replacement.
cf: https://doi.org/10.1016/j.ymeth.2010.06.011 It might be worth a try.
RNA perhaps inspires hatred because it habitually and bitterly mocks us in
silence.
William G. Scott
Professor, Department of Chemistry and Biochemistry
and The Center for the Molecular Biology of RNA
University of California at Santa Cruz
Santa Cruz, California 95064
USA
http://scottlab.ucsc.edu/SARS-CoV-2/
> On May 6, 2022, at 6:34 AM, Eleanor Dodson
> <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:
>
> How I hate RNA!
> However, structures have been solved..
>
> As others say:
> Look for twinning
> Look for translation non-cryst symmetry.
> It seems likely when you have a doubling of the a axis for the Zn derivative.
>
> I use CCP4I2 and the data processing report will do both these tests.
> Then you need to decide whether the SG is P6i or P6i22
>
> IF there is twinning then the apparent P6i22 symmetry could be due to this..
>
> Where are your sites? If they are related by crystal symmetry then it is hard
> to distinguish the hand.
> And low solvent content hampers DM
> Good luck Eleanor
>
>
>
>
> On Fri, 6 May 2022 at 12:51, Petr Kolenko wrote:
> Dear Charlie Nichols,
> when optimizing your SHELX runs, SHELIXIR may help you in some cases
> (https://kmlinux.fjfi.cvut.cz/~kolenpe1/shelixir).
> A couple of days ago, I created quick and dirty tutorial to SHELIXIR command
> line: https://www.youtube.com/watch?v=dqi5_yLhWOc and also the same quality
> tutorial to the GUI: https://youtu.be/CZIziPv28hA
> There may be some parameters to further optimize in which SHELIXIR may help
> you (trying more space groups, optimizing of high or low resolution cut-off,
> solvent content). However, SHELX C/D/E is generally known to have problems at
> lower resolution (say 3.5 AA and lower). To say a bit more about your
> problem, would you share the files off the list?
> Btw, the great thing about SHELX is that you do not even need to know the
> content of the AU in some cases!
> Best regards,
> Petr
>
> From: CCP4 bulletin board on behalf of Nichols,
> Charlie
> Sent: Friday, May 6, 2022 1:17:20 PM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] Phasing a difficult RNA heteroduplex structure
>
> Dear all,
>
> I am trying to solve the structure of an RNA heteroduplex + ligand with
> approximate MW of 6800.
>
> * Structure likely to have a core helical region and a couple of bases of
> single stranded material at both ends on both strands
>
> I have datasets from visually similar crystals with different, but related
> unit cells:
>
> Form1:
> 32.70 32.70 54.55 90.00 90.00 120.00 – best native ~2.9A
> - different pipelines reported P62 2 2, P62 and P32 from auto-indexing
> - P6222 impossible to fit 1 complete heteroduplex
> - P62, most consistent indexing choice, 37% solvent, low Matthews probability
> but possible to fit 1 heteroduplex
>
> However, Xia/Dials report tNCS
>
>
> * If the ASU only has room for 1 copy the heteroduplex there can’t be
> tNCS, does this therefore mean we must have twinning?
> * There is a rea
Re: [ccp4bb] Coot 0.9.5
I’ve compiled it, but am having trouble with the GUI. This is not a big sur problem per se, but rather is the newer GTK+3 X-windows-independent interface. When we get it working, it will be a much nicer mac interface. Apple threw OpenGL under the bus in the last couple of OS updates. > On Mar 18, 2021, at 2:10 AM, F.Xavier Gomis-Rüth wrote: > > Dear all, > any hint from where to get precomplied Coot 0.9.5 for Big Sur? > Best regards, > Xavier > -- > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] Issues in new Mac version 10.15
Which ones? All of the binaries in $CBIN I have say "Mach-O 64-bit executable x86_64” So that is unlikely the issue. I haven’t installed Catalina yet, as I only have one computer that is new enough. But one of the changes is they have locked down much of the file system, and are urging installation into /opt (which is where X11 now gets installed, for example). I have CCP4 installed in /opt/xtal/ccp4-7.0 You can do this with the tarball and manual install. I’m going to help a student here with this today. I’ll report back if it works. Also, reinstallation of X11 is probably a good idea. Sorry BTW to everyone for not keeping the Crystallography on OS X website more up to date. I will try to do so shortly. (The morale-sappers here finally got to me.) Peace and joy, Bill > On Oct 16, 2019, at 12:44 AM, Ruud Hovius wrote: > > Hello, > > this is the warning that our IT people gave us : > > > "Do not install the MAcOS upgrade to the new system CATALINA > > This system version will apparently NOT allow 32-bit applications to run, > which are still many , > see https://support.apple.com/en-us/HT208436 > > > Try to go back to the former MacOS > > A+ > > Ruud > > On 16/10/19 01:50, Werther, Rachel A wrote: >> Hello All, >> >> I downloaded the latest Mac Update, 10.15 Catalina, and then Coot wouldn’t >> open on my computer. >> >> Phenix opened as usual. I use the GUI, and the button that says “Open in >> COOT” was not greyed out, but would not launch the window. When I tried to >> open it directly from Finder, it also failed to open. The cartoon coot >> appeared on my recently opened section of my bottom-of-screen toolbar, but >> nothing happened. >> >> Next I downloaded the latest CCP4-7.0.077, and followed the instructions to >> remove the extended attributes: >> ATTENTION: If you are planning to install CCP4 from a tarball on Mac OS X >> version 10.13 or later (10.12 was not tested), you will have to remove >> extended attributes from the tar-gz-file before unpacking it, otherwise the >> app icons will not be functional (and you will be able to launch the CCP4 >> apps including ccp4i and ccp4i2 from the command line only). The extended >> attributes can be removed from the file _file_ using the command "xattr -c >> _file_". For example: xattr -c ccp4-7.0.065-macosx64.tar.gz >> >> But when I try to open CCP4, I get this message: >> Ccp4 cannot be opened because of a problem. >> Check with the developer to make sure ccp4 works with this version of macOS. >> You may need to reinstall the application. Be sure to install any available >> updates for the application and macOS. >> Click Report to see more detailed information and send a report to Apple. >> >> And when I try to open Coot from the Finder, I again just see the icon in my >> recently opened section of my bottom-of-screen toolbar, but it doesn’t open. >> >> Any advice? >> >> Many thanks, >> Rachel >> >> Rachel Werther / Research Technician III / Stoddard Lab / Basic Sciences / >> Fred Hutchinson Cancer Research Center / rwert...@fredhutch.org / >> 206-667-4066 >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 >> > > -- > > Ruud Hovius > EPFL SB ISIC LCBM > Office CH B3 424 > CH-1015 Lausanne > mobile : +41 79 435 34 73 > office : +41-21-693-3134 > > http://people.epfl.ch/ruud.hovius > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] [OT] Structure-related pun needed urgently
After reflecting on this a bit, I rejected anything dealing with glide planes, and although I initially thought I had something good involving a screw axis of evil, I decided it, too, would probably be lost in translation, not to mention a bit dated. Perhaps something more current, involving electrons, would help to resolve this? I'll give it some thought this morning as I bicyle up the worst hill in the region. Unfortunately, it is still very early here, and I don't yet have the inspiration I possessed for my crowning achievement during my postdoc, which was to place a small, inconspicuous label on the outside door of the toilet facility that read "MRC Lavoratory of Molecular Biology.” (I am flush with embarrassment every time I think of that.) Can this also involve nucleic acids? I’m afraid protein structure puns might be a bit outside my domain. — Bill > On Aug 15, 2019, at 4:42 AM, Gerard DVD Kleywegt > wrote: > > Dear CCP4BB-ers, > > Once again I turn to you in my hour of need. I *urgently* need a > side-splittingly funny, and ideally punny, structure-related > sentence/statement/claim/expression to put in a speech bubble attached to a > life-size bobblehead version of yours truly (don't ask)! > > I know there are some very funny people on CCP4BB. The best I've been able to > come up with myself so far is: "Protein structures are beautiful, but I try > to keep it platomic" - which is pretty lame, I know. > > Many thanks in advance! > > --Gerard > > ** > Gerard J. Kleywegt > > http://xray.bmc.uu.se/gerard mailto:ger...@xray.bmc.uu.se > ** > The opinions in this message are fictional. Any similarity > to actual opinions, living or dead, is purely coincidental. > ** > Little known gastromathematical curiosity: let "z" be the > radius and "a" the thickness of a pizza. Then the volume >of that pizza is equal to pi*z*z*a ! > ** > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] Sir Prof. Aaron Klug 1926 - 2018
Dear Miri: Thanks very much for your very thoughtful CCP4 post. Since I was one of his last (and perhaps least) postdocs, I felt a bit self-conscious and inadequate initiating discussion. I am very grateful to you for doing so. I would like to point out, for those who are interested, that Ken Holmes (a close colleague of Aaron’s) recently published an excellent and definitive biography entitled "Aaron Klug: A Long Way from Durban." It is extremely well-written, accurate and comprehensive. I got ahold of it here: https://www.amazon.com/Aaron-Klug-Long-Durban-Biography/dp/1107147379/ref=mt_hardcover Aaron's many contributions to our field included pioneering work on virus structures, which began in collaboration with Rosalind Franklin, structures of tRNA, the nucleosome, a ribozyme, discovery of zinc finger transcription factors and of course 3D image reconstruction. He initially learned crystallography from R. W. James in Cape Town. He also made contributions to many aspects of crystallography, including direct methods and heavy-atom phasing. From my personal perspective, he was truly an exceptional mentor. Despite obligations that included directorship of the MRC-LMB and then Pres. of the Royal Society, he always had time and a keen interest in what each of us in his small group was doing. When I first arrived (in 1993), I was supposed to work on a structure of a zinc finger/RNA complex, but he quickly deduced that my heart was still invested in getting a ribozyme structure, which I had struggled with for several years previously. He immediately appreciated its significance and encouraged me to make a fresh start of it, which eventually succeeded. At about the time I got the ribozyme phasing to work, my mother, back in Chicago, was treated for lung cancer. Aaron was very supportive and encouraged my frequent trips home to visit. When she recovered, he hosted her (along with me) for lunch in London at the Royal Society, which she (and I) greatly enjoyed and appreciated. (Perhaps because of this in some small part, she beat the odds and survived.) It remained one of her fondest memories. I last saw Aaron about 10 years ago when I gave a presentation at the LMB, and he was still very much engaged and helpfully critical of our work. His extraordinary intellect, informed by his remarkable dignity and humanity, is as much a legacy as his many exceptional contributions to science. Yours sincerely, William G. Scott Professor, Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA University of California at Santa Cruz Santa Cruz, California 95064 USA http://scottlab.ucsc.edu > On Dec 5, 2018, at 5:07 AM, Miri Hirshberg > <02897e8e9f0f-dmarc-requ...@jiscmail.ac.uk> wrote: > > Weds., Dec. 5th 2018 > London > > > Prof. Klug died November 20th, 2018, and was buried on November 26th > in Cambridge, UK. > https://www2.mrc-lmb.cam.ac.uk/aaron-klug-1926-2018/ > > He was among the founders of Structural Biology as we know it today. > > The title of his 1982 Nobel Prize lecture > > 'From Macromolecules To Biological Assemblies' > > sums part of his vast body of scientific work, from X-ray > crystallography to EM, nucleic acid structures to the Human Genome > Project. He also was a supporter of the PDB and the work carried out in > PDBe. > > I was privileged to have met him personally, over cups of tea, > both at Stanford California and in the LMB. His brilliant > scientific mind went hand in hand with his pleasant,civilised, > sometimes funny and immensely interesting persona. > > It is never too late to pay respects. > May he rest in peace > > Miri Hirshberg > > > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] Asn/Gln - pi-stacking prevalence
Hi Michael: It always makes me happy to see that there are people who care about this. 3.3 to 3.4 Å should be an ideal distance for this, and, as you note, the lone pair residing on the (sp^3-hybridized) nitrogen would have to be oriented for favorable overlap, which is a bit harder to deduce from your figure. The other rotomer would place oxygen at that position. Because it is double-bonded to the gamma carbon, the lone pairs are oriented differently, and the pi-bond would be approximately parallel to the plane containing the tryptophan, which would give a nice pi-stacking interaction similar to what is seen with adjacent base pairs in nucleic acids. Expectation bias, as well as having partial charges turned on during refinement, might influence the rotomeric state of examples from the PDB, so be careful of social consensus. With classical electostatics, N has a partial positive charge, and O has a partial negative charge. (If you think about it, all pi-stacking interactions, from the point of view of classical electrostatics, would be somewhat repulsive.) Good luck with this, and let us know of the outcome. Bill William G. Scott Director, Program in Biochemistry and Molecular Biology Professor, Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA University of California at Santa Cruz Santa Cruz, California 95064 USA http://scottlab.ucsc.edu > On Nov 10, 2018, at 1:45 AM, Michael Jarva wrote: > > Dear ccp4 community, > > I have recently been working with a structure that has an Asparagine that > makes a planar stacking connection with a Tryptophan ring > (pep_ASN-TRP_v2.png), that seem to be a true pi-stacking interaction and I'd > like to find more examples of this. > > I've found a few other examples in the literature but they are mostly amide > hydrogen-pi interactions (4PTI_ASN-TYR_v2.png and 1N4W_ASN-FAD_v2.png), which > can be seen by the way the Asn is dipping down into the pi-cloud. One > potential exception is of a DNA-binding protein where the orientation is more > planar (3HXQ_GLN-DNA_v2.png). > > So, I'm looking for examples of Asparagine or Glutamine pi-stacking and am > sure there are more of them out there and would greatly appreciate any > examples. > > best regards > Michael > > Michael Jarva, PhD > ACRF Chemical Biology Division > The Walter and Eliza Hall Institute of Medical Research > 1G Royal Parade > Parkville Victoria 3052 > Australia > Phone: +61 3 9345 2493 > Email: jarv...@wehi.edu.au | Web: http://www.wehi.edu.au/ > The ACRF Chemical Biology Division is supported by the > Australian Cancer Research Foundation > > ___ > > The information in this email is confidential and intended solely for the > addressee. > You must not disclose, forward, print or use it without the permission of the > sender. > > The Walter and Eliza Hall Institute acknowledges the Wurundjeri people of the > Kulin > Nation as the traditional owners of the land where our campuses are located > and > the continuing connection to country and community. > ___ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > <4PTI_ASN-TYR_v2.png><3HXQ_GLN-DNA_v2.png><1N4W_ASN-FAD_v2.png> To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] coot install problems under Mac OS X 11 (El Capitan)
Hi Barry: It is an X11.app bug that has persisted for years now. (It isn’t specific to coot). Briefly, this happens unless you uncheck the checkbox for “Displays have Separate Spaces” in System Preferences>Mission Control William G. Scott Director, Program in Biochemistry and Molecular Biology Professor, Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA University of California at Santa Cruz Santa Cruz, California 95064 USA http://scottlab.ucsc.edu > On Sep 23, 2017, at 12:11 PM, Barry Finzel <finze...@umn.edu> wrote: > > I've been trying to get coot running on my MacBook Pro after upgrading to OS > X El Capitan (10.11.6). I have installed as part of ccp4, Phenix (1.9-1692) > or standalone (0.8.8) (As provided by the Scott lab at UCSC). I'm also > running X11 (2.7.11). It seems to be fine, unless I have my big Mac Cinema HD > Display connected (via USB). When the big monitor is plugged in, all coot > windows just disappear. They reappear on the notebook screen if I disconnect > the remote monitor. > > Never had this problem with the same hardware and older versions of the Mac > OS, an have not had problems with windows from other software, either - just > coot. > > Is this a problem others have observed and/or dealt with? > > --Barry Finzel
Re: [ccp4bb] Coot no GUI
coot --no-graphics William G. Scott http://scottlab.ucsc.edu > On Jul 28, 2017, at 1:34 PM, Reza Khayat <rkha...@ccny.cuny.edu> wrote: > > Hi, > > Is it possible to run Coot without the use of GUI? We have some Coot scripts > for a pipeline and we’d like to do without the GUI. Thanks. > > Best wishes, > Reza > > Reza Khayat, PhD > Assistant Professor > Department of Chemistry > City College of New York > 85 Saint Nicholas Terrace, CDI 2.318 > New York, NY 10031 > http://www.khayatlab.org/ > 212-650-6070
[ccp4bb] Abraham Szöke
Dear Colleagues: Is is with great sadness that I report the recent passing of Abraham Szöke, a friend, colleague, informal mentor, and an exceptionally intelligent and energetic source of boundless intellectual enthusiasm. Abraham was a physicist at Livermore who helped to design nuclear weapons for a living, but he had many other interests. One of these was X-ray crystallography, and with his wife and collaborator Hanna Szöke, as well as John Somoza, he developed an approach to crystallographic real-space electron-density refinement and optimization, implemented in a program called EDEN, that produces electron density maps with minimal model bias in a robust manner. The source code, along with a brief explanation and extensive user's manual, is freely available: https://code.google.com/archive/p/edencrystallography/ https://github.com/wgscott/edencrystallography EDEN is written in C and is easy to compile on any unix platform. A fink package for OS X is also available, as are packages for various linux distributions. John and I first met Abraham and Hanna Szöke when we were graduate students at Berkeley. A few years later, I had the opportunity to collaborate with them and to put EDEN to the test. A single-particle version of EDEN was also under development, for use with electron microscopy. Abraham had a wide variety of interests in addition to electron density reconstruction, including many novel ideas about the origin of life. He enjoyed a multitude of fruitful and productive collaborations throughout a period most normal people would consider retirement. He passed away on Thursday at age 87 from an opportunistic infection while combatting lymphoma. William G. Scott Professor, Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA University of California at Santa Cruz Santa Cruz, California 95064 USA http://scottlab.ucsc.edu
Re: [ccp4bb] FW: [ccp4bb] Fwd: [ccp4bb] just out of totally idle curiosity ...
Dear Edward et al: I agree we shouldn’t engage in partisan arguments on the CCP4bb. However, I think it is a mistake, and perhaps a missed opportunity, to ignore politics completely. For example, Newt Gingrich is currently in the running for Sec HHS. He has previously written editorials in the NYT and Wall Street Journal advocating doubling the budget of the NIH. I think it is incumbent upon us to make our voices heard if such an opportunity arises, regardless of what one may happen to think about the individual’s political orientation, as it could potentially be of enormous benefit to the scientific community. Yours faithfully, William G. Scott Director, Program in Biochemistry and Molecular Biology Professor, Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA University of California at Santa Cruz Santa Cruz, California 95064 USA http://scottlab.ucsc.edu > On Nov 9, 2016, at 9:02 AM, Edward Snell <esn...@hwi.buffalo.edu> wrote: > > As a Brexit and Trumpet affected person having a foot in both countries ,this > topic is too far off the normal discussion on CCP4 and probably better taken > up privately. CCP4 is not a political discussion site. With CCP4 the signal > is unusually high and the noise low when compared to any discussion board. I > for one would like to keep it there. Political views aside, we’re all trying > to achieve the same scientific goals. Let’s remember that and keep that the > focus. > > Edward Snell Ph.D. > President and CEO Hauptman-Woodward Medical Research Institute > Assistant Prof. Department of Structural Biology, University at Buffalo > 700 Ellicott Street, Buffalo, NY 14203-1102 > Phone: (716) 898 8631 Fax: (716) 898 8660 > Skype: eddie.snell Email: esn...@hwi.buffalo.edu > > Heisenberg was probably here!
[ccp4bb] just out of totally idle curiosity ...
What’s the job situation in Europe looking like for refugee scientists these days? William G. Scott Director, Program in Biochemistry and Molecular Biology Professor, Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA University of California at Santa Cruz Santa Cruz, California 95064 USA http://scottlab.ucsc.edu
[ccp4bb] Latest XQuartz upgrade breaks Coot
More regarding" XQuartz upgrade breaks Coot” from people who know more than I do (which admittedly is most everyone, but I digress …): > > Today's Topics: > > 1. Xquartz 2.7.10-rc2 breakage (Jack Howarth) > 2. fink-0.41.0-101 du_sk.t build failure (Patrick Carmack) > > > -- > > >Xquartz is currently testing the upcoming 2.7.10 release which has the > following significant change > > libXt > > Both libXt.6.dylib and libXt.7.dylib are two-level-namespaced now > A flat_namespace version of libXt is available in > /opt/X11/lib/flat_namespace to help ease the transition (#96292) > > Set DYLD_LIBRARY_PATH=/opt/X11/lib/flat_namespace when executing older > non-compliant software (eg: Motif-based applications) > Motif users are encouraged to file bugs against Motif to encourage them to > fix that library > > Upstream is attempting to deprecate out the libXt.7.dylib with a > symlink to libXt.6.dylib (as both are now linked as two-level namespace). > Unfortunately, they didn't think this one through as it breaks all binaries > linked against libXt under Xquartz 2.7.9 (as those expect the library to > have the 8.0.0 soversion from libXt.7.dylib instead of the 7.0.0 one from > libXt.6.dylib). Currently you have to rebuild any packages built under > Xquartz 2.7.9 which linked libXt after upgrading to Xquartz 2.7.10-rc2. > > I've alerted upstream of this issue > > https://lists.macosforge.org/pipermail/xquartz-dev/2016-September/004008.html > > and expect they will solve this by releasing an -rc3 with the symlink for > libXt.7.dylib replaced by the actual shared library as in 2.7.9. Note that > in 2.7.10, libXt.dyib points at libXt.6.dylib since its flat-namespace > linkage has been replaced with two-level namespace linkage for both. >Jack > ps Note that the flat-namespace libXt.6.dylib provided by Xquartz in 2.7.10 > in /opt/X11/lib/flat_namespace can't be used for builds as the path in its > install name is intentionally set to /opt/X11/lib. > > I've placed proposed libxt-flat-namespace-shlibs packaging on fink tracker > to provide the missing flat-namespace libXt.6.dylib for use in builds of > and against openmotif4. I've also placed updated packaging for those > packages that use openmotif4 on fink tracking which uses this new > libxt-flat-namespace-shlibs package.
Re: [ccp4bb] SUMMARY: Equation Editor woes with Office 2011 for Mac
On May 20, 2015, at 5:38 AM, Randy Read rj...@cam.ac.uk wrote: Thanks, as always, to everyone for a thoughtful discussion! Alternatively, as a scientific community, perhaps it is finally time for us to untwist Clippy, bending him backwards and forwards until he snaps at those horrid beady little eyeballs, ditch the Comic Sans, flip Redmond the bird, HTFU and learn to use LaTeX equation markup, and ask that our journals do the same. It really isn’t any harder than learning basic HTML (and predates it as one of the original mark-up languages). Journals and funding agencies should not be demanding that we use crappy broken and restrictive proprietary formats for submitting papers and proposals. Ascii text documents provide the ultimate form of universal interchangeability. The syntax is actually quite straightforward and easy to learn (or look up), eg: http://en.wikibooks.org/wiki/LaTeX/Mathematics LaTeX allows you to focus on content rather than document formatting. Although it is definitely more badass to do this in vim, other ascii text editors often have very useful LaTeX functionality. (My favorite on OS X is TextMate, version 2 of which is now free. If you code on OS X, you should take a look at this.) Once you make the small investment of time learning LaTeX, it makes other tasks easier. For example, you can use jsMath to embed LaTeX-encoded equations (including chemistry symbols) in web pages, eg: http://www.math.union.edu/~dpvc/jsmath/examples/welcome.html
Re: [ccp4bb] Equation Editor woes with Office 2011 for Mac
On May 18, 2015, at 4:31 AM, Nicolas Soler nso...@mrc-lmb.cam.ac.uk wrote: You just have to learn the (easy) equation syntax or just use this: http://www.macupdate.com/app/mac/18172/tex-fog William G. Scott http://scottlab.ucsc.edu/~wgscott
Re: [ccp4bb] CCP4 and Coot Interface can not maximized to full screen on Macbookpro Yosemite
Glad it works! It sounds like they finally fixed an X11 bug that has been quite problematic these last few years. Bill William G. Scott http://scottlab.ucsc.edu/~wgscott On May 14, 2015, at 9:06 PM, Xiao Lei xiaolei...@gmail.com wrote: Dear William, I installed the X11 2.7.8_rc1 as you suggested, it turned out to be a great choice. With the newest X11, I can even check display in separated windows option without having any problem run on my mac. It did need me a restart to be effective. Thanks a lot for your input. Xiao On Mon, May 11, 2015 at 12:27 PM, William G. Scott wgsc...@ucsc.edu wrote: In System Preferences, under the idiotically-named “Mission Control” window, try unchecking “Displays have separate Spaces”. Screen Shot 2015-05-11 at 12.24.13 PM.png Also, if you aren’t running X11 2.7.8_rc1, you might want to try that (it is currently the newest version available). William G. Scott http://scottlab.ucsc.edu/~wgscott On May 11, 2015, at 11:05 AM, Xiao Lei xiaolei...@gmail.com wrote: Dear All, I came to a weird problem when I use CCP4 and coot on my macbook pro (Yosemite 10.10.3). I could not fully maximize the user interface to my screen, even after I click maximize button (the + sign on the up left corner), the interface only occupies around half of my screen (I attached the photos here). I could not adjust manually to increase the screen occupation of the interface from the vertically direction further. This makes viewing structure on coot very uncomfortable. I appreciate any input from you for this problem. Thanks ahead. Xiao Screen Shot 2015-05-11 at 10.52.49 AM.pngScreen Shot 2015-05-11 at 10.54.27 AM.png
Re: [ccp4bb] 3BDN, 16.5% Ramachandran Outliers!!!!!
Hi Robbie: Sorry, I just saw your email now. To make that figure, I just downloaded the automated refinement results manually from the server, loaded into coot, and took a screenshot. A couple of days later, after Gert mentioned you had since fixed it, I checked with the built-in coot interface, and, as you say, it looks fine now. In general, the problem seems to do with linking. Two examples (which both now appear to be corrected) in 3zp8 are the 5’-terminal GDP (one often gets GTP or GDP at the 5’-end of in vitro transcribed RNAs) and the modified nucleotide at the ribozyme cleavage site (2’-OMe). In some instances, these don’t get linked up the the rest of the nucleotide chain. I think the root problem is different refinement programs handle some of these things more or less gracefully by default, probably because the PDB standard (if there is one) is obscure. For example, GDP (or GTP) is often a separate cofactor, so I guess it doesn’t get linked by default. I’ve run into different subsets of this problem both with refmac and with phenix, although refmac run via coot seems to handle it gracefully. Phenix complains it can’t find the 2’-OMC cif file by default, but when pointed in the right direction, handles it, but it needs to be told to link the GDP at the 5’-terminus. PDB_REDO is a great service; certainly there is no reason to apologize for the results of an automated refinement. If it “goes wrong”, this really tells us that there is a more fundamental problem of standardization that needs to be addressed, because the automatic refinment program should run without any special knowledge, just as any interested user should be able to take the PDB and data and refine the structure for himself or herself manually without any special knowledge. All the best, Bill William G. Scott Professor, Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA University of California at Santa Cruz Santa Cruz, California 95064 USA http://scottlab.ucsc.edu/~wgscott On Apr 24, 2015, at 12:52 AM, Robbie Joosten robbie_joos...@hotmail.com wrote: Hi Bill, I have no Idea where you got that picture, the PDB_REDO entry for 3zp8 look pretty okay to me. You might need press F5 (or the OSX equivalent) when you check the entry page though ;) Apparently something went hideously wrong with the restraint generation in the previous run. It seems to work much better now. The modified residue stays nicely in density. Problems like this are bound to occur in automated pipelines like PDB_REDO, we cannot check all the entries by hand. So if you or anyone else finds problems with specific entries, feedback is always welcomed. We might be able to solve the problem and improve out software in the process. Cheers, Robbie Date: Thu, 23 Apr 2015 16:15:41 -0700 From: wgsc...@ucsc.edu Subject: Re: [ccp4bb] 3BDN, 16.5% Ramachandran Outliers! To: CCP4BB@JISCMAIL.AC.UK On Apr 23, 2015, at 11:43 AM, Keller, Jacob kell...@janelia.hhmi.org wrote: Is it in pdb redo? Take a look here: http://www.cmbi.ru.nl/pdb_redo/bd/3bdn/index.html JPK Sometimes it is worth checking the pdb_redo maps, in case it does something like it did to our 3zp8 (which has a modified nucleotide at the active site that apparently it can’t cope with): Screen Shot 2015-04-23 at 4.02.46 PM.png Maybe it just hates RNA and defaults to pdb_oyvey Bill William G. Scott http://scottlab.ucsc.edu/~wgscott
Re: [ccp4bb] PDBcur fails with error message
Hi Jeorge: My Luddite approach to such things: grep -v ANISOU original.pdbiso_only.pdb HTH, Bill William G. Scott http://scottlab.ucsc.edu/~wgscott On Apr 24, 2015, at 8:54 AM, jeorgemarley thomas kirtswab...@gmail.com wrote: Dear All, Here is the CCP4 version 6.5 installed, where I want to remove the ANISOU atoms from the pdb file, but its shows failed job with an error message : has failed with error message child process exited abnormally So I am not able to figure it out, how to rectify. Please suggest. Thank you Regards Jeorge
[ccp4bb] [OT]: Can anyone recommend a good reference for creating CVs or resumes for US biotech?
Apologies for the (somewhat) off-topic question. I’m trying to help someone (a virologist/immunologist) create a viable resume or cv for obtaining a biotech industrial job in the US. (Since she is from the UK, her idea is to construct a chronological life history dump, punctuated with bitter sarcasm and strange verb tenses.) If anyone has a good source for successful examples or templates, I would be incredibly grateful. Many thanks in advance. Bill William G. Scott http://scottlab.ucsc.edu/~wgscott
Re: [ccp4bb] OS X yosemite
Hi Mirek: I haven’t encountered anything (CCP4, phenix, coot. pymol, etc) that doesn’t work, but also haven’t found a single compelling advantage (or even a non-compelling advantage) to upgrading. You get to see more of the spinning beachball of death while waiting for file dialog boxes to materialize. YMMV, Bill William G. Scott Professor, Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA University of California at Santa Cruz Santa Cruz, California 95064 USA http://scottlab.ucsc.edu/~wgscott On Mar 17, 2015, at 4:30 PM, Cygler, Miroslaw miroslaw.cyg...@usask.ca wrote: Hi, I am thinking of upgrading the os on my mac to Yosemite. Are there any known issues for crystallographic software that I should pay attention to? Thanks, Mirek
Re: [ccp4bb] CCP4 PATH variable
On Mar 13, 2015, at 12:42 PM, Petr Leiman petr.lei...@epfl.ch wrote:
this is how we are supposed to use CCP4 today anyway.
I’ve never been big on doing what I am told I am supposed to do, so I have been
using this:
use this to put it at the end of the path:
ccp4_first_in_path=0
or this to put it at the beginning:
ccp4_first_in_path=1
with the following for bash and zsh:
if [[ $ZSH_NAME != zsh ]];then
# This is specific to bash, so protect it from zsh users
# CCP4 executables and scripts live in $CBIN and $CETC respectively; put
them
# on the path in an appropriate order for scripts to be used as wrappers for
# binaries of the same name. Put ccp4 stuff after the current path to avoid
# confusion with `.' or whatever in the path:
#
# This construct prevents the path getting longer each time ccp4.setup is
# executed (A. Perrakis)
#
ccp4pathlist=${CCP4}/etc ${CBIN}
#
for dir in ${ccp4pathlist}; do
if [[ `expr :${PATH}: : .*:${dir}:` -eq 0 ]]; then
if [[ $ccp4_first_in_path -eq 1 ]]; then
export PATH=${dir}:${PATH}
else
export PATH=${PATH}:${dir}
fi
fi
done
else
# This is specific to zsh, so protect it from bash users
if [[ $ccp4_first_in_path == 1 ]]; then
PATH=${CCP4}/etc:${CBIN}:$PATH
else
PATH=$PATH:${CCP4}/etc:${CBIN}
fi
typeset -U path # This construct prevents the path getting longer
each time
# ccp4.setup is executed in zsh.
export PATH
fi
Re: [ccp4bb] Basic Anomalous Scattering Theory
Hi Jacob: If you can find a copy of R. W. James, THE CRYSTALLINE STATE VOL II: THE OPTICAL PRINCIPLES OF THE DIFFRACTION OF X-RAYS. Hardcover – 1965, this gives a very good (albeit primarily classical) description. Blundell and Johnson also has a good, slightly more modern, description, which I think is derived in part from James’s treatment. (Someone has swiped both books from me, so I can’t double-check.) Having said that, I find an approach based on quantum scattering theory more intuitive. Everything we normally deal with is elastic scattering within the first-order Born approximation, which means a single photon collides exactly once with a billiard ball-like spherically symmetric hard-sphere electron cloud, neither gaining nor losing energy. Using the Poisson equation, you can then show that the electron density is the FT of the (completely real) potential. To treat absorption within this framework, an imaginary term is added to the potential as a small perturbation. Briefly, in the first case, a photon elastically scatters, and in the second case, there is a probability of absorption. (An absorbed photon, absorbed in the conventional way , in which an electron is promoted to an excited state, will be re-emitted as a new photon having less energy, which is how we are able to do fluorescent XAFS to find the absorption edge when collecting data.) Sorry, I will have to stop here to go teach something else I am equally unqualified to speak about — enzymology. Hopefully this will be something to get a start with. Bill William G. Scott Director, Program in Biochemistry and Molecular Biology Professor, Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA University of California at Santa Cruz Santa Cruz, California 95064 USA phone: +1-831-459-5367 (office) email:wgsc...@ucsc.edu On Mar 11, 2015, at 9:57 AM, Keller, Jacob kell...@janelia.hhmi.org wrote: Dear Crystallographers, I have had only a vague understanding of what specific things are happening with shell electrons at anomalous edges. Specifically, for example, to what energy of electron-transition does the x-ray k-edge correspond in terms of orbitals, and is that transition energy actually equal to the energy of the photon, suggesting that the photon is absorbed (or disappears?) in elevating the electron? I don't think we say it is absorbed, so how does the energy come back out, from the electron's falling back down, right? So then there's a new photon created, or the same one comes back out? Where was it? Further, I also have heard that the emerging anomalous/resonance photons are of the same wavelength as the incident radiation, but usually there is something lost in transitions (even non-fluorescence ones) I thought? Has it ever been definitively shown that the anomalous photons are of the same energy as the incident radiation? In the case of L-edges, why are there three separate edges? Further, if the resonance occurs when the energies are equal, why does resonance occur at energies greater than the edge? I don't think this happens in other resonance phenomena, or does it? If projects a middle-C-tone into a piano, do all of the lower notes resonate as well, according to the Kramers-Kronig relation? I think it may actually happen in the mammalian cochlea's travelling wave, but is it completely general to resonance phenomena? Just interested, and have wondered these things for a long time in the background of my mind... Jacob Keller *** Jacob Pearson Keller, PhD Looger Lab/HHMI Janelia Research Campus 19700 Helix Dr, Ashburn, VA 20147 email: kell...@janelia.hhmi.org ***
Re: [ccp4bb] Basic Anomalous Scattering Theory
On Mar 11, 2015, at 11:13 AM, Keller, Jacob kell...@janelia.hhmi.org wrote: Somebody sent me a pdf with such a mind-picture which describes the origin of the anomalous effect as arising from broken centrosymmetry of the anomalous atoms themselves: (p. 8) Under normal conditions, electron distributions within atoms are centrosymmetric...Under conditions of anomalous scattering, electrons are perturbed from their centrosymmetric distributions; electrons are jumping between orbitals. The breakdown of centrosymmetry in the scattering atoms is reflected in a loss of centrosymmetry in the pattern of scattered X-ray intensities. I think this is wrong. Unless I am mistaken, the diffraction pattern is centrosymmetric simply as a consequence of the electron density (and therefore the potential) being a purely real function. If the function is complex (i.e., including that small perturbation I spoke of this morning), then the diffraction pattern will no longer be centrosymmetric.
Re: [ccp4bb] different Kd and Km value
On Feb 26, 2015, at 4:51 PM, Srivastava, Dhiraj dhiraj-srivast...@uiowa.edu wrote: Hi I have a protein with two substrate. when I am doing the binding studies with the two substrate separately, I am finding one of the substrate to have similar kd and Km. however the km and kd values are almost 30 fold different for the other substrate. it binds 30 fold more tightly then you can think based on Km. I don't know how to explain this. Km and Kd can be different but does any one have seen that much difference in Kd and Km? Thank you Dhiraj If k+2 isn’t small compared to k-1, Km cannot be approximated by Kd.
Re: [ccp4bb] How to rename nucleic acid residues in PDB files
CCP4 has a number of such utilities, such as pdbset. http://www.ccp4.ac.uk/html/pdbset.html You can find others by looking here: http://www.ccp4.ac.uk/html/FUNCTION.html HTH, William G. Scott http://scottlab.ucsc.edu/~wgscott On Oct 7, 2014, at 11:01 AM, Sasha Pausch sashapau...@gmail.com wrote: Thank you Scott, I could change the nomenclature. But is there any way to change the numbering also? My PDB is not being accepted by NUCPLOT. Initially I suspected it is the nomenclature, even after changing nomenclature as per your suggestion program is not accepting the PDB. Now I am suspecting is the numbering of the bases different!! Please help on overcoming this problem. On Tue, Oct 7, 2014 at 12:58 AM, William G. Scott wgsc...@ucsc.edu wrote: On Oct 6, 2014, at 12:04 PM, Sasha Pausch sashapau...@gmail.com wrote: Hello All, I would like to know how to change the nomenclature of bases (for example from Ad to DA for adenosine triphosphate) in PDB file. perl -pi -e ‘s|Ad|DA|g’ your.pdb
Re: [ccp4bb] How to rename nucleic acid residues in PDB files
On Oct 6, 2014, at 12:04 PM, Sasha Pausch sashapau...@gmail.com wrote: Hello All, I would like to know how to change the nomenclature of bases (for example from Ad to DA for adenosine triphosphate) in PDB file. perl -pi -e ‘s|Ad|DA|g’ your.pdb
Re: [ccp4bb] paper
On Sep 2, 2014, at 9:10 PM, Avisek Mondal avisekmonda...@gmail.com wrote: please can you send me this paper... i can not subscribe it from my lab... Acta Cryst. (2014). F70, 1296-1302[ doi:10.1107/S2053230X14014381 ] No problem: http://tinyurl.com/n3gurpe
Re: [ccp4bb] negative density around disulfide bond
On Jun 1, 2014, at 10:08 PM, Eze Chivi ezech...@outlook.com.ar wrote: Hello, when I refine my structure, I see negative density around the disulfide bond. I have 7 copies per ASU, and I can see this density in many of them. In some cases, I see positive density also (negative in the center of the straight line linking S atoms, and positive in both sides). What can I try to solve it? Is it due to radiation damage? Alternative conformation (partial oxidation)? Incorrect disulfide geometry parameters? My resolution is 2.1 A, R/Rfree are around 0.220/0.243, and similar results with refmac5, phenix and PDBREDO. Please find two example pictures in attachment. Thanks for your help! Ezequiel disulfide.jpgdisulfide2.jpg Dear Ezequiel: I apologize if I missed some crucial fact, but the simplest naive explanation would be the disulfide bonds became reduced somewhere along the line, since that would push the non-bonded sulfur atoms apart, relative to where you have them. You should be able to tell with a denaturing gel (run in the absence of DTT or equivalent). I’ve found a bit of Cu(II)-1,10-phenanthroline can help keep the disulfides oxidized. Try re-refining without the disulfide linkages, and see if the difference densities go away. Bill
Re: [ccp4bb] crystallographic confusion
Dear Arnon et al: My understanding of the Shannon/Nyquist sampling theorem is admittedly extremely rudimentary, but I think aliasing can result if an arbitrary brick-wall resolution cut-off to the data is applied. So let’s say there are real data are to 2.0 Å resolution. Applying the 2.2 Å cutoff will result in aliasing artifacts in the electron density map corresponding to an outer shell reciprocal space volume equal but opposite to the cut out data. The alternative, which is to process and keep all the measured reflections, should help to minimize this. An effective resolution can be calculated and quoted. This becomes a significant problem with nucleic acids and their complexes, which often diffract with significant anisotropy. The idea that 85% completeness in the outer shell should dictate its rejection seems rather surprising and arbitrary. The aliasing artifacts in that case would probably be significant. The map image quality, after all, is what we are after, not beautiful Table 1 statistics. Bill William G. Scott Professor Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA University of California at Santa Cruz Santa Cruz, California 95064 USA http://scottlab.ucsc.edu/scottlab/ On Apr 18, 2014, at 5:22 PM, Lavie, Arnon la...@uic.edu wrote: Dear Kay. Arguably, the resolution of a structure is the most important number to look at; it is definitely the first to be examined, and often the only one examined by non-structural biologists. Since this number conveys so much concerning the quality/reliability of the the structure, it is not surprising that we need to get this one parameter right. Let us examine a hypothetical situation, in which a data set at the 2.2-2.0 resolution shell has 20% completeness. Is this a 2.0 A resolution structure? While you make a sound argument that including that data may result in a better refined model (more observations, more restraints), I would not consider that model the same quality as one refined against a data set that has 90% completeness at that resolution shell. As I see it, there are two issues here: one, is whether to include such data in refinement? I am not sure if low completeness (especially if not random) can be detrimental to a correct model, but I will let other weigh in on that. The second question is where to declare the resolution limit of a particular data set? To my mind, here high completeness (the term high needs a precise definition) better describes the true resolution limit of the diffraction, and with this what I can conclude about the quality of the refined model. My two cents. Arnon Lavie On Fri, April 18, 2014 6:51 pm, Kay Diederichs wrote: Hi everybody, since we seem to have a little Easter discussion about crystallographic statistics anyway, I would like to bring up one more topic. A recent email sent to me said: Another referee complained that the completeness in that bin was too low at 85% - my answer was that I consider the referee's assertion as indicating a (unfortunately not untypical case of) severe statistical confusion. Actually, there is no reason at all to discard a resolution shell just because it is not complete, and what would be a cutoff, if there were one? What constitutes too low? The benefit of including also incomplete resolution shells is that every reflection constitutes a restraint in refinement (and thus reduces overfitting), and contributes its little bit of detail to the electron density map. Some people may be mis-lead by a wrong understanding of the cats and ducks examples by Kevin Cowtan: omitting further data from maps makes Fourier ripples/artifacts worse, not better. The unfortunate consequence of the referee's opinion (and its enforcement and implementation in papers) is that the structures that result from the enforced re-refinement against truncated data are _worse_ than the original data that included the incomplete resolution shells. So could we as a community please abandon this inappropriate and un-justified practice - of course after proper discussion here? Kay
Re: [ccp4bb] install coot in mac through fink
I’m not sure what went wrong, but I have reindexed everything at my end and tested it with this command: sudo apt-get --reinstall install gcc48-shlibs You might want to delete the file /sw/var/cache/apt/archives/gcc48-shlibs_4.8.2-1001_darwin-x86%5f64.deb first in case the download became corrupted. Bill William G. Scott Professor Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA University of California at Santa Cruz Santa Cruz, California 95064 USA http://scottlab.ucsc.edu/scottlab/ On Apr 2, 2014, at 8:58 AM, Yamei Yu ymyux...@gmail.com wrote: Hi All I'm trying to install a coot for my new Mac. I followed the instructions from http://scottlab.ucsc.edu/~wgscott/xtal/wiki/index.php/Fink_for_10.9 when I execute the command :sudo apt-get install coot I got two errors: Get:23 http://psbmini.ucsc.edu stable/main gcc48-shlibs 4.8.2-1001 [33.0MB] Err http://psbmini.ucsc.edu stable/main gcc48-shlibs 4.8.2-1001 Connection timed out Fetched 240MB in 1h38m19s (40.7kB/s) Failed to fetch http://bindist.finkproject.org/10.9/dists/stable/main/binary-darwin-x86_64/languages/gcc48-shlibs_4.8.2-1001_darwin-x86_64.deb Size mismatch E: Unable to fetch some archives, maybe run apt-get update or try with --fix-missing? Could you please tell me How to solve these problems? Thanks so much! yamei
Re: [ccp4bb] OSX 10.9.2
On Mar 28, 2014, at 10:29 AM, Cygler, Miroslaw miroslaw.cyg...@usask.ca wrote: Hi, Does the ccp4 suite work with the latest OSX 10.9.2 operating system? Are there any known problems? Mirek As far as I can tell, it works fine. One problem I have heard (on the ccp4bb) with 10.9.X is that support for 3rd-party monitors may be problematic. Bill
Re: [ccp4bb] largest protein crystal ever grown?
I remember seeing an approx (5mm)^3 haemoglobin crystal in the MRC LMB crystal growing room, and the nucleosome crystals there were almost as big in their longest dimension. Bill On Oct 24, 2013, at 8:33 AM, Tobias Beck tobiasb...@gmail.com wrote: Dear all, I was just wondering if anyone has some information or references about the dimensions of the largest protein crystal ever grown? I am aware that for neutron protein crystallography one usually needs crystals with mm dimensions. I have found some information on crystallization under micro-gravity and how this can enlarge the crystal size. However, I would rather be interested in the dimensions for crystals obtained from a regular lab setup. Thanks, Tobias. -- ___ Dr. Tobias Beck ETH Zurich Laboratory of Organic Chemistry Wolfgang-Pauli-Str. 10, 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] Only refine Bs in Refmac?
On Sep 4, 2013, at 2:57 PM, Garib N Murshudov ga...@mrc-lmb.cam.ac.uk wrote: You may need to use the latest available version (5.8) from our LMB site Hi Garib: Would it be possible to add a link for the source code, so this could also be used with Coot? Thanks. Bill
Re: [ccp4bb] CCP4 package installation problem in Mac OS
Scroll up to see where it started failing. On Aug 3, 2013, at 11:22 AM, anil kumar anilkumar...@yahoo.co.in wrote: Dear members, I am attempting to install ccp4 package in my mac machine. The download of the files was directed in a temp folder and done via the package manager successfully. Upon installation there is an error message: mount list is unavailable. I am attaching the screenshot for your reference. Please advice how I can overcome this issue. Thanks, Anil Screen Shot 2013-08-04 at 2.09.29 AM.png Screen Shot 2013-08-04 at 2.13.19 AM.png
Re: [ccp4bb] Harmful effect of X-ray
On Jul 12, 2013, at 12:57 PM, Mark van der Woerd mjvdwo...@netscape.net wrote: I just re-wrote our safety plan because we have to renew our radiation license for our new in-house instrument. On this plan, they ask you to write a worst-case scenario. For an in-house sealed tube instrument, producing CuKa radiation, we calculated (with the help of the friendly manufacturer, thank you) that if you had a direct exposure to the beam, for example because your hand would be in the wrong place at the wrong time, you would burn a 7mm deep hole in your hand. Interestingly and surprisingly, when compared to our old rotating anode generator, the estimated worst case scenario for the old setup was an order of magnitude less severe (less than 1 mm deep burn). The constant improvement of instruments also makes them just a little more dangerous. The old days of 'tingle' are long gone and you *really* need to watch yourself, even on in-house instruments. Indeed, if you do not tinker with the safety system and have shielding in place at all time, as you say, the exposure is never above background. So: obey all the rules and worry very little. Although I've never knowingly stuck any bodily appendage into an X-ray beam, I recently had the delightful experience of having a skin cancer hacked off my hand. Even though it is hard to know if the cause was an X-ray beam, I've met other crystallographers who have had similarly located lesions, leading me to believe that this might be more common than we tend to acknowledge to ourselves or each other. So I would modify the last quoted sentence to Obey all the rules and worry anyway. Ionizing radiation, especially when collimated, it a significant hazard, ipso facto.
Re: [ccp4bb] RNA for crystallization
On May 20, 2013, at 7:20 AM, A K alek6...@gmail.com wrote: Dear all, I have a crystallization-related question. I am going to co-crystallize protein with RNA. I ordered a short (10 mer and 14 mer) RNA from Dharmacon but did not choose the purification option while ordering them due to the budget issues. How critical is to HPLC purify them before setting drops? Aren't RNA synthesis protocols reliable enough nowadays for such short RNAs? Thanks, Alex Dear Alex: The coupling steps are rather more inefficient than with DNA, so you may have some non-negligible N-1, N-2, .. contaminations, as well as potentially incompletely deprotected RNAs. If the RNA is involved in making lattice contacts, this might be problematic. However, crystallization is also a purification procedure, so you could always try it first and see if it works. In one case in our lab, having a contaminant like this present was absolutely essential for obtaining crystals. Gel purification is cheap and easy, and not too much of a burden if you can avoid getting skin cancer from the UV light needed for shadowing the RNA. A 20% acrylamide sequencing gel mix would give you the nucleotide resolution you might need. Good luck. Bill William G. Scott Professor Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA 228 Sinsheimer Laboratories University of California at Santa Cruz Santa Cruz, California 95064 USA
Re: [ccp4bb] delete subject
That last paragraph is great: Adam is the author of the book Surviving Your Stupid, Stupid Decision to Go to Grad School (Broadway Books, 2010) -- Bill On Mar 28, 2013, at 9:09 AM, Ian Tickle ianj...@gmail.com wrote: By coincidence this just landed in my Inbox: http://membercentral.aaas.org/multimedia/webinars/how-recruit-citizen-scientists-discovery So maybe after all Tom is way ahead of the rest of us in his structure-solving strategy - though I agree with others that his tactics need to be honed somewhat! Cheers -- Ian On 28 March 2013 14:43, Raji Edayathumangalam r...@brandeis.edu wrote: Ed, I very much agree with you. We've all had to learn that questions posted to ccp4bb and the ensuing discussions take on a life of their own. Once one posts a question on ccp4bb, there's no such thing as steering the direction of the discussion on the ccp4bb and there's no such thing as the equivalent of screaming Stop! Stop! Stop! on the ccp4bb. Also, I don't believe people simply woke up one day and posted irritating or mean comments to ccp4bb. Ed was spot on for why some folks reacted the way they did to the post so let's acknowledge that as well. I didn't get the impression that any of the replies suggested that students stop posting questions. There are many many students on this BB who are in small institutions without even the minimal help at arm's length and who get tons of help from posting questions to the ccp4bb. That situation is not all that distant in my own memory and I suspect for many other experts on this BB. But posting 10MB attachments and getting the entire ccp4bb community to crowdsource towards problem solving is all good, but only to a certain degree. It may be great to get things done quickly with the collective intellect of the ccp4bb but there comes a point when the correct answers may get fed back at such a rapid speed that if one doesn't go back and try to figure stuff out for oneself, including the reasons/theory/logic behind the answers/solutions that the community has posted, it may be to the detriment of one's own learning, especially if one is in the early stages of learning the subject matter. Cheers, Raji On Thu, Mar 28, 2013 at 9:09 AM, Ed Pozharski epozh...@umaryland.edu wrote: On Thu, 2013-03-28 at 12:15 +, Tom Van den Bergh wrote: I think this is a good time to end the discussion. As a general comment, discussions on boards like ccp4bb often digress and take direction different from you original intent. I may understand your desire to try to control the situation, but if people on this board feel that the questions of data sharing, student training, netiquette and proper choice of resolution cutoff are worthy of further discussion (that may not have much to do with specifics of your original request for assistance), it is their right too. What may have caused some extra grief is this unfortunate turn of phrase in your original post Could you try some refinement for me, because this is first structure that i need to solve as a student and i dont have too many experience with it. It goes a bit beyond the usual my R-values are too high what should I do question and may be instinctively construed as if you expect someone to actually do your work for you (I am sure that is not what you asked). So a bit of a vigorous reaction that you received likely results from misunderstanding your intent (albeit posting your data is very unusual and strengthens the impression) and perhaps misplaced feeling that you have abandoned attempts to resolve the problem independently too soon. I did *not* look at your data and therefore I may be completely wrong here, but it is my understanding that your actual issue was not realizing there could be more than one molecule in the asymmetric unit. More traditional route is to describe your situation in general terms and offer to provide data to those willing to take a closer look. Cheers, Ed. -- Hurry up before we all come back to our senses! Julian, King of Lemurs -- Raji Edayathumangalam Instructor in Neurology, Harvard Medical School Research Associate, Brigham and Women's Hospital Visiting Research Scholar, Brandeis University
Re: [ccp4bb] delete subject
Dear Tom et al: Although arriving too late to participate in the snark-fest, it occurred to me that maybe this is almost exactly how we should solve structures and educate graduate students (or others). Instead of attachments, the relevant files could be shared via dropbox. Those of generous spirit could help solve, refine, correct, critique or otherwise improve structures before formal peer review. (If everyone knows the source of the data, it is far less likely to be ripped off, not more.) It might cut down on the number of mistakes (or worse) that appear in the PDB and journals, new mentorships and collaborations might be established, in exceptional cases co-authorship, or more generally, an acknowledgement could be offered. For students like mine who are comparatively isolated in a small institution somewhat off the beaten path, it would be a real asset and advantage to them not to have to rely only upon my limited abilities and increasingly obsolete knowledge. We should all be able to learn from one anther without fear of reproach. All the best, Bill William G. Scott Professor Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA 228 Sinsheimer Laboratories University of California at Santa Cruz Santa Cruz, California 95064 USA On Mar 27, 2013, at 3:36 PM, Tom Van den Bergh tom.vandenbe...@student.kuleuven.be wrote: Is it possible to delete my post: refinement protein structure from ccp4 bb, i get too many bad reactions. I think its bettter to just delete the whole topic. Greetings, Tom
Re: [ccp4bb] RNA 3D structure alignment
I find that least-squares fitting of RNA in coot is fairly painless, robust and straightforward. It will move all of the contents of one pdb file, not just the RNA residues you select to align. On Mar 14, 2013, at 1:53 PM, Chen Zhao chenzhaoh...@gmail.com wrote: Dear all, I am now struggling to align two 3D RNA structures. I know there are a bunch of web servers, but they either just generated a pdb file with a single aligned structure, or they left the ligand out. Does any of you have some recommendations? Alternatively, is there some software that can calculate the transformation matrix between the coordinates in 2 pdb files? Then I could add the ligand back by myself. I suspect that Matlab is able to do this, but I would save it as the last resort. Thank you so much! Best, Chen
Re: [ccp4bb] Mac OS 10.8 Mountain Lion and CCP4?
Hi Brad: To the best of my knowledge, everything works on 10.8.X. If you have an older computer running 10.6.8, you might want to leave it there if you don't have at least 4, preferably 8 gig of memory. 10.8 is very resource-intensive. (10.7 seemed worse somehow. 10.7 introduced a few bugs, annoyances and 'features' that have been corrected in 10.8, so I either run 10.8.X or 10.6.8 on my computers in the lab.) Good luck. Bill William G. Scott Professor Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA 228 Sinsheimer Laboratories University of California at Santa Cruz Santa Cruz, California 95064 USA On Feb 22, 2013, at 7:18 AM, Brad Bennett bradbennet...@gmail.com wrote: Thanks to Jon, Huw, and Albert for quickly setting my mind at ease about upgrading our Mac OS to Mountain Lion and compatibility with CCP4. Just as an FYI, it seems most of the other commonly used software packages (i.e. Phenix v1.8, PyMol v1.5) are ok running on 10.8 as well. Best- Brad On Fri, Feb 22, 2013 at 10:01 AM, Jon Agirre jon.agi...@gmail.com wrote: The (on by default) versioning auto save is a PITA if you ever use textedit to edit scripts but apart from that 10.8 is a fairly painless upgrade. You'll probably know about this trick, but just in case there's someone else still suffering the autosave feature, here it goes: you can disable autosave and bring back the good old 'Save as...' command for a number of apps by executing the following commands: defaults write com.apple.TextEdit ApplePersistence -bool no defaults write com.apple.Preview ApplePersistence -bool no defaults write com.apple.iWork.Pages ApplePersistence -bool no defaults write com.apple.iWork.Numbers ApplePersistence -bool no defaults write com.apple.iWork.Keynote ApplePersistence -bool no Cheers, Jon -- Jon Agirre, PhD Unit of Biophysics (CSIC-UPV/EHU) http://sourceforge.net/projects/projectrecon/ +34656756888
Re: [ccp4bb] fink problem
It sounds like you have updated the OS system since last updating fink. Easiest thing is to blow it away and start over. I made some tarballs to remove the pain: http://scottlab.ucsc.edu/~wgscott/xtal/wiki/index.php/Installing_Fink_on_10.6_and_10.7#Installing_Fink_on_10.8 Or you can just install coot from here or CCP4 webpage. http://scottlab.ucsc.edu/~wgscott/xtal/wiki/index.php/Stand-Alone_Coot http://www.ccp4.ac.uk/download/#os=mac On Feb 19, 2013, at 7:23 PM, Yamei Yu ymyux...@gmail.com wrote: Hi all, I use this command fink -y install coot to install coot but I got the following error message arch: /usr/bin/perl5.10.0 isn't executable Then I check the folder /usr/bin/ I don't have perl5.10.0 I only have perl5.10 how to solve this problem? Thanks! yamei
Re: [ccp4bb] how to update phenix
On Feb 10, 2013, at 8:23 AM, LISA science...@gmail.com wrote: Hi all, My mac has the old version of phenix. How can i update to the new verison? Should I delete the old version and download the new version to install as the fist time ? Thanks lisa You can delete it and download a new version, or simply keep both. phenix has version labels on their binaries, for the enjoyment of those who use shell auto-completion. e.g.: fennario-% phenix.refine external command phenix.refine phenix.refine_1.8.1-1168 BTW, there is also a phenix bb. Asking about this here is kind of like asking my wife what I should get my (purely hypothetical) mistress for valentine's day.
Re: [ccp4bb] off topic:how to prevent DNA tetraplexe forming?
On Dec 20, 2012, at 8:16 PM, dengzq1987 dengzq1...@gmail.com wrote: Hi all, recently, i perform an EMSA experiment.when i prepared the DNA with a 5' poly(G)-tailed ,i find that it formed guanine tetraplexes .how can i prevent this happen,or has any method to disrupt the guanine tetraplexes structure? any suggestion is appreciation. dengzq Unless it has some other, more stable structure to compete it out, you will have this problem persist. Even GTP in solution will do this. Bill William G. Scott Professor Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA 228 Sinsheimer Laboratories University of California at Santa Cruz Santa Cruz, California 95064 USA
Re: [ccp4bb] Reading CCP4 maps into PyMol
Give it the suffix .ccp4 On Dec 7, 2012, at 10:52 AM, Harman, Christine christine.har...@fda.hhs.gov wrote: Hi, Can anyone tell me how to open a CCP4 map in Pymol. Thanks, Christine
[ccp4bb] Mg++ interactions
Hi folks: Are Mg++ ions ever observed to chelate primary amines? Are there any examples in crystal structures? Thanks. -- Bill William G. Scott Professor Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA 228 Sinsheimer Laboratories University of California at Santa Cruz Santa Cruz, California 95064 USA
Re: [ccp4bb] hkl2000 install
Make your life easier and use CCP4's imosflm (this is the CCP4 bb after all) On Nov 18, 2012, at 5:48 PM, 王瑞 wangrui...@gmail.com wrote: OK,thank you all of you. I have installed one copy of HKL2000 on our desktop computer. But for my notebook's low 1366*768 resolution, the HKL2000 can't work ! So what could I do to resolve it ? 2012/11/13 王瑞 wangrui...@gmail.com: 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
[ccp4bb] OT: Has anyone experienced problems with Apple laptop battery expansion?
Hi folks:I'm trying to get a sense for how frequently this sort of thing occurs:That was a macbook air that served me well for four years, but then self-destructed. (I took it to the Apple store. They generously offered to repair it for $800 or to sell me a new one, and suggested this was normal if you leave the power cord attached after the battery charges, even while giving a lecture or seminar.) It strikes me as a bit dangerous.--Bill ScottWilliam G. ScottProfessorDepartment of Chemistry and Biochemistryand The Center for the Molecular Biology of RNA228 Sinsheimer LaboratoriesUniversity of California at Santa CruzSanta Cruz, California 95064USA
Re: [ccp4bb] Glass Capillaries
On Nov 12, 2012, at 8:13 AM, Michael Roberts mrobert...@talktalk.net wrote: Dear All, I would be interested to learn of other crystallographers' experience in their use of glass capillaries for protein crystal growth and X-ray diffraction clarity. There are many types of glass available - quartz, soda glass, borosilicate, etc. Are there specific types which people prefer for best results overall? Best wishes, Michael Roberts Glass capillaries can be reactive with crystals. Quartz tends to be more neutral and has the advantage of being easier to cut, etc. as well. It does however create a higher background scatter, so the signal to noise ratio of the data collected might suffer a wee bit.
Re: [ccp4bb] CCP4-6.3.0 installtion
On Oct 18, 2012, at 3:39 PM, Kip Guja k...@pharm.stonybrook.edu wrote: If the output says: /bin/bash then do source /Applications/ccp4-6.3.0/bin/ccp4.setup-sh ccp4i If the output says: /bin/tcsh or /bin/csh then do source /Applications/ccp4-6.3.0/bin/ccp4.setup-csh ccp4i You need to replace with or with the return key.
Re: [ccp4bb] CCP4 update 6.3.0 006
Dear Ronan et al: I apologize if I have missed it, but is there a simple way to obtain the corresponding changes in the source code for those of us who compile ccp4 ourselves? I looked on the web site and the ftp site but can't seem to find it. Many thanks in advance. Bill On Oct 8, 2012, at 11:20 AM, ronan.kee...@stfc.ac.uk wrote: Dear CCP4 Users, A CCP4 update has just been released, consisting of the following changes: * MrBUMP: model building options added * PISA: new QT interface * AMPLE: bug fixes and expanded interface (Linux and MAC only) * tlsextract: correction of output format which broke parsing of output * DiffractionImage: corrections to reading of pilatus mini-cbf * ccp4i: New AMPLE (Linux and Mac) and MrBUMP interfaces, QT-PISA launcher and bug fixes * crank: bug fix (Windows only) The easiest way to obtain the update is to install the CCP4 update client, if you have not done so already. Note that auto-updates will work correctly only with CCP4 release 6.3.0, therefore upgrade if necessary. Report bugs to c...@stfc.ac.uk. Many thanks for using CCP4, -- Ronan Keegan -- Scanned by iCritical.
Re: [ccp4bb] Off-topic: Best Scripting Language
I'd just use a decent shell scripting language (like zsh) in conjunction with a unix tool like awk. But the gnuplot option sounds ideal. Bill William G. Scott Professor Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA 228 Sinsheimer Laboratories University of California at Santa Cruz Santa Cruz, California 95064 USA On Sep 12, 2012, at 7:32 AM, Jacob Keller j-kell...@fsm.northwestern.edu wrote: Dear List, since this probably comes up a lot in manipulation of pdb/reflection files and so on, I was curious what people thought would be the best language for the following: I have some huge (100s MB) tables of tab-delimited data on which I would like to do some math (averaging, sigmas, simple arithmetic, etc) as well as some sorting and rejecting. It can be done in Excel, but this is exceedingly slow even in 64-bit, so I am looking to do it through some scripting. Just as an example, a sort which takes 10 min in Excel takes ~10 sec max with the unix command sort (seems crazy, no?). Any suggestions? Thanks, and sorry for being off-topic, Jacob -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu ***
Re: [ccp4bb] CCP4 Update
On Sep 6, 2012, at 9:00 AM, eugene.krissi...@stfc.ac.uk wrote: If this does not work for you for any reason, please (re-)read update manual for details. If that does not help as well, please write to us. Dear Eugene: Will there be a way to get the corresponding changes to the source-code? -- Bill Scott
Re: [ccp4bb] Various OSes and Crystallography
I completely agree with Harry's observation about the glare screen feature. I find it is quite literally an almost instant headache. There is an option with the macbook pro to pay a ransom to get a usable screen, so my wife did. On my macbook air, I found putting a dull dark grey background for a desktop helps considerably to cut down on the reflection, perhaps in part because it reflects my personality. Instead of buying iMacs, we now get mac minis and pair them with Samsung LED matte screen monitors. The improvement is considerable, and they are a lot less expensive too. Bill On Aug 9, 2012, at 11:25 PM, Harry ha...@mrc-lmb.cam.ac.uk wrote: Hi My two ha'porth. For a laptop, this is the clincher for me - if you want to use your laptop anywhere that has reasonable light levels (e.g. demonstrating to anyone in an exhibition hall), you may well find that the beautiful shiny mirror that Apple put on the front of their screens on most of their laptops makes your investment almost useless in reasonable levels of ambient light. Unless I could buy a Macbook with a matt screen I doubt I'd want to buy another one. Sometimes I wonder if my Macbook was designed in California in a cave to paraphrase what it says on the sticker on the back... It runs all the software I want it to without problems, though, including WIndows stuff via wine or VMWare. And I do *really* like OSX as an interface. On 9 Aug 2012, at 16:18, Andreas Förster wrote: Mind that if you buy a MacBook, there's only one (hefty 15) model without a mirror-coated screen. Andreas On 09/08/2012 3:58, Nat Echols wrote: On Thu, Aug 9, 2012 at 6:55 AM, Jacob Keller j-kell...@fsm.northwestern.edu wrote: one. Are there any really reasonable arguments for preferring Mac over windows (or linux) with regard to crystallography? What can Mac/Linux do that windows cannot (especially considering that there is Cygwin)? What wonderful features am I missing? Mac vs. Linux: mostly a matter of personal preference, but I agree with Graeme. Most programs run equally well on either - with Coot a partial exception, apparently due to problems with the X11 implementation (but once you get used to these, it's not a big deal). Windows, on the other hand, simply doesn't support the full range of modern crystallography software. And in my experience, it has crippling flaws that mean some programs will always work better on Mac/Linux. I wouldn't ever endorse trying to use Windows for serious scientific computing unless you need to run an application that won't work on any other OS, and as far as I know there isn't a single (macromolecular) crystallography program that falls into this category. -Nat Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 0QH
Re: [ccp4bb] Problem with Coot on Mountain Lion
I'm unable to reproduce the error. Can you try it in a temporary new account that doesn't have anything modified, and see if it works? William G. Scott Professor Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA 228 Sinsheimer Laboratories University of California at Santa Cruz Santa Cruz, California 95064 USA On Aug 8, 2012, at 4:50 PM, Jinyi Zhu jinyi.c...@gmail.com wrote: Hi, I recently upgrade to Mountain Lion and update fink following the official instructions. After that, CCP4, Phenix and pymol all run well without problems. However, I could not start Coot. The error message is as following: DEBUG:: stating pydirectory /sw/share/coot/python INFO:: importing coot.py from /sw/share/coot/python/coot.py Importing python module coot using command from coot import * INFO:: coot.py imported Fatal Python error: PyThreadState_Get: no current thread /sw/bin/coot: line 6: 66155 Abort trap: 6 /sw/bin/coot-real $@ I have update all fink packages up to date and tried to re-install Coot by compiling after removing Coot completely. Does anyone have some good suggestion to make Coot work? Thanks! Best, Jinyi
Re: [ccp4bb] Question on stereo monitor: LG D2342P-PN
Dear Zhijie: I saw this for under $300 at Amazon's Showroom and wondered the same thing. I can verify that the LG TV will work with coot, etc., as long as you turn OFF all stereographic processing and allow the software to do the work. There is an extremely detailed review of this at http://www.amazon.com/LG-D2342P-PN-23-Inch-Widescreen-Passive/dp/B004WK3R4U/ref=cm_cr-mr-title by Bill Costa (he gives his email address at the end). He seems to suggest that the 3D glasses for the LG TV are not compatible with this, which left me scratching my head. Having said that, I'll bet it will work fine. If you can get it from Best Buy for under $300 and return it within 30 days for a full refund, it might be worth it. Either way, let us know. Bill William G. Scott Professor Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA 228 Sinsheimer Laboratories University of California at Santa Cruz Santa Cruz, California 95064 USA On Jul 23, 2012, at 11:42 AM, Zhijie Li wrote: Dear CCP4BBers: Sorry to bring up this highly repeated topic again. After some internet research, we are about to make the commitment to buy an LG D2342P-PN for setting up a stereo system. I would like to have a final confirmation from someone with real life experience that this model does work with COOT and Chimera the same way as the Zalman monitors. Thanks in advance. Zhijie
Re: [ccp4bb] Nucleophilic attack by the side-chain carboxyl group of Asp?
On Jul 21, 2012, at 11:52 AM, Justin Jones wrote: Unfortunately, their [sic] isn't a general rule for good versus bad nucleophiles. Actually, there is: The theory of hard and soft acids and bases, developed by Ralph Pearson, generalizes to nucleophiles and electrophiles (Lewis bases and acids, respectively). cf: http://en.wikipedia.org/wiki/HSAB_theory Briefly, hard nucleophiles prefer hard electrophiles, and interact primarily via electrostatic attraction, and soft nucleophiles prefer soft electrophiles, and orbital interactions dominate. So Mg++ prefers oxygen to sulphur, and Hg++ prefers sulphur to oxygen. William G. Scott Professor Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA 228 Sinsheimer Laboratories University of California at Santa Cruz Santa Cruz, California 95064 USA
Re: [ccp4bb] [COOT] CCP4 6.3.0 released
On Jul 17, 2012, at 6:25 AM, Felix Frolow wrote: I will wait for fink version if it will be one… :-\ Does anyone use or want this anymore? -- Bill William G. Scott Professor Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA 228 Sinsheimer Laboratories University of California at Santa Cruz Santa Cruz, California 95064 USA phone: +1-831-459-5367 (office) +1-831-459-5292 (lab) fax:+1-831-4593139 (fax) email:wgsc...@ucsc.edu
Re: [ccp4bb] Coot installing problem
If RedHat allows you to install a more current version of glibc, then do that. If not, switch to something like Ubuntu. William G. Scott Professor Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA 228 Sinsheimer Laboratories University of California at Santa Cruz Santa Cruz, California 95064 USA phone: +1-831-459-5367 (office) +1-831-459-5292 (lab) fax:+1-831-4593139 (fax) email:wgsc...@ucsc.edu On Jun 14, 2012, at 2:26 PM, Young-Jin Cho wrote: Hi, I am using old RedHat now and am having some problem for using new version of coot. When I downloaded coot-0.6.2-binary-Linux-i386-rhel-5-python-gtk2.tar.gz, and simply untared and went to bin directory. When I typed as following it gave me following message: $ ./coot COOT_PREFIX is /home2/yjcho/bin/coot-Linux-i386-rhel-5-gtk2-python ./coot-real ./coot-real: error while loading shared libraries: requires glibc 2.5 or later dynamic linker /home2/yjcho/bin/coot-Linux-i386-rhel-5-gtk2-python/bin/guile: error while loading shared libraries: requires glibc 2.5 or later dynamic linker It would be helpful to know how I can handle this problem. Thanks in advance. YoungJin
Re: [ccp4bb] Drawing reaction mechanism
xdrawchem is free and will do this. On May 31, 2012, at 8:01 PM, Appu kumar wrote: Dear ccp4 user, Sorry for offset question, Anyone please tell me the name of programme which can be used to draw enzyme reaction mechanism ( like Sn1 and Sn2). Your kind help will be much appreciated Thank you Appu
Re: [ccp4bb] Sad News
I thought it was some sort of allegory for tenure-track faculty positions. -- Bill On Feb 28, 2012, at 7:16 AM, Gerard Bricogne wrote: Dear Smita, For me, your story mostly illustrates the grave dangers of wanting to own a BMW while still in high school ... ;-) . With best wishes, Gerard. -- On Tue, Feb 28, 2012 at 09:02:42AM -0600, Smita Mohanty wrote: Yes, this is of course a scam. My husband was almost duped by someone who wrote in the name of a close friend saying that he got mugged in Europe and to send money to return to USA. My husband of course was ready to send for his colleague but just gave a call to his friend to make this not a scam. Of course, it was a scam. Only last night we saved ourselves from another scam. I think it is good share with the group. My son (in high school) found a 2005 BMW X5 on an internet site. The car's blue book price is $26,000 but the asking price by the seller is $2775. Sounds too good to be true. But when my son (who dreams to own a BMW) contacted the owner (Amanda Stone), she replied him immediately saying her son died two months back in an automobile accident hit by a drunk driver while riding his fiancee's car. She simply wants to sell the car so that someone else can use it and she is not interested in making money. She said that she has a deal with e-bay and that the car will be shipped by e-bay to the buyer once the buyer pays the price that will be hold by e-bay. The buyer has 5 days to check the car out and if decides not to buy, the car will be shipped back to e-bay at seller's cost and buyer gets back his money. She sent an invoice that was from e-bay with e-bay logo and exactly looking genuine. She sent car pictures and Vin and my husband checked the car out with car fax. She wanted the money to be sent to a e-bay financial expert through moneygram although she sent name and address of an e-bay expert. That is when my husband called up e-bay just to make sure before he send the moneygram out. That is when e-bay told him this is a scam and that e-bay never asks for moneygram. That all transactions are done on e-bay site only and that e-bay does not get any contract like the one we had. E-bay told us that their logo has/can be copied to make an invoice appears to have come from them. Of course, we went all communications and invoice to e-bay. We lost only $35 for car fax. Lesson: we need to be aware of any advertisements on internet or unsolicited e-mails. Here is a site to read about different scams- http://www.fbi.gov/scams-safety/be_crime_smart Thanks, Smita Vellieux Frederic frederic.velli...@ibs.fr 2/28/2012 7:01 AM From: regnicat@, reply to: regniica@... Somehow I don't believe someone in such a situation would write to ccp4bb instead of calling the family back home. Using Skype since there is apparently internet access ! And I rather view with my mind's eye someone sitting in an internet cafe in (say) Lagos, or the Paris suburbs or Kingston or... Fred Catherine Regni wrote: I'm writing this with tears in my eyes,my family and I came over here to Madrid,Spain for a short vacation. unfortunately,we were mugged at the park of the hotel where we stayed,all cash and credit card were stolen off us but luckily for us we still have our passports with us. We've been to the Embassy and the Police here but they're not helping issues at all and our flight leaves in few hours from now but we're having problems settling the hotel bills and the hotel manager won't let us leave until we settle the bills. Well I really need your financial assistance..Please, Let me know if you can help us out? Am freaked out at the Moment. Catherine Regni.. Catherine Regni, Ph.D.
Re: [ccp4bb] DNA length for crystallization
This paper is a favorite:http://www.ncbi.nlm.nih.gov/pubmed/2160019 J Mol Biol. 1990 May 5;213(1):159-66. Crystallization of Escherichia coli catabolite gene activator protein with its DNA binding site. The use of modular DNA. On Feb 15, 2012, at 12:06 AM, LISA wrote: Hi all, I have a DNA binding protein. I can get crystals when I mix 8-28 nt dsDNA with my protein. But neither of them has good diffraction. Some biochemical data said the longer of DNA, the tigher of the binding betwwen DNA and my protein. The binding is not sequence-specfic. Does anyone have suggestion of the optimization? What is the good length of DNA for crystallization? Thank you. Lisa
Re: [ccp4bb] All-D World
Hi Jacob: After giving this a great deal of reflection ….. I realized that you would face the same paradox that God had to resolve six thousand years ago at the Dawn of Creation, i.e., He needed D-deoxyribose DNA to code for L-amino acid proteins, and vice versa. Likewise, you would probably be faced with a situation where you need L-deoxyribose DNA to code for D-amino acid proteins, so once again, you need a ribozyme self-replicase to escape the Irreducible Complexity(™). (The Central Dogma at least is achiral.) At least it can be done six thousand years, which isn't unreasonable for a Ph.D. thesis project (especially when combined with an M.D.), and you, unlike Him, have access to a Sigma catalogue. All the best, Bill William G. Scott Professor Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA 228 Sinsheimer Laboratories University of California at Santa Cruz Santa Cruz, California 95064 USA On Feb 15, 2012, at 10:28 AM, Jacob Keller wrote: So who out there wants to start an all-D microbial culture by total synthesis, a la the bacterium with the synthetic genome a while back? Could it work, I wonder? I guess that would be a certain benchmark for Man's conquest of nature. JPK ps maybe if there is a broadly-acting amino-acid isomerase or set of isomerases of appropriate properties, this could be helpful for getting the culture started--or even for preying on the L world? On Wed, Feb 15, 2012 at 12:17 PM, David Schuller dj...@cornell.edu wrote: On 02/15/12 12:41, Jacob Keller wrote: Are there any all-D proteins out there, of known structure or otherwise? If so, do enantiomer-specific catalyses become inverted? JPK What do you mean by Out There? If you mean in the PDB, then yes. As of two weeks ago, there are ~ 14 racemic structures deposited; most in space group P -1, with one outlier in space group I -4 C 2. This includes RNA, DNA, and PNA, but 6 entries are actually protein. The longest is over 80 residues. Theoretically, enantiomer-specific catalysis ought to be inverted, but most of the structures solved are not enzymes. kaliotoxin, plectasin, antifreeze protein, monellin, villin, and a designed peptide. On the other hand, if by out there you meant in nature outside of biochemistry and organic chemistry labs; then no, I am not aware of any all-D proteins. There are a few protein/peptides which include a small number of D-residues, which is marked up to nonribosomal synthesis. The first paper I managed to Google: http://jb.asm.org/content/185/24/7036.full Learning from Nature's Drug Factories: Nonribosomal Synthesis of Macrocyclic Peptides doi: 10.1128/JB.185.24.7036-7043.2003 J. Bacteriol. December 2003 vol. 185 no. 24 7036-7043 If racemic crystallization isn't exciting enough for you, look into quasi-racemic crystallization. On Wed, Feb 15, 2012 at 8:05 AM, David Schuller dj...@cornell.edu wrote: Wukovitz Yeates (1995) Nature Struc. Biol. 2(12): 1062-1067 predicts that the most probable space group for macromolecular crystallization is P -1 (P 1-bar). All you have to do to try it out is synthesize the all-D enantiomer of your protein and get it to fold properly. On 02/14/12 18:36, Prem Kaushal wrote: Hi We have a protein that crystallized in P21212 space group. We are looking for some different crystal forms. We tried few things did not work. Now we are thinking to mutate surface residues. Anybody aware of any software which can predict the mutations that might help in crystallizing protein in different space group, please inform me. Thanks in advance Prem -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu ***
Re: [ccp4bb] 10 mM Na Acetate buffer preparation
http://en.wikipedia.org/wiki/Henderson–Hasselbalch_equation or any intro chemistry text William G. Scott Professor Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA 228 Sinsheimer Laboratories University of California at Santa Cruz Santa Cruz, California 95064 USA On Feb 3, 2012, at 6:42 PM, megha goyal wrote: Our recombinant product is formulated in 10 mM sodium acetate buffer at pH 4.0 and the std composition mentions sodium 0.035 mg and acetate 0.59 mg per ml of sample. It mentions Sodium acetate is formed by titrating glacial acetic acid with sodium hydroxide. Can anyone guide me on how this 10 mM buffer is prepared or on its calculation. What currently I do is the old method that we have been following i.,e Use 0.123 mg Na Acetate trihydrate + 0.476 µl Gl. Acetic acid, adjust pH to 4.0 using 5 N NaOH. But we do not know how these values have been arrived at and if this calculation is correct. Please guide me with this regards. Any help on this will be highly appreciated. thanks, Megha
Re: [ccp4bb] Coot on an SGI
Dear Gina: I think Coot 0.0.33 originated sometime early in the Nixon administration, and I finally parted with my SGIs a few years ago, so am not in a good position to advise. I seem vaguely to remember some non-canonical naming of the files. What happens if you make a symbolic link from the one you have to the one that is required? As I recall, coot on an SGI (at least on my R1, which I think has a processor almost as fast as that in my generation A iPod touch) was impossibly slow. By contrast, I can run the very latest svn revision of coot in stereo on a $270 Zalman monitor attached to a $600 mac mini. I'm sorry this doesn't answer your question, but I think an ancient version of coot on an ancient computer will just be a world of hurt. -- Bill William G. Scott Professor Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA 228 Sinsheimer Laboratories University of California at Santa Cruz Santa Cruz, California 95064 USA On Jan 26, 2012, at 8:59 AM, Clayton, Gina wrote: Hi there we are trying to install Coot onto one of our old SGIs and so we installed Coot 0.0.33 (IRIX). However when starting Coot, such as in the Coot (install) directory, we get an error message stating thatlib libgcc_s.so is required but can not be found. We have the sgi freeware gcc_lib installed (the link on the Coot page to sgi.freeware, is dead ) but can only find libgcc_a in our gcc_lib. Can someone tell us how we can get hold of the right library? Thanks so much for any help Gina NOTICE: This email message is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message.
Re: [ccp4bb] image compression
The mp3/music analogy might be quite appropriate. On some commercial music download sites, there are several options for purchase, ranging from audiophool-grade 24-bit, 192kHz sampled music, to CD-quality (16-bit, 44.1kHz), to mp3 compression and various lossy bit-rates. I am told that the resampling and compression is actually done on the fly by the server, from a single master, and the purchaser chooses what files to download based on cost, ability to play high-res data, degree of canine-like hearing, intolerance for lossy compression with its limited dynamic range, etc. Perhaps that would be the best way to handle it from a central repository, allowing the end-user to decide on the fly. The lossless files could somehow be tagged as such, to avoid confusion. Bill William G. Scott Professor Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA 228 Sinsheimer Laboratories University of California at Santa Cruz Santa Cruz, California 95064 USA phone: +1-831-459-5367 (office) +1-831-459-5292 (lab) fax:+1-831-4593139 (fax)
Re: [ccp4bb] not so good news (Steve Jobs RIP)
On Oct 5, 2011, at 5:52 PM, Bosch, Juergen wrote: http://www.apple.com/stevejobs/ May innovation continue to lead the future. Jürgen I've been quite saddened about this all evening. Even though we knew it was coming, it is still incredibly sad, especially at his age (only 56). Although I never met him, through OS X, he made a fairly significant impact upon my life and career development (such as it is). The advent of OS X has had a significant impact upon both my professional and personal lives. Although I have worked with unix systems since the mid 1980s, it was only when OS X came along, and I made the switch (from SGI's Irix, which many of us remember fondly as a total pig of an OS), did I really come to enjoy using computers. As a crystallographer, a unix operating system really is essential I think, and when OS X appeared, a fundamental change took place in my office as a young assistant professor: I only needed one computer. Before, I had an enormous SGI sitting on a table, for doing science. With its stereographic hardware and dials, it put me back (well, actually, the taxpayer) about $12K for an R10,000, which had a 150MHz RISC processor. The sony trinatron monitor did a good job heating the room, especially in the summer. Then I had this little colored hunk of plastic, the first generation bottom-of-the-line iMac, upon which I wrote my papers and grant proposals, sitting on my desk. This left very little room in my office to mope and feel sorry for myself, which my wife tells me are the only things I am good at. OS X came on an extra CD packaged with an iBook I bought just before the Sept 11th attack. I remember, because I gave my first presentation using OS X 10.0.3 or something like that on that day, in Grenada, Spain, right next to the Alhambra. It was the worst talk I ever gave, but it wasn't the fault of the software. I was excessively nervous, so much so that my arch-competitor I guess took pity and tried to calm me down. Maybe I sensed something bad was about to happen. Anyway, it was an inauspicious start. I eventually made it home and put it on that colored piece of plastic in my office and discovered it really was a real unix operating system, albeit in its infancy. I sort of got lost in it for months at a time, and was determined to get all of the software used in macromolecular crystallography running on OS X. O was about the only thing at the time that seemed ready. What evolved from that was a crystallography on os x website, which started off as a chronicle of my pain, which I seem to feel an almost moral obligation to share and inflict upon everyone around me. (I work at a university that, frankly, isn't very good at infrastructural support, to put it mildly, and I wound up having to learn to do everything the hard way, by myself.) I think it is fair to say that Steve Jobs and OS X were some of the main things that made this, and my survival, possible. I've primarily used OS X I guess from the bottom up, but at the same time I was a bit of an Apple fan-boy in the sense that I got the first iPod when it came out, the first iPod Touch, the first MacBook Air, the first iPad, etc. I've never regretted any of those purchases, nor the purchase of the 20 or so Apple computers that I've acquired for work and family over the last decade or so. My newest OS X adventure has been into computer audio. I really still don't know much of anything about it, but again Apple has made it an enjoyable experience. I bitch and moan about iTunes as much as the next guy, but if you stop to think about it, it transformed the entire music industry, and turned what began as a network of illegal file sharing (Napster), something I regrettably missed out completely, into a legitimate business model. Some might look at this as co-opting, but I think there is a bit more to it than that. In any case, both from the perspective of hardware and software, Apple/Jobs completely changed how I listen to music. During that same decade I was starting out as an academic scientist, I had more or less given up on music almost completely. My oldest son now likes music (Pearl Jam, Joy Division, REM), but at the time he couldn't handle listening to it at all, probably as a consequence of being somewhere on the autistic spectrum. OS X provided an escape from all that for me, but it eventually also provided a relief for him I think, and through it he came to enjoy (some) music and now plays cello and electric guitar. So, I guess Steve Jobs has had a large, albeit indirect, influence on my life, and that of my family and research group. I never met him, but I've learned a bit about him through a former VP. I doubt I would have liked him very much personally. Obsessive secrecy and temper tantrums aren't my favorite personality traits. But as I continue to age, I realize superficial likability isn't really that much of an asset. I'm kind of worried about
Re: [ccp4bb] Linux vs MacOS for crystallographic software
On Sep 28, 2011, at 5:26 PM, Jacqueline Vitali wrote: Dear colleagues, I need some advice for a new computer. (1) I have the option of an HP Z210 8 GB with a low end Quadro Nvidia 400 512 MB. --How does Coot run with this card? OK --I am happy with any Linux. However, the system needs updates for security purposes (the University requires it). Do I have to remake the NVidia driver every time there is a kernel update or is there a way around it for this NVidia card? Do you suggest another NVidia card (inexpensive) that is good for coot and automatically updates when the kernel is updated? Try Ubuntu (or Kubuntu or Xubuntu, etc). You can have Linux and proprietary drivers. (2) Second option is an IMAC 4 GB 2.5 GHz with AMD Radeon HD 6750M 512 MB GDDRS. --How does Coot work with this graphics card? OK --Should I get more memory for Lion? Max it out. Lion is a memory pig. --Is this platform advisable for crystallographic software for the next four years? It is essentially BSD unix. So it should be fine, unless they continue to lobotomize everything and make it into an iPod on a stick. Thank you in advance for any advice. Jackie Vitali Cleveland State University
Re: [ccp4bb] Desmond 3.0 Tutorial, Oct 5 in Boston, MA
On Sep 22, 2011, at 9:29 AM, Ben Eisenbraun wrote: Desmond 3.0 Tutorial 2.2 was quite impressive. (sorry.)
[ccp4bb] Rigaku high voltage tank
Hi Citizens: We seem to run through high voltage tanks on our Raxis IV like guano goes through a goose. Has anyone else had this problem, and, more importantly, what is the best way to protect them. I am assuming it might have something to do with our electrical supply, which is a bit unreliable. Also, does anyone have an extra used functional one they want to get rid of? We've run out of 7-11s to rob to pay for this, and our friendly and helpful radiation safety staff think the best way to deal with this problem is to hack apart the power cable, so it is a current (so to speak) source of frustration. Thanks in advance. Bill William G. Scott Professor Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA 228 Sinsheimer Laboratories University of California at Santa Cruz Santa Cruz, California 95064 USA
Re: [ccp4bb] Mac OSX 10.7 Lion
Dear Phil (and everyone): 1. I've now got automated build systems for coot for 10.7.1 and 10.6.8. I just haven't had a chance to get the 10.6.8 one on line. I'll try to do this today. (Also, the last few haven't build due to a change in the code with which the compiler can't cope, but hopefully that will be a thing of the past soon.) 2. Most things build on 10.6.X will run on 10.7.X. I haven't opened ccp4mg, but will give it a try after I wake up. 3. I've had trouble with stereo on coot with 10.7.1, but, oddly, the problem goes away if I have a second monitor. If you update to 10.7, keep a clone of 10.6 just in case it drives you nuts. There are all sorts of perverse changes, and (unlike the reversal in scrolling direction) not a lot of over-ride options. I guess this is a glimpse of the post-Jobs era, albeit one provided from an inconvenient vista. Peace and joy, Bill On Sep 16, 2011, at 6:33 AM, William G. Scott wrote: Dear Phil (and everyone): 1. I've now got automated build systems for coot for 10.7.1 and 10.6.8. I just haven't had a chance to get the 10.6.8 one on line. I'll try to do this today. (Also, the last few haven't build due to a change in the code with which the compiler can't cope, but hopefully that will be a thing of the past soon.) 2. Most things build on 10.6.X will run on 10.7.X. I haven't opened ccp4mg, but will give it a try after I wake up. 3. I've had trouble with stereo on coot with 10.7.1, but, oddly, the problem goes away if I have a second monitor. If you update to 10.7, keep a clone of 10.6 just in case it drives you nuts. There are all sorts of perverse changes, and (unlike the reversal in scrolling direction) not a lot of over-ride options. I guess this is a glimpse of the post-Jobs era, albeit one provided from an inconvenient vista. Peace and joy, Bill On Sep 16, 2011, at 5:48 AM, Phil Evans wrote: I use my MBP with external screen, keyboard mouse all the time. The new ones are fast, mine should easily cope with Lion My question about Lion was because 1. on the one hand as far as I can see Bill Scott only builds latest stand-alone Coots (0.7...) for Lion, and these don't work on 10.6 (is this true Bill?) 2. on the other hand, I had a report that ccp4mg doesn't work on Lion (is that true Stuart?) and I need both of these (and don't fancy building either myself) Phil (still on 10.6) On 11 Sep 2011, at 17:55, Sean Seaver wrote: Dear Herbert, I've come across quite a few people that are using mac books as their main development computer. This site ( http://usesthis.com/ ) can be an good way to learn about various setups. A popular trend seems to be using a mac book along with the apple thunderbolt display for more screen real estate. Take Care, Sean Seaver P212121 http://store.p212121.com/
Re: [ccp4bb] more Computer encryption matters
OS X 10.7 enables you to do whole-drive encryption. Here is a description from Arse Technica: http://arstechnica.com/apple/reviews/2011/07/mac-os-x-10-7.ars/13 I ain't never tried it myself. 10.7 seems to run slow enough as it is. -- Bill On Aug 18, 2011, at 5:34 AM, Andreas Förster wrote: Since we're on the subject... I've been tempted on and off to encrypt my hard drive, but after getting burned once a hundred years ago when encrypted data turned into garbled bytes all of a sudden I've been hesitant. I've gone so far as to install TrueCrypt (on a MacBook), but I haven't put it into action. Before I do, the big question: What software do people on the bb use for encryption? What can be recommended without hesitation? Thanks. Andreas On 18/08/2011 1:19, Eric Bennett wrote: John, Since so many people have said it's flawless, I'd like to point out this is not always the case. The particular version of the particular package that we have installs some system libraries that caused a program I use on a moderately frequent basis to crash every time I tried to open a file on a network drive. It took me about 9 months to figure out what the cause was, during which time I had to manually copy things to the local drive before I could open them in that particular program. The vendor of the encryption software has a newer version but our IT department is using an older version. There is another workaround but it's kind of a hack. So I'd say problems are very rare, but if you run into strange behavior, don't rule out encryption as a possible cause. -Eric -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk
Re: [ccp4bb] OSX Lion
On Jul 27, 2011, at 6:45 AM, Bosch, Juergen wrote: But Bill has updated his webpage http://sage.ucsc.edu/~wgscott/xtal/wiki/index.php/Lion_upgrade_notes
Re: [ccp4bb] fink unofficial fix for OSX 10.7 (Lion)
On Jul 22, 2011, at 4:24 AM, Xiaoguang Xue wrote: I noticed that the Fink repository will not run on the Lion system All the debian utilities work (as does the crystallography software), so it is just the fink perl wrapper script itself that doesn't work. Here is a cheap and easy, but unofficial, work-around: If you have everything in /sw, and it is 64-bit: curl -O http://psbmini.ucsc.edu/fink_intel_10.7_64bit_sw/debs/fink_0.31.99.cvs-20110723.1818_darwin-x86_64.deb sudo dpkg -i fink_0.31.99.cvs-20110723.1818_darwin-x86_64.deb If you have everything in /sw, gimmie about an hour, and you can do the same like this: curl -O http://psbmini.ucsc.edu/fink_intel_10.7_64bit_sw64/debs/fink_0.31.99.cvs-20110723.1818_darwin-x86_64.deb sudo dpkg -i fink_0.31.99.cvs-20110723.1818_darwin-x86_64.deb
Re: [ccp4bb] Coot Bad magic number errors
Sorry about this. Issue the command sudo perl -pi -e 's|/System/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6\:/System/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5\:||g' /Library/Coot/bin/coot and that will fix it. I'll make a new one. Bill On Mar 10, 2011, at 7:55 AM, Sampson, Jared wrote: Hi all - Two of the grad students in our structural biology course are having similar problems installing Coot on their Mac computers using the stand-alone packageshttp://sage.ucsc.edu/~wgscott/xtal/wiki/index.php/Stand-Alone_Coot from Bill Scott's Crystallography on OS X website. I've pasted the Terminal outputs below from each of their machines below. They're both getting Python magic number errors, which from what I know result from one Python version trying to run a .pyc file created with another Python version, but I'm not sure exactly how to work around it in the context of the stand-alone package. The students aren't planning to do much in the structural realm outside the course, and I don't want to have to go through installing Xcode and Fink to compile on their own, since they probably won't need it much past this one assignment. Any suggestions would be greatly appreciated. Thanks! Jared Sampson First student (3 week-old Macbook Pro, 10.6.6, stand-alone package for Version 0.6.2-pre-1-3250) $ coot Acquiring application resources from /Library/Coot/share/coot/cootrc INFO:: splash_screen_pixmap_dir /Library/Coot/share/coot/pixmaps INFO:: Colours file: /Library/Coot/share/coot/colours.def loaded There are 118 data in /Library/Coot/share/coot/lib/data/monomers/list/mon_lib_list.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/a/ALA.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/a/ASP.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/a/ASN.cif [... and a bunch more monomers ...] There are 2 data in /Library/Coot/share/coot/lib/data/monomers/u/UR.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/h/HOH.cif There are 1 data in /Library/Coot/share/coot/lib/data/monomers/ener_lib.cif sbase monomer dir: /share/sbase sbase files not found in /share/sbase Reading coordinate file: /Library/Coot/share/coot/standard-residues.pdb PDB file /Library/Coot/share/coot/standard-residues.pdb has been read. Spacegroup: P 1 Cell: 40.631 109.18 93.243 90 90 90 initalize graphics molecules...done. (filter-fileselection-filenames-state) (get-active-map-drag-flag) ImportError: Bad magic number in /System/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site.pyc second student (Macbook, 10.6.5, also Version 0.6.2-pre-1-3250) $ /usr/local/bin/coot Acquiring application resources from /Library/Coot/share/coot/cootrc INFO:: splash_screen_pixmap_dir /Library/Coot/share/coot/pixmaps INFO:: Colours file: /Library/Coot/share/coot/colours.def loaded There are 118 data in /Library/Coot/share/coot/lib/data/monomers/list/mon_lib_list.cif/ There are 2 data in /Library/Coot/share/coot/lib/data/monomers/a/ALA.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/a/ASP.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/a/ASN.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/c/CYS.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/g/GLN.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/g/GLY.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/g/GLU.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/p/PHE.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/h/HIS.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/i/ILE.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/l/LYS.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/l/LEU.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/m/MET.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/e/ETH.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/c/CIT.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/a/AR.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/a/AD.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/c/CR.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/c/CD.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/g/GR.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/g/GD.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/t/TD.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/u/UR.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/h/HOH.cif There are 1 data in /Library/Coot/share/coot/lib/data/monomers/ener_lib.cif sbase monomer dir:
Re: [ccp4bb] Detaching crystals from glass cover slides
Hi Wataru: I hope all is well. For the ones you already have grown, try very gently prying them off with a wedge-shaped needle. If you can grow more, try using a very thin smooth layer of vacuum grease, and apply the drop to that. I managed to get RNA crystals to grow that way that otherwise irreversibly adhered to the surface. All the best, Bill On Feb 8, 2011, at 6:06 PM, Wataru Kagawa wrote: Hi all, I have crystals growing by the hanging-drop method, using 24-well VDX plates and Hampton Research siliconized glass cover slides. Most crystals are attached to the cover slide, and I am having difficulties detaching the crystals (using a cryoloop) without breaking them. There are few smaller crystals floating in the drop, and they diffract X-rays pretty well (clean spots, ~3.5A resolution using RAXIS). However, I would like to try the bigger ones, because they may diffract to a higher resolution. Any suggestions for detaching crystals from cover slides will be greatly appreciated. Wataru
Re: [ccp4bb] Mg2+ or water
On Dec 20, 2010, at 1:16 PM, jlliu liu wrote: it is also within hydrogen bonding distance to the main chain N of another protein residue. This also strongly suggests it is not Mg2+, which prefers hard ligands such as charged oxygen, rather than softer ligands like uncharged backbone nitrogens (the interactions are primarily electrostatic, rather than orbital-mediated).
Re: [ccp4bb] CCP4 hey
On Dec 3, 2010, at 3:11 AM, U US wrote: Hello CCP4, long time no see! I wanted to show you this article. I've made over $2k in the past month and I barely work 4 hours a day. Grad school was the best 13 years of my life, too.
Re: [ccp4bb] vector and scalars
As usual, the Omniscient Wikipedia does a pretty good job of giving the standard mathematical definition of a vector: http://en.wikipedia.org/wiki/Vector_space#Definition If the thing fulfills the axioms, it's a vector. Complex numbers do, as well as scalars. It is a bit more complicated, unfortunately. cf: http://en.wikipedia.org/wiki/Complex_number#The_complex_plane http://en.wikipedia.org/wiki/Complex_number#Real_vector_space
Re: [ccp4bb] embarrassingly simple MAD phasing question (another)
On Oct 14, 2010, at 7:40 AM, Ed Pozharski wrote: On Thu, 2010-10-14 at 08:41 +0200, Tim Gruene wrote: This sounds as though you are saying that a single photon interacts with several electrons to give rise to a reflection. Not only with several - it shouldn't be much of an exaggeration to say that the photon senses all the electrons in the Universe as it travels between the source and detector. Once it hits detector, it's trajectory magically collapses into a specific one. Quantum physics is undeniably crazy stuff :) Cheers, Ed. Less ephemerally, the photon scatters from every scattering center in the crystal lattice. Under these (incoherent scattering) experimental conditions, it is my understanding that the individual photon only interferes with itself. The quantum weirdness creeps in from the fact that the wave describing the scattering is spherically symmetric, sampled by the reciprocal lattice. But if a photon is a particle, and you were to do a single photon experiment, the particle of light can only wind up in one of the diffraction spot locations, but the diffracted wave determines the propensity of the photon to wind up in that location. It is basically the generalization of the single photon double-split paradox. I've found the headaches start to go away if you don't take the duality part of wave-particle duality too seriously. -- Bill
Re: [ccp4bb] embarrassingly simple MAD phasing question (another)
On Oct 14, 2010, at 2:31 PM, Tim Gruene wrote: I would like to understand how the notion of a photon being scattered from all electrons in the crystal lattice explains the observation that radiation damage is localised to the size of the beam so that we can move the crystal along and shoot a different location. Modify it to all points in the lattice bathed in the beam. The double slit paradox is actually not a paradox, I agree with that, but for different reasons than what follows ... and a single photon is not scattered by both slits: if you reduce the light intensity so that you really detect single photons, you observe that each photon decides on exactly one slit that it goes through. Really? Why do you get interference fringes then? You need two (or more) slits to create the interference pattern, and the location of the subsidiary maxima in the interference pattern do not change with the intensity of the light source. If you dim it to the point where one photon per second emerges, and you wait long enough, you still get the identical interference pattern. You do not observe single-slit diffraction. However, if you put your used chewing gum in one of the slits, the pattern changes to that of a single-slit experiment. It is only the sum of many photons that create the typical pattering of the double slit experiment. No. That is false. That would give you the scalar sum of two intensity peaks with no interference patterns. You have to add the amplitudes with phases, not the intensities, to get the interference pattern. The photon knows it is both wave and particle, but depending on the experiment we carry out we observe only one of the two phenomena, but never both. That's also the idea behing Schroedinger's cat. Schrödinger actually developed the cat gedanken-experiment to illustrate that the conventional (Copenhagen) interpretation leads to absurd conclusions. But it sounds like you are talking about the Heisenberg uncertainty principle or scatter relation. Sure, you can observe both, or we couldn't count photons in individual diffraction spots (which is what we do when we measure their intensities). The scatter relation simply means you can't measure both simultaneously to arbitrary precision.
Re: [ccp4bb] [QUAR] Re: [ccp4bb] embarrassingly simple MAD phasing question (another)
On Oct 14, 2010, at 2:28 PM, Jacob Keller wrote: I have always found this angle independence difficult. Why, if the anomalous scattering is truly angle-independent, don't we just put the detector at 90 or 180deg and solve the HA substructure by Patterson or direct methods using the pure anomalous scattering intensities? Or why don't we see pure anomalous spots at really high resolution? I think Bart Hazes' B-factor idea is right, perhaps, but I think the lack of pure anomalous intensities needs to be explained before understanding the angle-independence argument. JPK Yo Jacob: I think one thing that got ignored as I followed the other irrelevant tangent is what f and F are. f is the atomic scattering factor, and F is the corresponding Fourier sum of all of the scattering centers. This holds for f_0 vs. F_0, f' vs. F' and f vs. F. The spots we are measure correspond to the capital Fs. Just like we add the f_o for each scatterer together and we get a sum (F) that has a non-zero phase angle, this also holds for F (that is the part I missed when I posted the original question my student asked me). The full scattered wave isn't given by f by the way. It is (1/r) * f(r) * exp(ikr) so the intensity of the scattered wave will still tail off due to the that denominator term (which is squared for the intensity). That holds for f_o, f' and f unless I missed something fundamental. People tend to forget that (1/r) term because we are always focusing on just the f(r) scattering factor. -- Bill
Re: [ccp4bb] embarrassingly simple MAD phasing question (another)
On Oct 13, 2010, at 4:21 PM, Jacob Keller wrote: While we are on embarrassingly simple questions, I have wondered for a long time what is the reference phase for reflections? I.e. a given phase of say 45deg is 45deg relative to what? Is it the centrosymmetric phases? Or a theoretical wave from the origin? Conventionally, the phase difference is defined in terms of the path difference between the path traveled by a photon scattering from a point at the origin and a photon scattering from a point displaced by some finite amount (usually a multiple of a unit cell vector) from the origin. The key is the only physically meaningful quantity is the difference in path length, not the absolute values. Hence, if that difference is zero, then the phase angle will be zero. So it is compared to the wave from the origin (which is not theoretical, although by the theory we use -- the First-Order Born Approximation -- it appears to violate conservation of energy. Fortunately, the beamstop prevents us from having to face that horrific reality.) -- Bill
Re: [ccp4bb] Summary : [ccp4bb] embarrassingly simple MAD phasing question
On Oct 13, 2010, at 3:09 PM, Tim Gruene wrote: Dear Bill, The discussion is becoming complicated because of the mixing of notations. There is a theory or model which describes the atomic scattering factor as f = f0 + f' +if from which the structure factor is calculated. That right angle that you see in the picture you sent us with that link is a consequence of that factor i in if, therefore I would not call it a fundamental requirement. Dear Tim: Sorry, I mean that it was a fundamental requirement (restriction) that the absorption term must remain 90 degrees out of phase with the dispersive term, regardless of the absolute phase angle of their resultant. (And it must be retarded, due to absorption and conservation of energy, as Bernhard pointed out). Now as you displace that particular atom from the origin, all three components receive the same phase which leaves Fa and Fa in the same relative orientation. That is what I was trying to say. (But on the drive home from work, I was plagued by renewed doubt, for why then would there be a relative angle between f0 and f' that was anything but 0 degrees or 180 degrees?) That sounds pretty much like your explanation, but I have the impression that we have different notions of the sources of effects. I started to reply to emails in the inverse order I received them, realized I had forgotten to go to a boring meeting that in the end never went down anyway, and mixed notation from that email and the figure (or my false memory of the figure). This could be, though, like a discussion about whether the chicken or the egg came first, meaning that neither is more or less correct than the other. Maybe to better understand your question you could explain what you think the origin ior source of that image actually is (technically, not in terms of copyright). Google image search. Someone pointed out it was Bernhard's originally. (Sorry!) My understanding of the origin of the effect illustrated in the figure is roughly as follows: 1. We treat X-ray scattering using the assumptions inherent in the First-Order Born Approximation to elastic scattering (the photon interacts with an electron described by a spherically symmetric potential that is purely real). The photon scatters once, and elastically, so the atomic scattering factor is simply the Fourier Transform of the spherically symmetric (real) potential, or, using a couple of algebra steps and Poisson's equation, it is the Fourier Transform of the (real) electron density. The reality and symmetry of the potential ultimately are manifested in Friedel symmetry. The scattering from a spherically symmetric potential (not an electron per se) at the origin has a purely real amplitude and a phase of 1 (phase angle of zero) and nonzero phase angles result from displacement of the real scattering potential from the origin, so for elastic (non-absorptive) scattering, the resultant phase is a consequence purely of spatial displacement. Hopefully I am right so far ... 2. Within the confines of the approximation we use (or, equivalently, Fraunhofer Diffraction, if you want to stick to a purely classical treatment), absorption is modeled with a complex potential. The imaginary term added to the potential could account for both emission and absorption, but conservation of energy dictates it be the latter (hence the absolute value of the orientation of f). There is a good treatment of this in James; Blundell and Johnson glosses over the some of the essential steps in the derivation. But the main point is that the F (the imaginary component) arises as a consequence of absorption, which we model as a complex potential. This is distinct from what arises from path length displacement. In a centrosymmetric structure, all phase angles are either 0degree or 180degree whyfore - as you already point out - the additional anomalous term does not affect the validity of Friedel's law. For basically the same reason you would not detect an anomalous signal from a crystal containing only one element, irrespective of the values of f' and f. The link you sent, by the way, rises the impression that in the absence of anomalous scattering phi(F) = phi(-F), but this should read phi(F) = -phi(-F). Furthermore the abbreviation -F instead of F(-h-k-l) is also misleading because F(-h-k-l) is not the same as -F(hkl). Here's the figures I made that I actually used in my lecture. I realize now the way I made the first one set me up for this confusion: http://sage.ucsc.edu/~chem200a/2009/slides/diffraction_004/diffraction_004.html_files/diffraction_004.022-001.jpg http://sage.ucsc.edu/~chem200a/2009/slides/diffraction_004/diffraction_004.html_files/diffraction_004.023-009.jpg These are actually composite images of several-step slides, and for some reason a couple of labels didn't appear when I exported from Keynote, so I looked for something else with
Re: [ccp4bb] OSX 10.6, Fink CCP4 install problem
Hi David: I think you need to start with the pure 64-bit fink from cvs in order to get this to work. All the errors are a consequence of using the 32-bit version. You can't mix them. I have no idea why they still don't have a binary installer, but they don't. Email me directly if you need more info. I'm on my way home, somewhere obscure that I can't pronounce in Northern California that appears to have been carefully preserved in leucite since the day Jerry Garcia became Dead, so it might take a day or so to respond... Bill David Shin wrote: Hi - Got a new computer, was trying to install CCP4 following the Scott Lab page (64 bit install) - http://sage.ucsc.edu/~wgscott/xtal/wiki/index.php/64-bit_Fink_for_10.5_and_10.6 First had to install fink - tried to follow that page, but didn't have the cvs command (forgot about the xcode, etc.). So installed Fink via: http://www.finkproject.org/download/srcdist.php This install put fink into the sw/ directory, not sw64/ So after fink was running, I went back to the http://sage.ucsc.edu/~wgscott/xtal/wiki/index.php/64-bit_Fink_for_10.5_and_10.6 page, and started from For now on, I will use /sw* to mean /sw or /sw64 as appropriate. ie. edited files: When it is done, edit /sw*/etc/fink.conf and change line 4 to look like this: ## Trees: local/main stable/main stable/crypto unstable/main unstable/crypto This activates the unstable branch. Then issue source /sw*/bin/init.sh fink selfupdate-cvs fink -y update-all fink scanpackages # everything was fine until I did this: First you need to edit the /sw64/etc/apt/sources.list file and add the following three lines to the bottom of that file (I changed the sources.list file in the sw/ directory) # deb http://sage.ucsc.edu/fink_intel_10.6_64bitstable main crypto deb http://sage.ucsc.edu/fink_intel_10.6_64bit unstable main crypto deb http://sage.ucsc.edu/fink_intel_10.6_64bit local main then wehn I tried to install coot and ccp4 using the next part: # fink scanpackages sudo apt-get update sudo apt-get dist-upgrade sudo apt-get install coot # I found out I killed fink. ie. here's the error message after running fink scanpackages: ERROR: Configuration file /sw64/etc/fink.conf not found. /sw/bin/dpkg: error processing fink (--configure): subprocess post-installation script returned error exit status 1 Errors were encountered while processing: fink E: Sub-process /sw/bin/dpkg returned an error code (1) I see that the previous edit made the update look for something in /sw64/ which of course didn't exist, but now my version of fink is dead... ie. I type fink scanpackages, or any fink command, and the command is not found. I type which fink and nothing returns, but everything is still in the sw/ directory. What do you think? now that I have the cvs command up and going, I just delete the sw/ directory and start over, or is there some fix I can do? Thanks, Dave
Re: [ccp4bb] imosflm conflict with mosflm (OS X/fink 32-bit)
Dear Engin: I've put placeholder packages for those entitled imosflm-aqua and mosflm in fink CVS that simply point back to what is in ccp4. The imosflm package remains a placeholder with dependencies on all the X11-based tcl/tk extensions required to get imosflm in ccp4 to work with an X11 display (which you might need if you don't have OS X 10.6, or if you want to remote-display the GUI). All the best, Bill On Jul 6, 2010, at 2:13 PM, Engin Özkan wrote: Thanks for clearing that. Setting the mosflm executable to the ccp4 version, in combination with either the fink or the system wish, gives a nicely working imosflm. And thanks for the fink packages... Engin On 7/6/10 6:36 AM, William G. Scott wrote: Remove both. On OS X, 10.6, imosflm uses the tcl/tk supplied with OS X, and the latest mosflm is in ccp4, so there is no need for any of that. Just use what is in ccp4. Sorry for this. On Jul 5, 2010, at 4:34 PM, Engin Özkan wrote: Hi everybody, I was doing a regular fink update (OS X 10.6.4, 32-bit fink) when I encountered a silly outcome, which I thought others might have observed. During the imosflm update, I get an error saying that imosflm depends on mosflm, and it also conflicts with mosflm at the same time. This was my list of mosflm-related packages: % fink list mosflm Information about 9265 packages read in 0 seconds. (i) imosflm 1:1.0.4-3 Installs mosflm GUI for use with X11 TclTk imosflm-aqua 1:1.0.4-3 Installs mosflm GUI for use with aqua TclTk i mosflm7.0.6-2X-ray data processing, large display And below is the error. A workaround is removing mosflm, and using ipmosflm from the ccp4 installation. Is any of this expected with these two packages under fink? Best, Engin The package 'imosflm' will be installed. Reading dependency for imosflm-1.0.4-3... The following package will be installed or updated: imosflm Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/unstable/main/binary-darwin-i386/sci/imosflm_1.0.4-3_darwin-i386.deb dpkg: considering removing mosflm in favour of imosflm ... dpkg: no, cannot remove mosflm (--auto-deconfigure will help): imosflm depends on mosflm (= 7.0.6) mosflm is to be removed. dpkg: regarding .../imosflm_1.0.4-3_darwin-i386.deb containing imosflm: imosflm conflicts with mosflm mosflm (version 7.0.6-2) is installed. /sw/bin/dpkg: error processing /sw/fink/dists/unstable/main/binary-darwin-i386/sci/imosflm_1.0.4-3_darwin-i386.deb (--install): conflicting packages - not installing imosflm Errors were encountered while processing: /sw/fink/dists/unstable/main/binary-darwin-i386/sci/imosflm_1.0.4-3_darwin-i386.deb ### execution of /sw/bin/dpkg-lockwait failed, exit code 1 Failed: can't install package imosflm-1.0.4-3 -- Engin Özkan Post-doctoral Scholar Laboratory of K. Christopher Garcia Howard Hughes Medical Institute Dept of Molecular and Cellular Physiology 279 Campus Drive, Beckman Center B173 Stanford School of Medicine Stanford, CA 94305 ph: (650)-498-7111 -- Engin Özkan Post-doctoral Scholar Laboratory of K. Christopher Garcia Howard Hughes Medical Institute Dept of Molecular and Cellular Physiology 279 Campus Drive, Beckman Center B173 Stanford School of Medicine Stanford, CA 94305 ph: (650)-498-7111
Re: [ccp4bb] imosflm conflict with mosflm (OS X/fink 32-bit)
Remove both. On OS X, 10.6, imosflm uses the tcl/tk supplied with OS X, and the latest mosflm is in ccp4, so there is no need for any of that. Just use what is in ccp4. Sorry for this. On Jul 5, 2010, at 4:34 PM, Engin Özkan wrote: Hi everybody, I was doing a regular fink update (OS X 10.6.4, 32-bit fink) when I encountered a silly outcome, which I thought others might have observed. During the imosflm update, I get an error saying that imosflm depends on mosflm, and it also conflicts with mosflm at the same time. This was my list of mosflm-related packages: % fink list mosflm Information about 9265 packages read in 0 seconds. (i) imosflm 1:1.0.4-3 Installs mosflm GUI for use with X11 TclTk imosflm-aqua 1:1.0.4-3 Installs mosflm GUI for use with aqua TclTk i mosflm7.0.6-2X-ray data processing, large display And below is the error. A workaround is removing mosflm, and using ipmosflm from the ccp4 installation. Is any of this expected with these two packages under fink? Best, Engin The package 'imosflm' will be installed. Reading dependency for imosflm-1.0.4-3... The following package will be installed or updated: imosflm Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/unstable/main/binary-darwin-i386/sci/imosflm_1.0.4-3_darwin-i386.deb dpkg: considering removing mosflm in favour of imosflm ... dpkg: no, cannot remove mosflm (--auto-deconfigure will help): imosflm depends on mosflm (= 7.0.6) mosflm is to be removed. dpkg: regarding .../imosflm_1.0.4-3_darwin-i386.deb containing imosflm: imosflm conflicts with mosflm mosflm (version 7.0.6-2) is installed. /sw/bin/dpkg: error processing /sw/fink/dists/unstable/main/binary-darwin-i386/sci/imosflm_1.0.4-3_darwin-i386.deb (--install): conflicting packages - not installing imosflm Errors were encountered while processing: /sw/fink/dists/unstable/main/binary-darwin-i386/sci/imosflm_1.0.4-3_darwin-i386.deb ### execution of /sw/bin/dpkg-lockwait failed, exit code 1 Failed: can't install package imosflm-1.0.4-3 -- Engin Özkan Post-doctoral Scholar Laboratory of K. Christopher Garcia Howard Hughes Medical Institute Dept of Molecular and Cellular Physiology 279 Campus Drive, Beckman Center B173 Stanford School of Medicine Stanford, CA 94305 ph: (650)-498-7111
Re: [ccp4bb] imosflm conflict with mosflm (OS X/fink 32-bit)
Dear Harry et al: I'm sorry, I've been immersed in grant renewal/resubmission hell. I obviously screwed something up in a rush. Briefly, if you have 10.6.X, ccp4 and OS X have everything you need for a nice, fully-functioning OS X aqua imosflm gui. Bill PS: The 64-bit ccp4 and mosflm work great. On Jul 6, 2010, at 3:25 AM, Harry Powell wrote: Hi Engin This is almost certainly a Bill Scott issue, so you'll have to wait until he reads his e-mail this morning! Unfortunately, the Mosflm developers (i.e. me) have no experience of setting Fink dependencies so we can't help you. We don't use Fink for our distros of iMosflm and Mosflm, and have no plans to do so. On 5 Jul 2010, at 23:34, Engin Özkan wrote: Hi everybody, I was doing a regular fink update (OS X 10.6.4, 32-bit fink) when I encountered a silly outcome, which I thought others might have observed. During the imosflm update, I get an error saying that imosflm depends on mosflm, and it also conflicts with mosflm at the same time. This was my list of mosflm-related packages: % fink list mosflm Information about 9265 packages read in 0 seconds. (i) imosflm 1:1.0.4-3 Installs mosflm GUI for use with X11 TclTk imosflm-aqua 1:1.0.4-3 Installs mosflm GUI for use with aqua TclTk i mosflm7.0.6-2X-ray data processing, large display And below is the error. A workaround is removing mosflm, and using ipmosflm from the ccp4 installation. Is any of this expected with these two packages under fink? Best, Engin The package 'imosflm' will be installed. Reading dependency for imosflm-1.0.4-3... The following package will be installed or updated: imosflm Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/unstable/main/binary-darwin-i386/sci/imosflm_1.0.4-3_darwin-i386.deb dpkg: considering removing mosflm in favour of imosflm ... dpkg: no, cannot remove mosflm (--auto-deconfigure will help): imosflm depends on mosflm (= 7.0.6) mosflm is to be removed. dpkg: regarding .../imosflm_1.0.4-3_darwin-i386.deb containing imosflm: imosflm conflicts with mosflm mosflm (version 7.0.6-2) is installed. /sw/bin/dpkg: error processing /sw/fink/dists/unstable/main/binary-darwin-i386/sci/imosflm_1.0.4-3_darwin-i386.deb (--install): conflicting packages - not installing imosflm Errors were encountered while processing: /sw/fink/dists/unstable/main/binary-darwin-i386/sci/imosflm_1.0.4-3_darwin-i386.deb ### execution of /sw/bin/dpkg-lockwait failed, exit code 1 Failed: can't install package imosflm-1.0.4-3 -- Engin Özkan Post-doctoral Scholar Laboratory of K. Christopher Garcia Howard Hughes Medical Institute Dept of Molecular and Cellular Physiology 279 Campus Drive, Beckman Center B173 Stanford School of Medicine Stanford, CA 94305 ph: (650)-498-7111 Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 0QH
Re: [ccp4bb] Cryo tongs/manipulator
When searching, avoid the almost overwhelming temptation to spell it as vile manipulator or you will just wind up with a listing of university administrators. Bandaranayake, Rajintha wrote: Hello all, Does anyone know where one could purchase cryo-vial tongs/manipulatos with the plastic coated handles (See attached image)? We have checked with Blake Industries (where I think we originally got them eons ago), however their new catalog does not list them any more. Thanks in advance. -Rajintha
[ccp4bb] Off-topic: Univ California boycott of Nature publishing group
Hi folks: Sorry about the off-topic nature (so to speak) of this post, especially given that it is not yet Friday, but I am interested what our community thinks of this: http://library.ucsc.edu/sites/default/files/Nature_Faculty_Letter.pdf Something similar happened with UC and Cell Press a few years ago. I worry about the monopolistic tendencies of these journals, but I also worry about the consequences of trying to restrict faculty, students, postdocs, etc from publishing where they see fit. (Admittedly our department already holds it against you if you publish in Nature, so this may be a bit of a moot point.) At the very least, it should be amusing to watch the two beasts do battle. Well? -- Bill
Re: [ccp4bb] Should I be worried about negative electron density?
On May 18, 2010, at 4:13 PM, Jay Pan wrote: Hello Everyone, I have a reasonably well fitted electron density map through molecular replacement. However, there is always some red region left no matter how hard I tried when the mtz file is loaded into Coot. Is this because my model is still not good enough or it’s natural to most model fittings. Negative density (with absolute value above 2 sigma) sitting on atoms is much more of a concern than random negative peaks floating in the solvent breeze, as it indicates misplacement of the model. In another word, should I be worried about the red region? Thanks in advance. I've alway found it very helpful to worry about absolutely everything obsessively to the point where it causes endoderm to bleed. Which is why, I suppose, Paul chose red. Jay
Re: [ccp4bb] Please remove me from this list
Although not as dramatic, there is a simple, private, method one can use to unsubscribe, and it possesses the additional merit of actually doing what you want: http://www.ccp4.ac.uk/ccp4bb.php Colapietro, Anne-Marie wrote: Please remove me from this list. Thank you, Anne-Marie -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Randy Byrne Sent: Sunday, April 25, 2010 6:39 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Please remove me from this list __ This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you have received this email in error please notify the originator of the message. Any views expressed in this message are those of the individual sender, except where the sender specifies and with authority, states them to be the views of Malvern Instruments. http://www.malvern.com __
Re: [ccp4bb] Rejected posting to CCP4BB@JISCMAIL.AC.UK
Yo Hari: The symbolic link won't solve the problem. I managed to scrape together a blt for tcltk 8.5 on OSX, so it is possible. Most of the hacks in turn came from a different Linux distro (gentoo) so it should be possible on ubuntu. Here by the way is the patch: http://fink.cvs.sourceforge.net/viewvc/fink/dists/10.4/unstable/main/finkinfo/x11/blt-x86_64.patch debian and ubuntu distribute blt without the bltwish executable, and I apparently put a huge weed up their arse a couple of years ago by reporting this as a bug. They are totally inflexible. Like IT support people, the maintainers think you work for them rather than vice versa. It might be worth flooding them with complaints and bug reports. Bill On Apr 14, 2010, at 7:49 AM, hari jayaram hari...@gmail.com wrote: Hi Tim, Thanks a tonne Tim for the pointer on how bltwish is handled in debian. A symlink from /usr/bin/wish to /usr/bin/bltwish. Seems to at-least start ccp4i. Now to see if it will also plot my graphs Hari
Re: [ccp4bb] low resolution phasing protocols
This was done in total despair: http://sage.ucsc.edu/scottlab/reprints/2008_Scott_ActaCrystD.pdf Francis E Reyes wrote: Hi all I'm in search of literature *detailing* low resolution [4-5A] phasing protocols. Heck I'll take detailed thesis chapters (since they tend to be more detailed than pubs anyway). If you ribosome people are on this board I'd love to hear from you. [sarcasm]Searching for 'grasping at straws', 'last ditch efforts', 'making something out of nothing' failed to yield anything productive[/sarcasm]. By detailed I'm hoping for discussions on how the authors knew progress was being made, software and scripts used, etc. Thanks! FR - Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D
Re: [ccp4bb] linux question
On Feb 28, 2010, at 5:11 PM, Damon Colbert wrote: I have a persistent Kubuntu 8.10 .. it took a week to work out some problems. The main one being that with limited space on the thumb drive, one cannot do a complete update of Kubuntu. Therefore many libraries are missing and dependancy errors crop up during crystallography software installation. You might want to look at Xubuntu. It uses the rather more lightweight xfce4 windowing system, which is nice and simple and basic and lightweight and clean and responsive. I prefer it over kde and gnome, even on hardware that can easily handle the overhead of all the extra features.
Re: [ccp4bb] linux question
On Feb 27, 2010, at 7:10 PM, David Roberts wrote: I have a quick question about linux for all. Is there anybody running a windows pc with linux on a bootable cd or bootable drive/flash drive/??? that works for crystallography apps? I have a colleague who does molecular dynamics calculations and he needs some conversion programs that are unix based (not pc based - they just haven't been ported and that's not my area). We have linux computers that he can use, but I thought in the end it might be easiest if he could just boot up a linux flash drive to run his conversion, then go back to his pc and windows. Something like damn small linux or ?? Any thoughts on this? Thanks Dave A slightly different approach would be to install Cygwin, and then you can do unixy things within windoze. http://www.cygwin.com/
Re: [ccp4bb] slow graphic in mac 10.6
Dear Rui: Did you by any chance install an old ppc version of X11 onto an intel machine? If so, it might be running via Rosetta, which is an emulator provided for transition, but could account for lousy performance. OS X 10.6 comes with X11 installed by default, so you might have clobbered it with something else if you installed X11. If that is the case, simply reinstalling the X11 on the 10.6 install disk should fix your problem. Also, run the command file /whatever/path/to/bin/coot-real If it returns Mach-O executable ppc then you need to use an intel-compatible coot for best performance. HTH, Bill On Feb 12, 2010, at 9:10 PM, rui wrote: HI,Dear All, sorry for this non-crystallgraphic question, but I think people here may know how to fix this problem. Several days ago, I posted a question about slow coot in my mac and people suggested me change some settings in coot which does help. However, I still feel something is wrong. I noticed the slow speed when I installed x11,( I switched from ppc to macpro and need to reinstall x11 and coot etc ). Since then, I noticed that when I open a terminal , it's very slow and if I type glxgears, it only shows about 1400 FPS. If I open pymol, I can actually see the images are flashing. Does anyone know why? Thanks a bunch. Rui
Re: [ccp4bb] Displaying electron density in PYMOL
You have to make sure the asymmetric unit for the maps is the same as for your molecule (which it probably isn't). The easiest way is to extend the map so it covers all the atoms with a few angstrom border. Coot calculates the map on the fly from the mtz file (I am guessing this is the difference) so you don't run into this problem. Raja Dey wrote: Hi, I need someone expert in PYMOL. I am getting a trouble to prepare a figure to display electron density for some water molecules. I can see clear density in COOT at sigma level 2.5. But, I could not see the density in PYMOL even at sigma level 1.0 Here is what I have done in PYMOL 1. fileâ¦â¦.open â¦â¦..pdb and map files. I can see these two objects on the right column. 2. Then I selected the waters for which I want to display the electron density and created an object named âwatâ 3. In the command line I wrote âisomesh mesh1, 3fo2fc.map, 1.0, wat, carve=1.6â and it creates an object âmesh1â that shows the electron density of some of the waters (not all) selected in âwatâ. I tried with other sigma levels, but the problem persists. I could not understand why for some waters electron density did not show up in PYMOL, but it does in COOT. I also noticed the same problem remains for part of this molecule, not just for some waters. I checked the pdb file, which looks fine and have the standard format. Does anyone have any idea, whatâs going wrong? Thanks⦠Raja Your Mail works best with the New Yahoo Optimized IE8. Get it NOW! http://downloads.yahoo.com/in/internetexplorer/
Re: [ccp4bb] Alternatives to ChemDraw 3D?
On Feb 7, 2010, at 11:13 PM, Wataru Kagawa wrote: Hi all, I would like to create a pdb file for a chemical compound (FW ~600) that was created in our chemistry department. ChemDraw 3D appears capable of doing this, but I would like to know if there are free alternatives that work great on Macs. Any info would be greatly appreciated. Thanks. Wataru Hi Wataru-san: Three easy steps: 1. Define a SMILES string for your compound. The java molecular editor makes this easy: http://www.molinspiration.com/jme/ 2. Paste the smiles string into COOT, or feed it into phenix.elbow 3. Output the pdb file. COOT is faster but phenix.elbow allows you to minimize the structure, even using third-party QM programs like GAMESS. I trust all is well. Bill
Re: [ccp4bb] problem of imosflm in ccp4
The easiest thing to do is: export MOSFLM_WISH=/usr/bin/wish8.4 or fink install imosflm-aqua will make sure everything is set up ok for 10.6, where the supplied aqua TclTK plays well with imosflm. Yamei Yu wrote: Hi all, I use fink to install ccp4-6.1.2 on my Mac OS X 10.6. All programs in ccp4 works well except imosflm. when I run it, it gives me the following error message Top level CCP4 directory is /sw64/share/xtal/ccp4-6.1.2 Using CCP4 programs from /sw64/share/xtal/ccp4-6.1.2/bin MOSDIR is /Users/yamei/mosdir Error in startup script: unknown namespace in import pattern itcl::* while executing namespace import itcl::* (file /sw64/share/xtal/ccp4-6.1.2/ccp4i/imosflm/src/imosflm.tcl line 91) invoked from within source $env(IMOSFLM) (file /sw64/share/xtal/ccp4-6.1.2/ccp4i/imosflm/imosflm.tcl line 117) Dose any one know how to fix this problem? Thank you very much! yamei
