Re: [ccp4bb] desktop models

. Thank you for your assistance. __ -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http

[ccp4bb] largest distance between atoms

Hey all, is there a script out there that computes the longest extent of a molecule and determines which atoms define the 'space diagonal'. In other words, I'm looking for the two atoms in a molecule that are most distant from each other. Thanks. Andreas -- Andreas Förster

Re: [ccp4bb] Update X11 in macbook

in advance for all the help... Raja Connect with friends all over the world. Get Yahoo! India Messenger at http://in.messenger.yahoo.com/?wm=n/ -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London

Re: [ccp4bb] To identify specific type of interaction

they are. Thanks in advance! Saraboji -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London

Re: [ccp4bb] putting in methionines for SeMet crystals

of the protein is not compromised. Any suggestions would be of great help. Thanks in advance, -- Amit Sharma, Ph.D. Research Associate, Department of Biology, University of York, YO10 5DD UK -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department

Re: [ccp4bb] Small lines in diffraction pattern (more info)

-- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London

Re: [ccp4bb] Fwd: Twinning

Phone: +44 (0) 20 7594 3908 Fax: +44 (0) 20 7594 3906 -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London

Re: [ccp4bb] iMosflm in 6.1 under OS X

This doesn't seem to be a general phenomenon. My xquartz is still 2.3.1 after installing the latest service pack (Leopard 6). Andreas William G. Scott wrote: Please, we all need to mention this to the Apple people. This is totally unacceptable. On Dec 17, 2008, at 2:54 PM, Engin Ozkan

Re: [ccp4bb] R pim and Rmeans

Will someone knowledgeable shed light on these issues at the ccp4 meeting next month? Thanks Andreas Frank von Delft wrote: Hi Manfred thanks a lot for your comments, since they raise some interesting points. R_pim should give the precision of the averaged measurement, hence the name.

[ccp4bb] refinement of half molecules

was solved by MR with one molecule per au but doesn't refine. There is good density for the MR solution, but the solution shifted by 1/2 z fits the density nearly as well. -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial

Re: [ccp4bb] Progresss with Stereo 3D under Mac OS X Leopard

for everyone, but I certainly think everyone benefits from having it as an option on as many platforms as possible. So keep it legal. -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London

Re: [ccp4bb] Facebook for Neerds

of Washington Dept. of Biochemistry, K-426 1705 NE Pacific Street Seattle, WA 98195 Box 357742 Phone: +1-206-616-4510 FAX: +1-206-685-7002 Web: http://faculty.washington.edu/jbosch -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department

Re: [ccp4bb] interface energetics

or corrections? I've only had 7 hours of sleep since Saturday. ~Steve -- Steven Darnell Univeristy of Wisconsin-Madison Madison, WI USA [EMAIL PROTECTED] -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London

[ccp4bb] interface energetics

if what I've done makes sense and if there are alternative methods for minimizing and calculating interface energies. I don't necessarily need docking algorithms as the interface is known. I just want to get an energetic description. Thank you. Andreas -- Andreas Förster, Research

[ccp4bb] more on thermofluor

Hey there, we've been demoing real-time PCR machines for use in differential scanning fluorimetry. Stratagene's Mx3005p has been mentioned before on this list. It seems to do the job well, and there is great software support from Frank Niesen at Oxford. However, we've really come to like

Re: [ccp4bb] pH gradient in Mono Q

Hey Matt, it seems to me that what you're asking for is chromatofocusing. See the official GE documentation: http://www6.gelifesciences.com/aptrix/upp00919.nsf/Content/WD:Chromatofocusin(260949098-R350) The proprietary buffers are a bit expensive, but as you found out, they're a bit

Re: [ccp4bb] How many reflections for Rfree?

When we ran into reviewer complaints a while back we referred to Methods in Enzymology, 277:366-396. I can't lay my hands onto this to verify the statement, but back then it was good enough to placate the reviewer. Full QnA with reviewer: 3) Why were only 1% of the reflections included in

Re: [ccp4bb] Two off-topic questions

Do we eally have to idicule postes to the ccp4 boad because of a missing lette? If evey post with a othogaphic mistake elicited such a eaction, I doubt anyone would cae to post to the bulletin boad. Andeas Frank von Delft wrote: only tried once). Does any body have ideas about how to

[ccp4bb] scala on mac osx - off topic, really

Hey all, a colleague is running ccp4 6.0.2 on a MacBook with Timid Tiger. Built-in Scala is 3.2.25. Because of a bug, he wants to upgrade Scala. Running Scala 3.3.2-beta5 or 3.2.34 (phil's binaries) fails because gcc shared libraries are missing. Here's the setup:

Re: [ccp4bb] ccp4 install on Leopard

A few month's back, and a few moments before almost throwing my Powerbook out the window, I enabled the root account, as officially described (http://docs.info.apple.com/article.html?artnum=106290): How to enable the root user Mac OS X 10.5 or later 1. From the Finder's Go menu, choose

Re: [ccp4bb] upgrade coot via fink on OS X

Hey Klaus, after I installed coot 0.5 via fink for the first time, I encountered stalling during startup as well. However, this resolved itself within a minute. Startup resumed, and the next time around, everything was back to normal. Were you patient enough during startup? Andreas

Re: [ccp4bb] bash terminal freezes after quit from 'O' 11.0.5

Documents/ More Applications/ Music/ (dyn1210-244) ~: Andreas Andreas Förster wrote: Hey Raja, this might not be directly helpful, but... I remember the same problem. I had to quit the terminal after shutting down O (11.0.5, Build 070605, on OSX 5.2). When I tried to recreate

Re: [ccp4bb] first week of CCP4 community wiki

Hey Kay, I'm not even sure I see a problem with reposting. All ccp4 posts are archived, and the archive is public. So, by posting to the list, you're already implicitly consenting to having your comment made public. How is this different from being included in the wiki? That said, I

Re: [ccp4bb] Thermofluor experiment

Dear Kornelius, I found the idea of doing Thermofluor on membrane proteins really intriguing - for identifying the best buffer and detergent, secondary detergents, even for checking crystallization drops that stayed clear. (This latter experiment should theoretically be possible with large

[ccp4bb] summary: sgi dials on intel mac

Juergen Bosch and Ben Eisenbraun were quick to forward my request to Dave Gohara who's at WUSTL now. Dave was equally quick in pointing out that a universal binary of the USB-to-serial driver resides on his homepage (http://smackfumaster.com) in the Software - Crystallography and EM Binaries

[ccp4bb] sgi dials on intel mac

Hey all, I've been trying to get SGI dials to work with a MacBook Pro running Leopard. I can't get my digitus USB-to-serial adaptor to work. The supplied driver is PPC only. As the chip is from Prolific, I tried the driver from sbgrid (David Gohara's work). That also seems to be PPC only. I

Re: [ccp4bb] Protein-protein docking

Hey Josiah, if you're into self-flagellation, try RosettaDock (http://www.rosettacommons.org/software/). The program is viciously obfuscated and the learning curve correspondingly steep, but once you've figured things out, it's quite powerful. Take the published protocols with a grain of

Re: [ccp4bb] crystallization robot

What Jan says (in brackets) is true and very important. If you go to great lengths finding the best robot, you might as well use the best plates, and the MRC plates are the best by far that I've ever used. http://www.innovadyne.com/products_iplateSD2.html Andreas Jan Lšowe wrote: Since

Re: [ccp4bb] ideal bond length and bong angel

Hey Gerard, wikipedia might tell you how to angle for fishes, but I fear it falls short of teaching you how to fish for angels. Andreas Imperial College of Aquatic and Fisheries Sciences London Gerard DVD Kleywegt wrote: Can you explain the define of the bond length and bond

Re: [ccp4bb] Protein interface prediction tool?

Hey Karen, Pisa analyzes oligomerization interfaces. http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html Andreas karen yates wrote: Hi, I would like to find a bioinformatic tool that will allow me to predict the dimerisation interface of a protein. A structural model has been generated,

[ccp4bb] more on dimerization interface analysis

are likely to form heterooligomers. There is some experimental evidence for that. I'm grateful for suggestions. Andreas -- Andreas Förster Imperial College London https://wasatch.biochem.utah.edu/~andreas

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