[ccp4bb] xprep vs shelxc

Dear All, A very simple stupid question: is it worth while getting xprep instead of shelxc to do the same job? i realize xprep does a lot of other things, but also seem to get the idea from some places that it does a better job than shelxc at preparing data from shelxd, or is there any differenc

Re: [ccp4bb] an over refined structure

Dale Tronrud wrote: In summary, this argument depends on two assertions that you can argue with me about: 1) When a parameter is being used to fit the signal it was designed for, the resulting model develops predictive power and can lower both the working and free R. When a signal

Re: [ccp4bb] Fit2D?

You can download the latest FIT2D executables from: http://ftp.esrf.eu/pub/expg/FIT2D/ Make sure to use the http protocol to download the files, ftp will not work. The most recent version of FIT2D is for MacOSX. Updates and support for other OS were apparently discontinued. Alexander Johs OR

[ccp4bb] AW: [ccp4bb] Thermofluor

Hi Jeroen, I assume you are planning to use Sypro Orange. We are using the Roche LC480 (simply because it's around in the lab next door) and it does the job although it's a little inconvenient to tweak the settings. Many people use the iCycler from Biorad. This machine is a little more flexibl

Re: [ccp4bb] an over refined structure

Edward Berry wrote: Dirk Kostrewa wrote: Dear Dean and others, Peter Zwart gave me a similar reply. This is very interesting discussion, and I would like to have a somewhat closer look to this to maybe make things a little bit clearer (please, excuse the general explanations - this might be

Re: [ccp4bb] summary: sgi dials on intel mac

The protocol (ftp://)from the link is wrong, ftp is not supported by the esrf site (which one is told when actually ftp'ing there. Try http://ftp.esrf.eu/pub/expg/FIT2D/, it works for me Tim -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A

Re: [ccp4bb] Thermofluor

Hi Jeroen, We just bought a Stratagene Mx3005p for the Thermofluor method (also known as differential scanning fluorimetry). This was after talking to Martin, among others, he he... We haven't had it long and did our first experiments last Friday, but it produced good results straight awa

Re: [ccp4bb] Thermofluor

Hi Jeroen, We used a BioRad iCycler iQ for the measurements in "Thermofluor-based high-throughput stability optimization of proteins for structural studies." Ericsson, et. al. Analytical Biochemistry (2006) 357:289-298. The wavelengths for excitation and detection were ~490 and ~575 nm, resp

[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] Fit2D?

I've been trying to get a copy of Fit2D for MacOSX, but the esrf web site with the executables has been unavailable for some time. The actual documentation is still online, including mirrors, but not the link to the executable. The author has also not responded. Anyone know what's up with F

Re: [ccp4bb] sgi dials on intel mac

On Tue, Feb 12, 2008 at 05:16:14PM +, Andreas Förster wrote: > 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 sbgr

[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

[ccp4bb] 13th Annual UTMB Sealy Center for Structural Biology Symposium

Dear Colleague: You and your colleagues are cordially invited to join us for the 13th Annual Structural Biology Symposium to be held at the University of Texas Medical Branch at Galveston on May 16th and 17th, 2008. The meeting is organized by the Sealy Center for Structural Biology & Molecula

[ccp4bb] Thermofluor

Sorry for the off-topic but can somebody recommend highly a sensitive RT-PCR machine for the thermofluor experiment (sypro orange). That would imply excitation below 500 nm (ideally 470) and detection at about 570 nm, right? I know several simple machines have a problem with the 570 nm... Jero

[ccp4bb] Protein-protein docking

I would recommend giving Dave Ritchie's Hex program a go - it is blisteringly quick. It's limited to local searches so it is best if you have a reasonable idea where you expect the docking surface to be (mutations, NMR shift data etc). We used it to refine solutions from searches with crosslinki

Re: [ccp4bb] Does NCS bias a randomly-chosen test set (even if not enforced)?

Dear Ed, my head starts smoking ;-) While it's clear that the Rfree goes down when a structure becomes better during refinement, I think, its not the correlation of the _changes_ of |Fobs-Fcalc|, but correlation of the _final_ |Fobs- Fcalc| that is important here. I don't know the answer rig

Re: [ccp4bb] shipping heavy-atom solutions using Fedex

"Does anyone has experience in shipping these compounds" Try Hampton Research. Christopher J. Law, PhD., Skirball Institute, NYU Medical Center, New York, NY 10016, U.S.A On 11/02/2008, David Aragao <[EMAIL PROTECTED]> wrote: > Dear All, > > We need to ship small amounts (< 100ul, [ ] < 5mM)