[ccp4bb] Annoying coot issue

Anyone have undefined symbols (referenced from ImageIO) in the libjpeg provided by coot 0.3.2? Running OS X 10.4.10. Maybe there is a libjpeg dylib to drop in? Here is the traceback: % coot current_exe_dir is /usr/programs/coot/g5/coot-0.3.2/bin COOT_PREFIX is

Re: [ccp4bb] Annoying coot issue

I finked the 0.4 pre-release. It seems to work. I think the binaries are broken, so don't waste your time with them. James On Nov 26, 2007, at 1:38 AM, James Stroud wrote: Anyone have undefined symbols (referenced from ImageIO) in the libjpeg provided by coot 0.3.2? Running OS X 10.4.10.

Re: [ccp4bb] Annoying coot issue

James Stroud wrote: I finked the 0.4 pre-release. It seems to work. Good. Do use wm_ffm for a less irritating experience. I think the binaries are broken, I think so too. Apple broke them. AFAICS. so don't waste your time with them. That is more or less the advice in the Coot FAQ.

Re: [ccp4bb] To bathe or not to bathe.

To bathers and non bathers This is an interesting discussion with several relevant points. I agree that, if small beams can pick up the best bits of the crystal that is a very good reason for using them. The background arguments can be relevant and having the beam size at the detector matched

Re: [ccp4bb] difference of R_work and R_free as a function of resolution

Dear Kay. If it is still relevant, the following article by Kleywegt and Jones also look at the correlation between R and Rfree as a function of resolution and find it to be: Rfree = 1.065*R + 0.036. Kleywegt GJ, Jones TA. Homo crystallographicus--quo vadis? Structure. 2002 Apr;10(4):465-72.

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Re: [ccp4bb] To bathe or not to bathe.

I just noticed this thread. I should make a few comments. We regularly provide microbeam with and without Helium here at MacCHESS. Yes, there are cases in which microbeam can give you good diffraction on large crystals when a larger beam cannot. Just last week we had a user group

Re: [ccp4bb] To bathe or not to bathe.

Richard Gillilan wrote: I am currently working on guidelines for when helium and microbeam are necessary (based on both simulations and explicit measurements). At the present time, my feeling is that crystals below 50 micron can certainly make the extra hassle worthwhile. It really

Re: [ccp4bb] To bathe or not to bathe.

Note the density of air is approximately 1000 times less than a protein crystal. The total scatter for a beam going through a 50 micron thick crystal will be similar to that from 50mm air. Most beamlines will have a path length less than this but nevertheless the air scatter will be significant

Re: [ccp4bb] To bathe or not to bathe.

Hi Juergen, the original calculation was done with I/SIG's from scala. Yes, I am aware of the problems obtaining reliable and meaningful I/SIG with CCD data. I have gone through the exercise of trying to get agreement between scala and scalepack by optimizing error model parameters ...

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Re: [ccp4bb] Cif file in coot

Hello Yang, You need dictionary for the residue 'abc' which will have all the geometric restraints defined. You can read the residue co-ordinates in Monomer Library Sketcher in CCP4i and writeout the dictionary file using LIBCHECK. You will be able to refine abc once you import monomer CIF

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Re: [ccp4bb] To bathe or not to bathe.

In our current helium box, there is a total of about 28 mm of beam exposed. 10 mm from the aperture of the optic and 18 mm from sample to beamstop. The 10 mm side working distance is very tight for hand mounting (little room for tongs) and falls just outside the shield stream for cryo.

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Re: [ccp4bb] To bathe or not to bathe.

Concerning the bathing, I think there is at least this point, which I do not think has been mentioned, to wit: Considering that radiation damage is now present, I would guess, in virtually all synchrotron-collected datasets, and considering that probably this information could be used in

Re: [ccp4bb] To bathe or not to bathe.

Folks, As expected, discussion about to bathe or not to bathe are starting to expand into other aspects of data collection and processing. Along the way I saw reference to how we use our small beams on GM/CA beamlines in sector 23 of APS. Without going into discussions of advantages and

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Re: [ccp4bb] To bathe or not to bathe.

- Original Message - From: Nave, C (Colin) [EMAIL PROTECTED] Several have raised the issue of radiation damage. The strategy which Bob mentions can make sense, ensuring fresh parts of the crystal are regularly brought in to the beam. I would have thought 5-10 micron beams were rather

[ccp4bb] Genome Biology 2007 8:103

Dear All, UCI does not subscribe to Genome Biology - I'd be grateful if someone might share a pdf of: And the second shall be first Gregory A Petsko Genome Biology 2007 8:103 Thx, br - Bernhard Rupp 001 (925) 209-7429 +43 (676)

Re: [ccp4bb] Genome Biology 2007 8:103

thanks to all - got it ! br -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Bernhard Rupp Sent: Monday, November 26, 2007 4:45 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Genome Biology 2007 8:103

Re: [ccp4bb] To bathe or not to bathe.

Manjasetty, Babu wrote: Hi there, 1. See attached for life-time of crystals (How long will my crystal lost?) at various beamlines in the world. 2. The citations for the beauty and quality of the datasets from bending magnet beamlines. Please read most of the papers from Dauter group.