Re: [ccp4bb] crystallography teaching advice: f(S) ?

William G. Scott wrote: On Oct 6, 2009, at 1:32 AM, Morten Kjeldgaard wrote: teleports the students across the hermeneutic circle ;-) (As a consequence, I recommended the postmodernism generator website to the students: http://www.elsewhere.org/pomo/ ) It is easy to mock postmodernism,

[ccp4bb] Nobel prize for chemistry 2009

BB members may be interested to know that the 2009 Nobel prize for chemistry has been awarded to Venki Ramakrishnan, Tom Steitz and Ada Yonath for their structural work on the bacterial ribosome.

[ccp4bb] problem with truncate

Dear fellow crystallographers, (nice work on the ribosome, and this award is going to be good for our science) We have the following problem when running truncate: FORMATTED OLD file opened on unit 45 Logical name: ATOMSF, Filename: /work/prog/ccp4/lib/data/atomsf.lib TRUNCATE:

Re: [ccp4bb] problem with truncate

Hmm - truncate guesses the unit cell contents as containing atom types C N O and H and retrieves their formfactors from ATOMSF.lib. Has the H labelling been changed somewhere? Eleanor Vellieux Frederic wrote: Dear fellow crystallographers, (nice work on the ribosome, and this award is going

Re: [ccp4bb] problem with truncate

Dear Eleanor, Hope all is well with you (and with Guy). We haven't touched the atomsf.lib file. It is the same in all versions of ccp4 we have lying around here. Will go on looking for a solution (perhaps the problem lies with the fact that the input MTZ file already contains columns for FP

Re: [ccp4bb] Nobel prize for chemistry 2009

A Leslie wrote: BB members may be interested to know that the 2009 Nobel prize for chemistry has been awarded to Venki Ramakrishnan, Tom Steitz and Ada Yonath for their structural work on the bacterial ribosome. It is a great piece of work, and well deserves a Prize. And nice that the

Re: [ccp4bb] problem with truncate

Hi Charles (I remember you associated with another e-mail address, whappened?). It is a ccp4 binary. Fred. charles.ball...@stfc.ac.uk wrote: Hi Fred we have seen this before with some over optimisation in the logic. Is it a roll your own installation or a ccp4 binary? Also, if you rolled

Re: [ccp4bb] gpp4 version 1.2 released

On 10:36 Mon 05 Oct , Kevin Cowtan wrote: Given that the current CCP4 build system is somewhat non-standard, I might be prepared to support an effort which provided an alternative build system to work with the CCP4 provided source code, however. I made about half of such an effort a few

Re: [ccp4bb] problem with truncate

Eleanor, I downloaded again ccp4-4.2.2_Linux.tar.gz and re-installed truncate. It worked this time. Perhaps the file got corrupted during ftp transfer? Anyway, thanks for your help. All the best, Fred. Eleanor Dodson wrote: I dont understand it - it works for me.. Here is the log file -

Re: [ccp4bb] the low correlation factor after final refinement

Hi Carl, the R-factors seem reasonable given the resolution... Try running phenix.validate from the latest version: it will do all Molprobity analysis, compute map CC for each residue, draw POLYGON image, and do many other validation staff. That might help to spot if there is anything not right.

Re: [ccp4bb] B values bottomed out

Are you using TLS? If so I usually start with all Bs reset to the Wilson B ( see GUI) It can still happen but not so often.. Eleanor# Gloria Borgstahl wrote: Hello ccp4-ers, We are refining a 1.55 angstrom cryocooled structure with REFMAC. In analyzing the occupancy of ligands in the active

Re: [ccp4bb] gpp4 version 1.2 released

On 07/10/2009, at 16.19, Donnie Berkholz wrote: On 10:36 Mon 05 Oct , Kevin Cowtan wrote: Given that the current CCP4 build system is somewhat non-standard, I might be prepared to support an effort which provided an alternative build system to work with the CCP4 provided source code,

[ccp4bb] Questions about cryoprotectant

Hi, I am trying to find an appropriate cryo-condition for my protein crystals. The mother liquid is 2-2.5M Ammonium phosphate dibasic 100mM TrisHCL pH8. The room-temperature diffraction looks not bad (mosaicity 0.8, resolution 2.6) But the diffraction turned to be very mosaic if I freeze the

Re: [ccp4bb] Questions about cryoprotectant

You have options: 1. Paratone-N (rarely works for me when other methods don't also work) 2. ML + 25-30% glucose (one of my favorite and reliable methods) 3. ML + 25-30% EG, maybe DMSO PEG400 is not likely to work here because its solubility in high sulfate solutions is limited. In 2 M AmSO4,

Re: [ccp4bb] Questions about cryoprotectant

I have had a fair amount of success using 2.1-2.3 M Na Malonate as a cryo protectant for crystals from high salt conditions like yours. Fluorinated oils are also an option, they generally are a little easier to work with then Paratone. Good Luck Leonard Thomas Ph.D. Macromolecular

Re: [ccp4bb] Questions about cryoprotectant

re : Paratone-N oil. 1) I find it much easier to work with if you cut it 50:50 with light mineral oil. 2) he stress of moving mechanically weak crystals (needles or thin plates) from a crystallisation liquor to the more viscous Paratone can cause the crystal to visibly bend - which might not be

[ccp4bb] Program for Neutrons in Biology Conference in Santa Fe

Dear Colleagues, please find below the final program for the International Conference on Neutrons in Biology, to be held in Santa Fe October 25th-28th 2009. If you work on biological systems or renewable energy and the environment, then I would like to encourage you to register for the

Re: [ccp4bb] Questions about cryoprotectant

Different suggestion: I assume you don't have problems obtaining crystals, so I'd setup a 24 or 96 well plate with your preferred condition then add to each row or column a different know cryo at low concentration e.g. 1-10%. Then under the conditions in which you still get crystals in the

[ccp4bb] Questions about cryoprotectants

Hi, Thank you for all your suggestions! I will test them and let you know what happens! Yuan