[ccp4bb] ccp4-6.0.99d-3, clapham test release

Dear All there is a slim 800 lb tarball at ftp://ftp.ccp4.ac.uk/ccp4/6.1/ccp4-6.0.99d-src.tar.gz this is to test the build and arrangement of files. If you want balbes you will have to manually install PyXML (run the setup.py in PyXML-... using python setup.py build followed by python

[ccp4bb] is it Ok to freeze

Dear Scientists and Friends, I am not sure, whether organic crystals need to be in cryo stream necessarily during data collection from an in house xray machine . How most of the organic crystals have been solved mostly? -- S.Jayashankar (A bit confused new generation researcher).

Re: [ccp4bb] is it Ok to freeze

Hi If you mean organic small molecules, then the opinion for the last 15 years at least is probably yes, unless you know you'll have a phase change. Most small molecule crystals don't have the same problems with needing cryoprotectants as macromolecules, due in large part to not having

Re: [ccp4bb] is it Ok to freeze

Harry Can you clarify why you get a substantially better structure at cryo temperatures e.g higher intensity at high resolution due to reduction in B factors, reduction in radiation damage, anything else? Colin -Original Message- From: CCP4 bulletin board

Re: [ccp4bb] is it Ok to freeze

Hi Colin yes, both of those. Plus freezing out multiple conformations so you can model them properly - bear in mind that a small molecule structure at a resolution worse than 1Å would be challenging to get past the normal criteria of referees, so you should be able to see them at least

Re: [ccp4bb] is it Ok to freeze

Hi I just noticed I scrambled that first paragraph. I didn't intend to imply you should be able to see your referees (or their criteria) at least some of the time. It should have read something more like- yes, both of those. Plus freezing out multiple conformations so that you can model

Re: [ccp4bb] is it Ok to freeze

Typically crystals of small organic compounds do not require freezing as there are no solvent channels. They do in general not suffer from radiation damage at room temperature the way protein crystals do. Occasionally they are mounted in a capillary instead of simply glueing them to a

Re: [ccp4bb] is it Ok to freeze

Hi Without wishing to start an argument, I've been checking with some of my colleagues who are chemical crystallographers - the reply I get is that, for routine structural analysis, pretty well all datasets are collected at 100K unless the crystals fall apart at low T, or if the

Re: [ccp4bb] is it Ok to freeze

This fellow below is presumably and Indian, writing in English at a German University, a very confused new generation researcher, indeed. Maybe this will help: S.Jayashankar (Ein wenig verwirrter Forscher der neuen Generation) Forschungsstudent Institut fuer Biophysikalische Chemie Medizinische

Re: [ccp4bb] How to change R-free set?

I am currently refining a high-resolution structure that has many reflections (~180,000). I would like to halve the R-free set from 5% to 2.5%, and am unsure how to do so. Any advice will be greatly appreciated. there is a bunch of commands in dataman to do this (and other things) to your

Re: [ccp4bb] is it Ok to freeze

I would go along with Harry friends, I used crystal cooling when I was at Aafje Vos' Struktuurchemie lab in Groningen in 1972, when the technique had already been in routine use there for at least 10 years, in order to study compounds that are liquid at ambient temp (of course it was custom-built

[ccp4bb] Coot and Hs

Dear all, a problem possibly at the coot/mmdb interface... If one uploads a pdb file (from phenix.refine in the example below) that contains Hs into Coot and then writes it out (with or without any modification done on it) Coot shifts the HG2n of THR on the right by one column space.

Re: [ccp4bb] is it Ok to freeze

Every small molecule dataset I collected as a graduate student in chemistry back in the mid to late 1980's was at 100K. I never had to worry about crystal slippage during collection, organic solvent evaporation, air oxidation of the sample (organometallic metal clusters) or secondary

Re: [ccp4bb] is it Ok to freeze

I typically collect data at -50C on all small molecule samples. I've had quite a few cases where there are phase transitions, and you can damage the crystals, especially when the molecules are packed in a pi-pi stacking motif, or I'm dealing with alloy systems. I've also collected data at 16K, so

Re: [ccp4bb] Coot and Hs

Dear Roberto, Roberto Steiner wrote: Dear all, a problem possibly at the coot/mmdb interface... Indeed. If one uploads a pdb file (from phenix.refine in the example below) that contains Hs into Coot and then writes it out (with or without any modification done on it) Coot shifts the HG2n

Re: [ccp4bb] Coot and Hs

Hi Paul, How can I add Hs (hydrogens) stereochemically to protein or peptide using COOT without altering the coordinates of non-hydrogen atoms. Thanks. Sam. Date: Thu, 19 Jun 2008 15:57:46 +0100 From: [EMAIL PROTECTED] Subject: Re: [ccp4bb] Coot and

[ccp4bb] adding hydrogens without altering coordinates of non-hydrogen atoms

Any idea is appreciated how to add Hs (hydrogens) stereochemically to protein or peptide without altering the coordinates of non-hydrogen atoms. Does COOT have any option to do this ? Thanks. Sam.

Re: [ccp4bb] Coot and Hs

I think that we will have to 'remediate' Coot (and the whole of CCP4 for good measure). I advise all SHELXL users NEVER to deposit hydrogen atoms, it saves lots of hassle. George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077

Re: [ccp4bb] is it Ok to freeze

Ha, everyone seems to be bragging about how far back cryo- crystallography really goes. In that vain, I'd like to mention that, in Martinsried, we had a room that was lined with insulated steel walls and that could be flushed with liquid nitrogen. It was requested (demanded, really...) by

Re: [ccp4bb] is it Ok to freeze

... room that was lined with insulated steel walls and that could be flushed with liquid nitrogen. I'm trying to picture this ... did you guys have some kind of LN2- proof SCUBA diving equipment to work in there? Klaus

Re: [ccp4bb] is it Ok to freeze

Sadly, I have never seen the room being used. Perhaps one of the 'older' Martinsrieder on the forum has seen it. MM On Jun 19, 2008, at 12:11 PM, Klaus Futterer wrote: ... room that was lined with insulated steel walls and that could be flushed with liquid nitrogen. I'm trying to picture

Re: [ccp4bb] is it Ok to freeze

I've been in that cold room / hutch. I never heard of it being flushed with LN2. I think that is just to make the room sound cooler. Jim On Thu, 19 Jun 2008, Mischa Machius wrote: Sadly, I have never seen the room being used. Perhaps one of the 'older' Martinsrieder on the forum has seen

Re: [ccp4bb] Coot and Hs

Roberto, An also less than optimal work around might be to take your refined .pdb from PHENIX or CCP4 and run it through the downgrade utility on MolProbity to change to PDBv2.3 format before working in Coot. I don't think it is necessary to convert back to PDBv3.0 for phenix.refine, but

Re: [ccp4bb] is it Ok to freeze

Dick Dickerson tried to do the same thing at Caltech around the same time. The major problem with cooling equipment was that the Picker goniometer had lots of metal in it, and each of the metal pieces cooled and contracted differently, so the alignment was always off. Nice idea, but not useful.

[ccp4bb] PhD Scholarship opportunity

Structure-Function Studies of Protein Trafficking The Role: A PhD scholarship is available immediately in the lab of Dr. Brett Collins at the Institute for Molecular Bioscience, University of Queensland, Brisbane (Australia). The successful applicant will join a team using