Re: [ccp4bb] summary: off topic: advice for crystallography workstation/server

Hi, First of all, thanks for all the suggestions and comments! I'll sum up a few of the replies here. It seems that most people would favor going for the route of having multiple, individual computers (iMacs, mac minis, etc) instead of having one workhorse. This mainly due to the fact that any

Re: [ccp4bb] cryoprotectant for protein crystal grown from Di-sodium hydrogen phosphate

80% saturated lithium sulfate should have about the correct ionic strength to match your crystallization conditions. The crystals need to be transfered with as little mother liquor as possible to avoid lithium phosphate crystallization. Robert Kirchdoerfer suggestion is also excellent, but c

Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms

Dale > The reward of the > full calculation is that all the complications you describe disappear. > An atom that sits 0.001 A from a special position is not unstable > in the least. That's indeed a very interesting observation, I have to admit that I didn't think that would be achievable. But th

Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms

> I think this is how the Oxford CRYSTALS software ( > http://www.xtl.ox.ac.uk/crystals.html ), which has been around for at > least 30 years, deals with this issue, so I can't accept that it can't > be made to work, even if I haven't got all the precise details > straight of how it's done in pract

Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms

Or you could write and ask the author, who is always willing to help (sorry, David!)... On 16 Dec 2010, at 11:24, Ian Tickle wrote: >> I think this is how the Oxford CRYSTALS software ( >> http://www.xtl.ox.ac.uk/crystals.html ), which has been around for at >> least 30 years, deals with this is

Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms

Dear Ian, You still have an arbitrary threshold: at high resolution you see two disordered atoms off-axis and at low resolution you see one ordered atom on-axis. However, somewhere in between you or the program has to decide whether you still see two atoms or if the data (resolution) does not w

Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms

> You still have an arbitrary threshold: at high resolution you see two > disordered atoms off-axis and at low resolution you see one ordered atom > on-axis. However, somewhere in between you or the program has to decide > whether you still see two atoms or if the data (resolution) does not warr

Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms

On 16/12/2010 12:24, Ian Tickle wrote: I think this is how the Oxford CRYSTALS software ( http://www.xtl.ox.ac.uk/crystals.html ), which has been around for at least 30 years, deals with this issue, so I can't accept that it can't be made to work, even if I haven't got all the precise details str

Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms

Hi Jon, try this: http://www.xtl.ox.ac.uk/download.html -- Ian On Thu, Dec 16, 2010 at 1:14 PM, Jon Wright wrote: > On 16/12/2010 12:24, Ian Tickle wrote: >>> >>> I think this is how the Oxford CRYSTALS software ( >>> http://www.xtl.ox.ac.uk/crystals.html ), which has been around for at >>> lea

Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms

Dear Ian, Of course there is no dicontinuity, but you create one the moment you decide that certain symmetry operators no longer apply to certain atoms. Confusion arises e.g. when you download a pdb file of fairly high resolution and find a water molecule with an occupancy of e.g. 0.45 at 0.02 Å

Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms

Ooops sorry that's only the executable, I guess to have to contact David for the source. -- Ian On Thu, Dec 16, 2010 at 1:14 PM, Jon Wright wrote: > On 16/12/2010 12:24, Ian Tickle wrote: >>> >>> I think this is how the Oxford CRYSTALS software ( >>> http://www.xtl.ox.ac.uk/crystals.html ), whic

[ccp4bb] Postdoctoral position available in Bethesda, Maryland

A postdoctoral position is available immediately at the Department of Biochemistry, Uniformed Services University to perform structural and biochemical research on potential drug target proteins from Mycobacterium tuberculosis. The candidate will be involved in recombinant protein expression and p

Re: [ccp4bb] Map Sharpening

On Thu, 2010-12-16 at 03:53 +0100, Raspudin wrote: > I hope, am not mixing up different things together. Perhaps you are. Map sharpening (iiuc) is done by applying B-factor-like correction to amplitudes and has only, according to coot manual, an educational value. Meaning that it's great if it h

Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms

On Thu, Dec 16, 2010 at 1:18 PM, wrote: > Of course there is no dicontinuity, but you create one the moment you decide > that certain symmetry operators no longer apply to certain atoms. Change 'atoms' in that statement to 'reflections', or to 'map grid points', then read it again. Does the (-

[ccp4bb] Fw: Virus alert

- Forwarded Message From: Dean Palmer To: Rex Palmer Sent: Thursday, 16 December, 2010 12:08:20 Subject: FW: Virus alert   From: amanda.po...@uk.henkel.com [amanda.po...@uk.henkel.com] Sent: 16 December 2010 10:20 To: dpal...@bucksgfl.org.uk Subjec

Re: [ccp4bb] Fw: Virus alert

Well, there are postcard viruses, which is why you should always open e-cards through the company's web site rather than by clicking on the link in the e-mail message. This particular message, however, is a hoax (http://www.snopes.com/computer/virus/postcard.asp). Eric --

Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms

On 12/16/10 03:06, Ian Tickle wrote: > Dale > >> The reward of the >> full calculation is that all the complications you describe disappear. >> An atom that sits 0.001 A from a special position is not unstable >> in the least. > > That's indeed a very interesting observation, I have to admit that

Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms

>   If the difference is insignificant, it may as well be off-axis.  I > guess if the difference is insignificant it just comes down to personal > preferences. My point was that if you're being strictly parsimonious with your parameters then you shouldn't be varying 2 additional parameters if it p

Re: [ccp4bb] Cys auxotroph

For those interested in our paper using non-auxotroph strains for SE-Cys labelling, it's now published: http://journals.iucr.org/d/issues/2011/01/00/dz5216/index.html Please cite this reference if you use our method in the future. B

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Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms

On 12/16/10 06:47, Ian Tickle wrote: > > For the sake of argument let's say that 0.02 Ang is too big to be > rounding error. So if you see that big a shift then the intention of > the refinement program (or rather the programmer) which allowed such a > value to be appear in the output should be t

[ccp4bb] Coot 0.6.2 CRYST1 problems ?

Dear BB, I finked my MacPro (Snow Leopard)ti the latest and greatest version of Coot 0.6.2-pre-1 (revision 3290) [with guile 1.8.7 embedded] [with python 2.7.1 embedded] and found out that I can not display any symmetry related molecules anymore. Coot complains about a problem in the CRYST card.