Re: [ccp4bb] Mg2+ or water

the peak height of anomalous signal (e.g Ca2+, K+) is a hint, but one has to be careful in the case there is not full occupancy. HTH Guenter *Subject:* [ccp4bb] Mg2+ or water Hi All, I am refining a structure and encountered a problem of modeling a difference density as water or Mg2

Re: [ccp4bb] Mg2+ or water

On Dec 21, 2010, at 2:08 AM, Vellieux Frederic wrote: > Programs that check viruses in incoming emails remove all files that carry > double extensions because this is a way to "hide" the real nature of the file. This doesn't sound correct, at least not for any antivirus package that is worth th

Re: [ccp4bb] Mg2+ or water

On Dec 20, 2010, at 1:16 PM, jlliu liu wrote: > it is also within hydrogen bonding distance to the main > chain N of another protein residue. This also strongly suggests it is not Mg2+, which prefers hard ligands such as charged oxygen, rather than softer ligands like uncharged backbone nitroge

Re: [ccp4bb] Mg2+ or water

Another option would be to collect data at the Mn K edge (1.89A) - at this wavelength Mg has a weak anomalous signal that you should still be able to detect. I've used Mn K edge to successfully distinguish between Mg, Mn and Ca ions as well as identify them as ions and not waters by looking at pea

Re: [ccp4bb] Mg2+ or water

Hi, I'm not sure if it has been mentioned yet, but you could take an experimental approach if you still have crystals. You could soak them with EDTA/EGTA and if the density disappears that is good evidence it was Mg (or other divalent cation), if not then putatively water. You could also soak wi

Re: [ccp4bb] Mg2+ or water

I agree. It is very unlikely to be Magnesium ion; may be an ordered water! I'd recommend to have a look at the following paper which discusses the different properties of Mg2+, Mn2+, and Zn2+. Charles W. Bock, Amy Kaufman Katz, George D. Markham, and Jenny P. Glusker. Manganese as a replaceme

Re: [ccp4bb] Mg2+ or water

, 2010 4:16 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Mg2+ or water Hi All, I am refining a structure and encountered a problem of modeling a difference density as water or Mg2+, and would like to hear opinions from the community. It has the following coordinations (attached): the water

Re: [ccp4bb] Mg2+ or water

-- Ian >> >> On Tue, Dec 21, 2010 at 8:55 AM, Robbie Joosten >> wrote: >> > You could also try the original WASP here (also for coloured Indo-dutch >> > catholics): http://xray.bmc.uu.se/cgi-bin/gerard/rama_server.pl or you can >> > use the latest WHAT

Re: [ccp4bb] Mg2+ or water

and Di > > Cera's algorithm. > > > > Cheers, > > Robbie > > > >> Date: Mon, 20 Dec 2010 22:59:53 + > >> From: paul.ems...@bioch.ox.ac.uk > >> Subject: Re: [ccp4bb] Mg2+ or water > >> To: CCP4BB@JISCMAIL.AC.UK > &g

Re: [ccp4bb] Mg2+ or water

gt;> From: paul.ems...@bioch.ox.ac.uk >> Subject: Re: [ccp4bb] Mg2+ or water >> To: CCP4BB@JISCMAIL.AC.UK >> >> On 20/12/10 21:48, Robbie Joosten wrote: >> > >> > >> > Also note that Mg2+ is significantly smaller than water. It fits in >> > pla

Re: [ccp4bb] Mg2+ or water

[christmas flame] The 'hiding' only applies to Windows, and that's your own fault then... and your responsibility to look after it. And since attachments are deprecated on this list it further imposes no real problem at all. [/christmas flame] ;-> Tim On Tue, Dec 21, 2010 at 11:08:27AM +0100, V

Re: [ccp4bb] Mg2+ or water

James Stroud wrote: On Dec 20, 2010, at 1:53 PM, Jacob Keller wrote: what is the .odp file extension? http://tinyurl.com/mjokqs A .odp file is an "open document presentation". It is the open version of a power point presentation. http://en.wikipedia.org/wiki/OpenDocument An .odp fi

Re: [ccp4bb] Mg2+ or water

annot go. This doesn't look like a magnesium site on first >> glance. If you can (privately) give the PDBid of the previous publication, I >> can have a look in 3D. >> >> Cheers, >> Robbie >> >>> Date: Mon, 20 Dec 2010 21:31:58 + >>>

Re: [ccp4bb] Mg2+ or water

21, 2010 9:55 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Mg2+ or water You could also try the original WASP here (also for coloured Indo-dutch catholics): http://xray.bmc.uu.se/cgi-bin/gerard/rama_server.pl or you can use the latest WHAT_CHECK that also has an implementation of Nayal and

Re: [ccp4bb] Mg2+ or water

22:59:53 + > From: paul.ems...@bioch.ox.ac.uk > Subject: Re: [ccp4bb] Mg2+ or water > To: CCP4BB@JISCMAIL.AC.UK > > On 20/12/10 21:48, Robbie Joosten wrote: > > > > > > Also note that Mg2+ is significantly smaller than water. It fits in > > places where wate

Re: [ccp4bb] Mg2+ or water

Sorry, the attachment is in here. Doesn't look like Mg2+ at all. Distances are too long, Mg is never coordinated by amides and if it were Mg you would have seen waters around it. Looks like tightly bound water to me. - Dima On Mon, Dec 20, 2010 at 4:16 PM, jlliu liu <

Re: [ccp4bb] Mg2+ or water

On 20/12/10 21:48, Robbie Joosten wrote: Also note that Mg2+ is significantly smaller than water. It fits in places where water cannot go. This doesn't look like a magnesium site on first glance. I tend to agree with Robbie. I wonder what WASP would say... (if you use Coot, you can try th

Re: [ccp4bb] Mg2+ or water

If it's more than likely Mg and it's easy to grow crystals, try soaking/cogrowing BaCl2/BaOAc. At least in the RNA world, Mg sites can easily be displaced by Ba. The latter of course has anomalous signal on the home sources. Place your divalents using the anomalous diff map. Have no clue w

Re: [ccp4bb] Mg2+ or water

f you can (privately) give the PDBid of the previous publication, I > can have a look in 3D. > > Cheers, > Robbie > >> Date: Mon, 20 Dec 2010 21:31:58 + >> From: p...@mrc-lmb.cam.ac.uk >> Subject: Re: [ccp4bb] Mg2+ or water >> To: CCP4BB@JISCMAIL.AC.UK >

Re: [ccp4bb] Mg2+ or water

gt; Date: Mon, 20 Dec 2010 21:31:58 + > From: p...@mrc-lmb.cam.ac.uk > Subject: Re: [ccp4bb] Mg2+ or water > To: CCP4BB@JISCMAIL.AC.UK > > Mg2+ is (almost) aways octahedrally coordinated, usually by oxygen atoms, > with distances of ~2A. > Phil > > On 20 Dec 2010, a

Re: [ccp4bb] Mg2+ or water

Mg2+ is (almost) aways octahedrally coordinated, usually by oxygen atoms, with distances of ~2A. Phil On 20 Dec 2010, at 21:16, jlliu liu wrote: > Hi All, > > I am refining a structure and encountered a problem of modeling a difference > density as water or Mg2+, and would like to hear opinio