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 file is an ISO standard--like the country code you dial when you call
your favorite Aunt.
You can open a .odp file with the free office suit called OpenOffice. Just
download it from http://www.openoffice.org/ and start double-clicking to open
the file just like you would if you were using some other presentation software.
Also, Jlliu Liu set a good example by sending the document in an open format so
anyone can open it (even though some may not have heard of an odp file before).
By using an open format, Jlliu Liu has catered to convenience rather than
catering to ignorance, and has increased the range of people who can provide
him with help.
James
>
>
>
> JPK
>
> On Mon, Dec 20, 2010 at 3:48 PM, Robbie Joosten
> <robbie_joos...@hotmail.com> wrote:
>> Dear jlliu liu,
>>
>> 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. 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 +0000
>>> 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, 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 opinions from
>>>> the community. It has the following coordinations (attached): the
>>>> water/Mg2+
>>>> forms salt bridge/H-bonding interaction with a carboxylate group from the
>>>> ligand, it also forms salt bridge/H-bonding interaction with a Glu residue
>>>> from the protein, it is also within hydrogen bonding distance to the main
>>>> chain N of another protein residue. In provious publication, it was
>>>> modelled
>>>> as a Mg2+ and the author reasoned the dual salt-bridge stabilizes the
>>>> liganding binding, also the Mg2+ is present in the protein solution for
>>>> crystallization. For my case, I have no Mg2+ present in the protein buffer,
>>>> also modelling it with water refines perfectly with no indication of
>>>> positive difference density even at 2.0 sigma cut off. Should I modelled
>>>> this density as water or as Mg2+. Your opinions are appreciated.
>>>>
>>>> JL
>>>>
>>>>
>>>> <test.png.odp>
>>
>
>
>
> --
> *******************************************
> Jacob Pearson Keller
> Northwestern University
> Medical Scientist Training Program
> cel: 773.608.9185
> email: j-kell...@northwestern.edu
> *******************************************
