Re: [ccp4bb] Nitrate versus Carbonate

[Gulcin Gulten]

Similarly, how do you differentiate a phosphate ion than sulfate just based
on electron density if data is not at atomic resolution?

Thanks!


On Fri, Nov 11, 2016 at 3:52 AM, Harry Powell 
wrote:

> Hi all
>
> Sticking to the first question, if you don't restrict yourself to _X-ray_
> crystallography but use your local neutron source instead, it should be
> straightforward (subject to all the normal caveats).
>
> On 10 Nov 2016, at 23:02, Tim Gruene wrote:
>
> Dear JPK,
>
> to answer your first question, at atomic resolution you would notice a
> density
> difference between N and C. At a little less resolution you might still
> measure difference in bond length.
>
> Regrds,
> Tim
>
> On Thursday, November 10, 2016 8:41:43 PM CET Keller, Jacob wrote:
>
> Dear Crystallographers,
>
>
> I don't think there is any feasible way crystallographically to distinguish
>
> between nitrate and carbonate or bicarbonate-correct? But that is not my
>
> main question.
>
>
> My main question is: given that nitrate and carbonate are both very
>
> important and also very different physiologically, and therefore they must
>
> be distinguished/recognized by cells, how is this done, since the ions are
>
> so similar in structure? Is there some aspect of these ions that differs
>
> dramatically of which I am not aware? What kind of "handles" could a
>
> protein grab onto to distinguish between nitrate and carbonate/bicarbonate?
>
>
> JPK
>
>
>
> ***
>
> Jacob Pearson Keller, PhD
>
> Research Scientist
>
> HHMI Janelia Research Campus / Looger lab
>
> Phone: (571)209-4000 x3159
>
> Email: kell...@janelia.hhmi.org >
>
> ***
>
>
>
> --
> --
> Paul Scherrer Institut
> Tim Gruene
> - persoenlich -
> OFLC/102
> CH-5232 Villigen PSI
> phone: +41 (0)56 310 5297
>
> GPG Key ID = A46BEE1A
>
>
> Harry
> --
> Dr Harry Powell
> Chairman of International Union of Crystallography Commission on
> Crystallographic Computing
> Chairman of European Crystallographic Association SIG9 (Crystallographic
> Computing)
>
>
>
>
>
>
>
>
>
>
>
>


-- 
Post-Doctoral Research Associate
Texas A&M University
Dept. of Biochemistry and Biophysics
Interdisciplinary Life Sciences Building
301 Old Main Drive, Lab 2138
College Station, Texas 77843

Re: [ccp4bb] Offtopic: Software to closely visualize interacting partnets in protein complex

[Gulcin Gulten]

Hi,

PDBsum (http://www.ebi.ac.uk/pdbsum/)  can also analyze and make a summary
of interactions between partners of a protein-protein complex. Just submit
your pdb by clicking the 'generate' option from the left menu on the main
page.

Best,

Gulcin Gulten, Ph.D.

On Tue, Mar 10, 2015 at 11:57 AM, gert  wrote:

> Dear Debasish,
>
> The WHAT IF software can do some things for you. As you probably don't
> want to install a thirty year old package just for some inter-chain
> contacts, I added a server for you to the WHAT IF servers that are
> available at http://swift.cmbi.ru.nl/ look under contacts, it is the
> bottom server on that page.
>
> Greetings
> Gert
>
>> Dear All,
>>
>> Apologies for this little off-topic inquiry. I want to closely
>> visualize the interacting residues in an multimeric protein complex to
>> understand the nature of interactions. Is there any good software to
>> give this information with good clarity.
>> Any suggestion is highly appreciated.
>>
>> Thanks,
>> Best !!!
>>
>> Debasish Kumar Ghosh
>>
>>
> Het Radboudumc staat geregistreerd bij de Kamer van Koophandel in het
> handelsregister onder nummer 41055629.
> The Radboud university medical center is listed in the Commercial Register
> of the Chamber of Commerce under file number 41055629.
>



-- 
Post-Doctoral Research Associate
Texas A&M University
Dept. of Biochemistry and Biophysics
Interdisciplinary Life Sciences Building
301 Old Main Drive, Lab 2138
College Station, Texas 77843