Phoebe,
I'm red green blind myself, and it is not as straight forward as it
sounds. The problem is that we "see" red and green despite lacking one
of the color receptors (I actually prepared a figure using red and green
once and got a referee comment that red/green blind people would have
difficu
FYI
Kevin Cowtan has a web page that discusses using color diagrams with respect to
the color blind interpretation.
http://www.ysbl.york.ac.uk/~cowtan/colour/colour.html
-Bryan
Thank you Mark for the link, this is really helpful.
Jürgen
..
Jürgen Bosch
Johns Hopkins University
Bloomberg School of Public Health
Department of Biochemistry & Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W8708
Baltimore, MD 21205
Offic
Professor Rice,
When publishing in NAR (Nucleic Acids Research), it was recommended that we use
"colors friendly to the color blind". You can read about it here:
http://jfly.iam.u-tokyo.ac.jp/html/color_blind/
It is quite nice that they went to the trouble of showing us "how they see it".
And
On Friday, May 31, 2013 01:34:51 pm Phoebe A. Rice wrote:
> I feel badly that one of my undergrads had trouble telling an O from a C in a
> pymol homework set because he's color blind. (The assignment involved telling
> me why the a GTP analog (GDPCP) wasn't hydrolyzed).
> Is there a handy by-ato
Why not use yellow carbons (colour by atom menu) and hit the builder button in
pymol which shows bond order (carbonyls).
You could also type colour gray, name o, this colours the carbonyls gray (or
any other colour that works) "name o* colours all oxygens
Hope this helps
From: CCP4 bulletin boa
I feel badly that one of my undergrads had trouble telling an O from a C in a
pymol homework set because he's color blind. (The assignment involved telling
me why the a GTP analog (GDPCP) wasn't hydrolyzed).
Is there a handy by-atom coloring scheme I can recommend that works for the
red-green co
The international PhD program of the Biozentrum, University of Basel,
Switzerland, is open for applications until June, 30th.
Successful candidates in this competitive program will have a chance to do two
lab rotations of two month each before selecting a host lab at the Biozentrum
for their P
Hi Wei
The sarco(endo)plasmic reticulum Calcium ATPase (SERCA) require Calcium
as a substrate to be functional.
Preben
On 5/31/13 12:25 PM, Wei Liu wrote:
Dear all,
As we all know, many proteins contain calcium ions. Does anyone know if there
are reported cases where calcium ions play a catal
Hi,
Also Secreated Phospholipase A2 enzyme requires Calcium
for its catalysis.
Regards
Kavya
>
> On 5/31/13, Patrick Loll wrote:
>> staph nuclease
>>
>> On 31 May 2013, at 6:25 AM, Wei Liu wrote:
>>
>>> Dear all,
>>>
>>> As we all know, many proteins contain calcium ions. Does anyone know if
>>>
We had a case where Calcium facilitates productive ATP binding (Nat Struct
Mol Biol. 12 (2005), 32-7) ... not sure whether one would call that a
"catalytic function", but it's certainly not "structural"
Best
Clemens
> -Ursprüngliche Nachricht-
> Von: CCP4 bulletin board [mailto:CCP4BB@JIS
Hi Liu,
A complex example is oxygen envolving complex of photosystem II..
Biochemistry 2003, 42, 6209-6217
http://www.rsc.org/chemistryworld/News/2011/August/05081101.asp
-Vandu...
On 5/31/13, Patrick Loll wrote:
> staph nuclease
>
> On 31 May 2013, at 6:25 AM, Wei Liu wrote:
>
>> Dear all,
>
staph nuclease
On 31 May 2013, at 6:25 AM, Wei Liu wrote:
> Dear all,
>
> As we all know, many proteins contain calcium ions. Does anyone know if there
> are reported cases where calcium ions play a catalytic role rather than a
> structural role in enzymes?
>
> Best
> Wei Liu
-
In our case, the Ca ion is essential for activity but not correct folding. The
enzyme requires Ca2+ (Mg or Mn) for activity. The crystal structure shows a
single Ca2+ ion coordinated by a key catalytic aspartate and two backbone
carbonyls. Mutagenesis of the key Asparate abolishes enzyme activit
I would think a Google search would make some suggestions for you. There
are lots of cases of proteins which require Calcium to function, but it is
a bit chicken-and-egg-y - can the protein only function after it folds
correctly, and is the Ca essential for that folding?
On 31 May 2013 11:54, R
My work with colicin M class bacteriocins shows that they require Ca2+ (or Mg
or Mn) for catalysis:
1 Grinter, R., Roszak, A. W., Cogdell, R. J., Milner, J. J. and Walker,
D. (2012) The Crystal Structure of the Lipid II-degrading Bacteriocin
Syringacin M Suggests Unexpected Evolutionary R
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Hi Sebastiano,
that's good to know. Thanks for the comment!
Tim
On 05/30/2013 06:58 PM, Sebastiano Pasqualato wrote:
>
> Tim, if I'm not wrong, if you judo type "dss" on the pymol command
> line you will apply dssp to your pdb and have your model c
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