Dear Dilip,
it's difficult to exactly analyse the coordination of your metal in 2D. But, my
suggestion is :
Try another metal like Zn, which maybe is a contamination (from the plastic of
eppendorf for example). Zn has more electron than Mg maybe that's the reason
why it's still green.
I
Dear Almudena,
I have some questions to help you, how many molecules are presents in the ASU ?
If more than one, maybe you can try to find NCS in the substructure. To perform
that it could be necessary to increase (more than 20) the radius of NCS
research parameters.
You can try to find NCS
Hi Saleem,
in my own experience with the yosemite update, after the update, i have had to
do that :
1) Xcode via apple store (itunes) you have to create or use you apple ID etc...
2) Install XQuartz :
http://xquartz.macosforge.org/downloads/SL/XQuartz-2.7.7.dmg
3) Install ccp4 :
Dear Vijay,
Have you try to use superpose in ccp4 ? In superpose it's possible to select
exactly what you want (atoms, residues...) .
In your case if you use only the atoms or the nucleotids that you want to be
superpose, it could be ok.
Hope to help.
Nicolas
]
Envoyé : mardi 26 mai 2015 14:56
À : FOOS Nicolas
Objet : Re: [ccp4bb] Hi
Dear Nicolas,
I ahd tried in superpose but it is not alligning and simultaenousli I had given
only the pdb
containing only the nucleotide but both of them dosen't work.
regards
Vijay
On Tuesday, 26 May 2015 6:22 PM, FOOS
Hi Charles,
I have some differents suggestions, maybe it could be a good idea to reconsider
the criteria for keep or discard data : Diederichs, K., et P. A. Karplus. «
Better Models by Discarding Data? ». Acta Crystallographica Section D:
Biological Crystallography 69, nᵒ 7 (1 juillet 2013):
Hi Ivan,
according to my experience, if you remove at the same time GuHCl and Triton,
you have huge risk of precipitation if the protein is not properly folded.
In my opinion, you have to do something like re-folding. It seems that your
protein could be solubilized from inclusion-body. In the
Dear Lu,
one simple solution is to remove the water molecules with text editor for
example. It depend of how-many times you have multiply water molecules and if
your model have several or more water molecules.
In coot you can remove it graphically, but according to my knowledge not
Hi Manjalu,
In my opinion, one way is to use iEX column. Depending of the Pi of you protein
and the one of the BSA, if they are sufficiently different, Ion exchange is on
possible way.
To separate your protein from BSA, you have to give us more information about
your protein if it's possible.
Hi Gajanan,
i never try Qhelix, but i use Chimera to do that. It's possible to mesure
angle, distance etc between helix.
Hope to help.
Nicolas
De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de Gajanan Arbade
[gajanan_pbi...@diat.ac.in]
Dear Sasha,
i try to answer one by one your question :
1) Not sur to understand what you mean by validate DNA constraints, if it's
about the geometry parameters liken angle bond length, you have to use
Moleprobity for example.
2) Fitting DNA in density, you can use coot, it's exactly the
...@gmail.com]
Envoyé : jeudi 24 juillet 2014 14:46
À : FOOS Nicolas
Cc : CCP4BB@JISCMAIL.AC.UK
Objet : Re: Problem in molecular replacement
How do I use DNA as search model? Can I use it in molrep or phaser?
On Thursday, July 24, 2014, FOOS Nicolas
nicolas.f...@synchrotron-soleil.frmailto:nicolas.f
Dear Sajid,
one first problem in your study is how-to adress if the deltaH mesured is
caused by the ligand interaction, or by the modification of dimer-monomer
equilibrium.
You have to well caracterise your system dimer-monomer. One other problem is
about the accessibility of the interaction
it depend of what you expected as information :
In this case your measure is resulting from ligand binding AND dimerization
(except if all the protein is already dimerized). I am not sur to understand,
do you know how many binding sites exists on one monomer ?
You should be able to determine the
Hello,
i cited this program with :
Hubbard, S.J., and Thornton, J.M. (1993). NACCESS (Computer Program, Department
of Biochemistry and Molecular Biology, University College London.).
I am not absolutly certain that's th best way.
Nicolas
De : CCP4
Dear Gajana,
you can use . PISA ((Krissinel and Henrick, 2007) (EMBL server)
and NACCESS (Hubbard and Thornton, 1993). (not for windows i think).
Hope to help
Nicolas
De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de Gajanan Arbade
Dear Meisam,
i don't know exactly what you need to do after the transfert, but if you want
collect without frozen, maybe you can try to use capillar.
Maybe can you mount your crystall in capillar before the travel ?
It's simple suggestion, i never did that.
Nicolas
Dear Almudena,
i think your problems com from the Flag in your input.mtz . You have to check
if your mtz has the correct column name. And you have to designate the one
which correspond to PHIB.
It depend from which programm com your input.mtz .
Hope to help.
Nicolas
Dear Antony,
Have you try to use the option - parralel 1, to see what hapen. Maybe it's
problem with the parallelism option. If you try this option you force to use
only one core and i think you decrease your need in memory. If this solution
help, you probably have to check the xdsInput
Hi Almudena,
you can also try mosflm as said Harry.
And you can try different setting in the XDS.INP, you can try to reduce the
STRONG_PIXEL (because you said spots are weak) number or/and
MINIMUM_NUMBER_OF_PIXELS_IN_A_SPOT (if the spot are small).
Nicolas
Hi Remi,
you place the pointer (pink cube) at the place where you want put the atom.
After you click on Place atom at pointer (yellow square with blue cross).
HTH
Nicolas
De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de Remie
Fawaz-Touma
along Y, you
replace and it should be good.
Finnaly, you have to turn your model in different position and replace the
pointer at the right place.
De : Edward A. Berry [ber...@upstate.edu]
Envoyé : mardi 18 mars 2014 17:50
À : FOOS Nicolas; CCP4BB
Hi Raji,
i the kit i used for this purpose was from Pierce it's call Protein BCA RAC
assay. BCA : for the colorimetric parts, en ad the RAC is for Reducing agent
compatibility. This RAC is also efficient with detergent. (according my
remember)
But you if you use at the same time detergent
The problem is that if you put detergent or reducing agent in Bradford or BCA,
the reaction is complet also without protein. You can't determine the color
gradient because every tubes are blue or purple.
De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK]
I agree with Dave, and i suggest one more method to estimate Kd,
The intrinsic fluorescence of proteins thanks to the aromatic chain side.
Maybe it's also possible to have an estimation with native gels if you use prot
A concentration as fixed and B protein concentration as variable. I am not
hello Andy,
i have different questions about your problem :
Is the hetero-dimer co-expressed ? Or the two partners are express separately ?
Have you controlled where are you proteins after the lysis, because if you
have many of your proteins in the pellet, it's not a good sign for the folding
Hi Thomas,
maybe you can try to use AMBER programs. http://ambermd.org/
I think these programs allow you to use different forcefield to minimise the
energy of your model.
Hope to Help
Nicolas
De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part
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