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Nicolas Foos PhD - ARISE fellow
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EMBL Grenoble, McCarthy Team
71 av. des
e named giant.logs"
So I tried to fixed it myself, without success up to now. Maybe I am
missing something obvious.
I did search on the ccp4bb archive. Someone had exactly the same issue.
But I couldn't find any answer.
If someone could help me.
Have a nice day.
Nicolas
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DNA not have to be blunt ended?
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EMBL Grenoble, McCarthy Team
71 av. des Martyrs,
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Hi Almudena,
did you cut the res. after the merge of your "individual" datasets ? or you cut
for each and then you merged?
Because I will probably go for the first, I merge and then I decide where to
cut. If you cut for each, maybe you "miss" the gain provide by the redundancy
you have cumula
Hi Kahkashan,
did you consider to use ccCluster. This program is very helpful. It's designed
exactly for what you want. It allow an easy and quick analysis of which data
sets you should merge.
You can find it here : [ https://github.com/gsantoni/ccCluster |
https://github.com/gsantoni/ccClust
Dear Simone,
I think here is what you are looking for :
https://www.mitegen.com/product/dual-thickness-micromounts/
Best,
Nicolas
Nicolas Foos
PhD
Structural Biology Group
European Synchrotron Radiation Facility (E.S.R.F)
71, avenue des Martyrs
CS 40220
38043 GRENOBLE Cedex 9
+33 (0)6 76
at
relatively "low" resolution.
Hope this help.
Nicolas
Nicolas Foos
PhD
Structural Biology Group
European Synchrotron Radiation Facility (E.S.R.F)
71, avenue des Martyrs
CS 40220
38043 GRENOBLE Cedex 9
+33 (0)6 76 88 14 87
+33 (0)4 76 88 45 19
On 08/03/2019 10:36, Tereza Skalo
that works very well.
Nicolas
Nicolas Foos
PhD
Structural Biology Group
European Synchrotron Radiation Facility (E.S.R.F)
71, avenue des Martyrs
CS 40220
38043 GRENOBLE Cedex 9
+33 (0)6 76 88 14 87
+33 (0)4 76 88 45 19
On 06/06/2018 14:25, Kay Diederichs wrote:
Dear all,
I haven't tried t
I lkije the riddle, so:
I guess it's something for Signal Noise Ratio (?) (help by the context)
;-)
Nicolas
Nicolas Foos
PhD
Structural Biology Group
European Synchrotron Radiation Facility (E.S.R.F)
71, avenue des Martyrs
CS 40220
38043 GRENOBLE Cedex 9
+33 (0)6 76 88 14 87
+33 (0)4
quence and create a pdb model. Once you have this, you can fit it with you
favorites program or manually. Depending of your strategy, you will need to
merge your current model with the DNA one and continue to refine.
HTH
Nicolas
Nicolas Foos
PhD
Structural Biology Group
European Synchrotron Radiatio
understand what is going on.
Hope this finally help.
Nicolas
Nicolas Foos
PhD
Structural Biology Group
European Synchrotron Radiation Facility (E.S.R.F)
71, avenue des Martyrs
CS 40220
38043 GRENOBLE Cedex 9
+33 (0)6 76 88 14 87
+33 (0)4 76 88 45 19
On 29/01/2018 20:28, Peng wrote:
Hello, every
Hello,
I am not sure but I had the same kind of problem using ccp4 on Linux "exotic"
distribution which use python 3 by default.
Check that your Linux installation has python 2.x as default python in your
environement.
Hope this guide a bit the trouble shooting.
Nicolas
Horrell, Sam
ssibility let's try.
Hope to help.
Nicolas
Nicolas Foos
PhD
Structural Biology Group
European Synchrotron Radiation Facility (E.S.R.F)
71, avenue des Martyrs
CS 40220
38043 GRENOBLE Cedex 9
+33 (0)6 76 88 14 87
+33 (0)4 76 88 45 19
On 21/06/2017 09:34, Chen WeiFei wrote:
Dear All,
W
maybe are they already good enough to do some in-situ data
collection or serial synchrotron experiment.
Hope to help
Nicolas
Nicolas Foos
PhD
Structural Biology Group
European Synchrotron Radiation Facility (E.S.R.F)
71, avenue des Martyrs
CS 40220
38043 GRENOBLE Cedex 9
+33 (0)6 76 88 14 87
plain of
Xtriage about outlier is due to this high mosaicity. What is the
diagnostic of Xtriage in terms of possible twinning? I am also wondering
about a pseudo translation.
Maybe try to re-processed your data in this direction.
Hope to help.
Nicolas
Nicolas Foos
PhD
Structural Biology
view,
surface only... and if you consider to discuss small variations the
resolution of the data and the reliability of your model may have
important influence.
Nicolas
Nicolas Foos
PhD
Structural Biology Group
European Synchrotron Radiation Facility (E.S.R.F)
71, avenue des Martyrs
CS 40220
discriminate "interaction with resin" that you suspect from oligomerization.
Nicolas
Nicolas Foos
PhD
Structural Biology Group
European Synchrotron Radiation Facility (E.S.R.F)
71, avenue des Martyrs
CS 40220
38043 GRENOBLE Cedex 9
+33 (0)6 76 88 14 87
+33 (0)4 76 88 45 19
On 12/01/2017 01:50, C
ch easier for the rest to line up (this is consistent with
Patrick's explanation).
Cheers,
Tim
On Wednesday 04 January 2017 05:45:50 PM Nicolas FOOS wrote:
Dear Evette,
If I was is your situation (explaining nucleation and other concept). I
will discuss in terms of energy.
I mean obtainin
you
mixed orange with water melon it's difficult to obtain nice pyramid.
For crystallization experiment which work, I have no Idea out of the one
you already mentioned.
Hope this help.
Nicolas
Nicolas Foos
PhD
Structural Biology Group
European Synchrotron Radiation Facility (E.S.R.F)
71, avenu
Dear Paul,
I am currently not working under Ubuntu OS, so I can't try your fix.
But if my memory is still good, it was exactly the problem (the dynamic
menus). And I am sure that some ccp4bb reader will be happy to find and
try this solution.
Thank you.
Nicolas
Nicolas Foos
PhD
Struc
well with numbers of hardware
configuration especially if you activate the proprietary repository in
the packet manager.
I used for a long time Xubuntu without any issues and was very happy
with it. CCP4 and other soft are perfectly packed for this OS.
HTH
Nicolas
Nicolas Foos
PhD
Structur
hese
axis.
Nicolas
Nicolas Foos
PhD
Structural Biology Group
European Synchrotron Radiation Facility (E.S.R.F)
71, avenue des Martyrs
CS 40220
38043 GRENOBLE Cedex 9
+33 (0)6 76 88 14 87
+33 (0)4 76 88 45 19
On 17/11/2016 23:48, Paul Emsley wrote:
On 18/11/2016 03:57, chemocev marker wrote:
Hi
ystal
structures. Acta Crystallographica D /70/, 1104–1114.
Nicolas
Nicolas Foos
PhD
Structural Biology Group
European Synchrotron Radiation Facility (E.S.R.F)
71, avenue des Martyrs
CS 40220
38043 GRENOBLE Cedex 9
+33 (0)6 76 88 14 87
+33 (0)4 76 88 45 19
On 25/10/2016 11:04, ansuman biswas wrote
Hello,
you can try Nucplot. http://www.ebi.ac.uk/thornton-srv/software/NUCPLOT/
Very usefull and tunnable to find and show dsDNA/protein complex.
Hope to help.
Nicolas
Le 16/10/13 21:23, Eike Schulz a écrit :
Hello everyone,
I would like to display the interactions of a protein dsDNA complex
Dear Yu,
in the CORRECT.LP,
The I/Sig is very low for the resolution higher than 4.17 . If i were
you i probably cut the resolution around 4 Å not 2.8 Å. Because of the
I/sig and CC.
This explain probably the bad electron density. Because, you have not
strong information for the resolution
Dear Appu,
one direction of your cristal has very anistropic diffraction. I think
your cristal has grown like multi-layer. The problem is probably due to
the DNA. If the different "layer" of your cristal are not very well
aligned, you have this type of problem.
In my opinion, you can try to
Dear wei,
i think you have to keep in mind what do you have in your cristal
growing condition, and in you protein buffer.
Because maybe you can find which molecules this ligand could be.
It's difficult to help more, because we don't know you level of sigma
for the map and the resolution of you
Hi Rafal,
have you try ADXV ?
I never try to use idiffdisplay, but i know that ADXV can display
resolution circles.
If your software is able to open the image, but can't show the circles.
I think it's not really a problem with the image format, but with the
information in the Header of your
Dear Alex,
i work with Purifier.
To my mind, this is a very nice system. High reliability. We are a lot
of differents users and we share the same system, some of us are not
very implicated in the cleaning and maintenance procedure, nonetheless
the Akta works well. Akta Purifier with 3 waveleng
Hi Wei,
If you have an interpretable density, the efficientest way in my
opinion, is to construct manually (only 6bp).
You can use coot and the button "add residue". Coot can add nucleotide
directly at the extremity of your existing nucleic acid model.
Hope to help you.
Nicolas
Le 18/03/1
Dear Chen,
you can find lsqkab and Topp in ccp4 : coordinates utility and superpose
molecule (if you use the GUI).
Hope to help you.
Nicolas
Le 14/03/13 21:53, Chen Zhao a écrit :
Dear all,
I am now struggling to align two 3D RNA structures. I know there are a
bunch of web servers, but th
Dear Wei,
If i understand your different experiment, you try to obtain your
protein DNA complex at different salt concentration with different
method to reach the final concentration.
I read that you try 150 mM KCl + 150 mM NaCl as high concentration salt,
it result in 300 mM cations and 300
Dear Chang,
i have seen ATP diffraction, it's not very different of your image.
Maybe you have only ATP in your crystals?
Best regard
Nicolas
Le 12/10/12 14:56, Chang Qing a écrit :
Dear Tim
I think your explanation is logical. But I tried ADP as ligand first
and got crystals and diffracti
Dear Leo,
I use "*superpose*" included in the ccp4 programms suite. You can manage
a lot of parameters.
In my case for exemple, i use the "superpose specified atoms/residues"
I defined the model which move et the one wich is the reference.
I precise the residues range (in DNA case residue me
Hi,
I find some information here :
http://www.csb.yale.edu/userguides/datamanip/xplor/xplorman/htmlman.html
And for a more usefull answer, they explain that :
The hbuild statement tries to build the position of any selected
hydrogen based on the position of the heavy atom antecedents (Brünge
Hello Bashir,
Maybe it's because your dataset present too much weak diffraction spots.
You can try to change the setting for the strong pixel detection. You
can Try to decrease a little bit de I/sigma. Have you define the
resolution range?
I read on your message that you resolution start at
Hi,
i think that this option for the real space refinement is for _all_ the
torsion angle.
You can find more informations with this link :
http://www.ysbl.york.ac.uk/~emsley/coot/doc/chapters/user-manual_5.html#SEC92
In the 5.1 section.
Hope to help you.
Nicolas
Le 24/07/11 02:24, zhang yu
Hello Afshan,
Maybe the programm that you use for refinement need specific entry with
restraint for your modified amino acids.
More precisely, i think about the *.cif file for exemple.
HTH.
Nicolas
Le 21/07/11 17:13, Afshan Begum a écrit :
Dear all,
I have facing one problem during the ref
Hello Edward,
I am not really certain for my explanation, but your error message about
the namelist could be provoked by a problem in your input files. In fact
you have to oriented each strand and define limits of the two strands.
If you do a mistake with the orientation you can have this typ
Hi Meg,
If the bigger peak is appearing when you wash with 1M NaOH, i think your
protein is precipitated on the the column. If you have your protein
relatively pure after the precedent step, maybe you can try different
buffer. You can probably find a better buffer than this one. If your
prot
Hi,
maybe you solved your problem,
if not, you can try this : You prepare your protein at high salt
concentration. After that you add your ssDNA directly and you proceed by
dialysis. You prepare your dialysis with a low salt concentration
buffer. You can use different buffer by step in order
Hi Rex,
If you have to mutate only few bases, maybe you can proceed manualy with
coot. And maybe after mutate refine at less for geometricals parameters
of your "new" base.
Nicolas.
Le 13/09/10 16:43, Rex Palmer a écrit :
Does anyone know of a program that will mutate a given base in the pd
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