Dear Dr. Philippe,
There is no symmetry axis nearby the density. I did not computed anomalous
map for this structure. In this structure, the occupancy of Co is only 0.4
(May be because I have added less Co). We have proved the presence of Co
in one of our another crystal structure of same protein
The Université of Paris-Saclay is pleased to present the MOOC " Voyage au cœur
du vivant avec les rayons X : la cristallographie", which results from a tight
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The use of three-dimensional structures o
Hi Anamika,
As it was said before, a cocktail of protease inhibitors should be
fine. But let`s say you can not overcome the problem. It is not specified
if you are doing this dialysis to cleave or not your His-tagged protein but
even this you could try getting samples in 1 hour interval
suppose protease is the issue, then avoid overnight dialysis
发自网易邮箱大师
在2017年10月26日 22:18，Anamika Singh 写道：
Dear All,
I am purifying the His-tagged proteins ( 21Kda) using buffer 20mM Tris, 150mM
Nacl, and 5mM MgCl2 with 500mM imidazole. Earlier I was facing the
precipitation problem during
Dear Johan
one more copy :-)
Yes, you can get it from
http://www-ibmc.u-strasbg.fr/spip-arn/spip.php?rubrique2&lang=en
Sorry for inconvenience and answering so late...
Luca, Daniel and Pavel, many thanks for your help !
Sacha Urzhumtsev
- Le 26 Oct 17, à 18:50, Hattne, Johan a écri
Dear Johan
one more copy :-)
Yes, you can get it from
http://www-ibmc.u-strasbg.fr/spip-arn/spip.php?rubrique2&lang=en
Sorry for inconvenience...
Luca, Daniel and Pavel, m
- Le 26 Oct 17, à 17:39, Hattne, Johan a écrit :
> Dear all;
> Would anybody know where I can find efresol (a
Dear All,
Thanks. I tried PDBemotif, indeed, it works very well!
On Thu, Oct 26, 2017 at 10:04 AM, Andrew Lovering <
andrewleelover...@googlemail.com> wrote:
> The backbone psi phi angle option in pdbemotif should limit hits to a
> particular secondary structure.
>
> Good luck!
> Andy
>
> On 26
The backbone angle search in pdbemotif should limit it to particular secondary
structure.
Good luck!
Andy
From: xiaolei...@gmail.com [xiaolei...@gmail.com]
Sent: October 26, 2017 5:53 PM
To: Andrew Lovering; Joana Pereira
Cc: CCP4BB@JISCMAIL.AC.UK
Subject:
Dear All,
Thanks for the suggestions! I tried MPI pattern search, MOTIF2 as Andrew
suggested, they worked fine to pull out of the PDB containing short
sequences. What I need to do is a little bit more, I'd also like to know my
hit region's secondary structure (helix, sheet, or loop), MPI and MOTI
Thanks a lot, Luca, Pavel, and Daniel! I now have sufficiently many copies to
last me well into 2020!
// Cheers; Johan
> On Oct 26, 2017, at 11:58, Bonsor, Daniel wrote:
>
> Is this not it?
>
> http://www-ibmc.u-strasbg.fr/spip-arn/rubrique257?lang=en
>
> At the bottom of the page.
>
>
I agree that the difference density isn’t “noise". However, just because it’s
not noise doesn’t mean that it is modellable (with an atomic model) — the
crystallographic density is an average over billions of molecules, and if its
not obvious at 1.6Å what is bound, then it’s probably a superposit
Is this not it?
http://www-ibmc.u-strasbg.fr/spip-arn/rubrique257?lang=en
At the bottom of the page.
Daniel A Bonsor PhD.
Sundberg Lab
Institute of Human Virology
University of Maryland, Baltimore
725 W Lombard Street N370
Baltimore
Maryland
MD 21201
Tel: (410) 706-7457
From: CCP4 bulletin bo
Johan,
core functionality described in that paper is implemented in cctbx. Re the
stand-alone program -- I'm cc'ing to the author.
Pavel
On Thu, Oct 26, 2017 at 8:39 AM, Hattne, Johan
wrote:
> Dear all;
>
> Would anybody know where I can find efresol (as detailed in
> http://dx.doi.org/10.1107
Dear all;
Would anybody know where I can find efresol (as detailed in
http://dx.doi.org/10.1107/S0907444913016673) these days? Googling lead me to a
2014 post
(https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1406&L=ccp4bb&F=&S=&P=155751),
but those links result in 403 Forbidden as of right
Hi,
Given the weakness and shapelessness of the density I doubt it is "one
conformation of one thing", but rather a superposition of "one or more
conformations of one or more things”. If that is the case then there probably
isn’t enough information in the electron density or enough prior inform
Hi Vijay,
Why there is no 2mFo-DFc (blue) feature on this mFo-DFc (green) map?!! Is
the contour level for blue map set high?!! If there is no 2mFo-DFc density,
should this be consider as noise?!!
Hope this helps,
Best Wishes,
Partha
On Thu, Oct 26, 2017 at 10:23 AM, Vijaykumar Pillalamarri <
vi
Dear Dr. Vaheh,
I tried fitting waters around Co but the positive density is still present
even after refinement.
Thanks,
Vijaykumar
On 26 October 2017 at 20:19, Oganesyan, Vaheh
wrote:
> Water molecules completing Co coordination?
>
>
>
> *Regards,*
>
>
>
> *Vaheh Oganesyan*
>
> *www.medimmun
Hello,
PMSF inhibits only 1 class of proteinases
You can try to add other inhibitors :
e.g. for purification from yeast I used the following in addition to PMSF:
1000 x stock individual inhibitors
pepstatin5 mg/ml methanol
chymostatin1 mg/mlDMSO
antipain3 mg/mlmethanol (sonicate to dissolve)
Dear All,
I am purifying the His-tagged proteins ( 21Kda) using buffer 20mM Tris,
150mM Nacl, and 5mM MgCl2 with 500mM imidazole. Earlier I was facing the
precipitation problem during dialysis but with the addition of 50mM L-Arg
somehow managed to overcome the precipitation issue. But this time I
Sorry all this was obviously meant for the helpdesk...
Best wishes Graeme
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Graeme Winter
[graeme.win...@diamond.ac.uk]
Sent: 26 October 2017 14:56
To: ccp4bb
Subject: [ccp4bb] mtzdmp gives segme
Folks
I have a data set with 50 wavelengths in - mtzdmp dies as follows:
mtzdmp
/dls/mx-scratch/gw56/LCY/50/process-all-merge-sep/LCY15/scale/LCY_LCY15_sorted.mtz
###
#
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I would guess that you want to search PDB for a small motif you've observed in
a structure of yours, looking to find examples of it used in same context?
If that's true, I would recommend PDBemotif, put the sequence in, and then use
the backbone psi phi angles of your motif as a secondary constra
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