Dear Paul,
Thank you
Regards
Devbrat
On Thu, Jun 6, 2024, 8:53 AM Paul Emsley wrote:
>
> On 06/06/2024 04:00, Devbrat Kumar wrote:
>
>
> --
> Dear Paul,
>
> Thank you for your response. I wanted to compare a Coulomb potential map
> to an electron density map. Before aligning these maps, I need
On 06/06/2024 04:00, Devbrat Kumar wrote:
--
Dear Paul,
Thank you for your response. I wanted to compare a Coulomb potential
map to an electron density map. Before aligning these maps, I need to
bring them to similar parameters, which requires rescaling one map to
match the other. After t
Dear Paul,
Thank you for your response. I wanted to compare a Coulomb potential map to
an electron density map. Before aligning these maps, I need to bring them
to similar parameters, which requires rescaling one map to match the other.
After that, I can proceed with density subtraction.
I hope t
Dear Jon
I will keep this in mind while working on it.
Thank you.
Regards
Devbrat
On Wed, Jun 5, 2024, 7:11 PM Jon Cooper <
488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:
> Another factor might be that ccpem uses a different axis order to gemmi
> and ccp4 ;-0
>
> Best wishes, Jon Cooper.
Dear Guillaume
I will keep that in mind while trying.
Thank you
Regards
Devbrat
On Wed, Jun 5, 2024, 5:21 PM Guillaume Gaullier <
guillaume.gaull...@kemi.uu.se> wrote:
> With a cryoEM map, it's easier to do the rigid-body fitting of step 2 in
> real space (this is trivial to do interactively in
Hello Eleanor,
Thank you for your consistent response to my inquiry. I will follow your
suggestions and willl tell you the updates.
Regards
Devbrat
On Wed, Jun 5, 2024, 5:10 PM Eleanor Dodson <
176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:
> Hmm - rather tricky! I would do an MR search
Hello Martin,
Thank you for your email and I will look into it.
Regards
Devbrat
On Wed, Jun 5, 2024, 4:16 PM Martin Malý wrote:
> Dear Devbrat,
>
> I am now playing with a similar problem but I don't have a simple solution
> for you as I'm also quite stuck. You can check these software tools
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people m
At this resolution you should be able to infer differences between C and O
based on the map levels at each location. Another dead giveaway is the bond
lengths and the asymmetry of the top region - that is not a carboxylic acid
to me.
This looks lime MPD to me, very classic shape.
Artem
On Wed, J
Oooops, correct, got my reasoning turned around too…. But it could still be a
betain if the water is more distant… We need a different view!
Best
J.
__.
Dr. math. et dis. nat. Jeroen R. Mesters
Biological Safety Officer (BBS)
Deputy, Lecturer, Program Coordinator Infection Biology
Visiting Pro
I sent my last response too soon….
The ‘top’ end of the molecule in the image looks more like a carboxylic acid
accepting H-bonds from two backbone amides (supporting the betaine assignment,
and not MPD), but the ‘bottom’ end of the molecule looks like it is forming an
H-bond with a well-ordere
Yes! That is why I excluded MPD as there is the water molecule close-by…. But
we need a different view….
Best
J.
__
Dr. math. et dis. nat. Jeroen R. Mesters
Biological Safety Officer (BBS)
Deputy, Lecturer, Program Coordinator Infection Biology
Visiting Professorship in Biophysics South Bohemia
It is pretty well-ordered, so I would expect the H-bonding pattern to
distinguish between betaine and MPD.
Best regards,
Z
***
Zachary A. Wood, Ph.D. (He/Him)
Professor and Graduate Coordinator
Josiah Meigs Distinguished Teaching Professor
Associ
Or, it could be MPD ;-?
Best wishes, Jon Cooper.
jon.b.coo...@protonmail.com
Sent from Proton Mail Android
Original Message
On 05/06/2024 17:54, Jeroen Mesters wrote:
> Thank you for this intriguing information!
>
> At the same time, this also implies that not all entities tha
Thank you for this intriguing information!
At the same time, this also implies that not all entities that have been
modelled as MPD are actually MDP but could also be a betain, right!?…..
Best,
Jeroen
__
Dr. math. et dis. nat. Jeroen R. Mesters
Biological Safety Officer (BBS)
Deputy, Lecturer,
"but another view might help."
I second that. I would specifically like to be assured that it is not sitting
on a special symmetry position.
===
All Things Serve the Beam
===
Hello Everyone,
It does look like trimethylglycine (betaine), but another view might help. If
it is, it is also made in ecoli and PEOPLE. It is a pretty common metabolite in
the microbial and animal kingdom…useful for balancing osmotic stress and
stabilizing protein structure (it is a strong ko
Hi,
proteins my pick up ligands from the „source" from which they were isolated….
Looks to me like trimethylglycine, an amino-acid derivative found in plants…
Regards,
Jeroen
__
https://orcid.org/-0001-8532-6699
Am 05.06.2024 um 17:44 schrieb Khadijah Ameen Khan
:
Dear All,
I am a first
On 05/06/2024 07:00, Devbrat Kumar wrote:
--
Hello Everyone,
Hello Devbrat,
I have a query regarding the resampling of cryoEM density to match
crystal density to obtain a density difference map. Specifically, I am
trying to determine if it is feasible to resample a cryoEM map with an
X
Many thanks to all who took out some time to reply.
Summary:
you can also use
https://www.neb.com/en/products/c3037-nebexpress-iq-competent-e-coli-high-efficiency
this has LacIq, we use it with all our pQE bassed vectors.
Gentauer may still sell those…
https://maxanim.com/strains/m15-prep4-esch
Another factor might be that ccpem uses a different axis order to gemmi and
ccp4 ;-0
Best wishes, Jon Cooper.
jon.b.coo...@protonmail.com
Sent from Proton Mail Android
Original Message
On 05/06/2024 12:51, Guillaume Gaullier wrote:
> With a cryoEM map, it's easier to do the
With a cryoEM map, it's easier to do the rigid-body fitting of step 2 in real
space (this is trivial to do interactively in ChimeraX) rather than by MR.
From: CCP4 bulletin board on behalf of Eleanor Dodson
<176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>
Sent: W
Hmm - rather tricky! I would do an MR search with the crystal model v the
EM density,
Steps would be:
1) convert EM density to "structure factors". - there are tools which do
this ..
1a) You need to go back to ccp4i - program sfall to read map to generate
SFs from map - then cad or sftools to add
Dear Devbrat,
I am now playing with a similar problem but I don't have a simple
solution for you as I'm also quite stuck. You can check these software
tools which involve some scripting in Python (NumPy, SciPy) and C++:
EMDA (for cryoEM maps, included in CCP-EM)
https://gitlab.com/ccpem/emda
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