Hi
I would appreciate it if someone could share with me a step by step
protocol for making a stable GDP.BeF3 solution which is often used as a
transition state analogue for structural studies of a protein complex ?
Or a vendor from where it can be purchased directly.
Regards
Firdous
Hi everyone
In ChimeraX I am not able to show Gly simultaneously as a stick and
cartoon. If I am trying to show Gly as a stick then the cartoon line breaks
up at this position. And this is for all structures if you see. By showing
a cartoon and stick together, the sticks for all amino acids show
Hi
Does anybody know how to make thioester bonds in Chimera or ChimeraX ?
I am unable to make a bond between Cys321 in mol A with Gly1 in mol B
(S-glycyl-L-cysteine) using Chimera or ChimeraX.
I tried Isolde in ChimeraX and Build Structure in Chimera to make a bond
between selected atoms but so
Do the mass spec of your crystal to identify the other protein. Once done
solve your structure and build the complete model. This should be straight
forward and quick.
Best Wishes
On Sat, 4 Nov 2023, 09:05 Sam Tang, wrote:
> Dear community,
>
> I am solving the structure of a complex between
Hi
I am getting the following error while running the class ranker program for
automatically selecting the 2D classes. Can anybody please suggest where
the issue is ?
PYTHON ERROR: The required python module 'torch' was not found.
in: /usr/local/relion-4.0-source/src/class_ranker.cpp, line 1954
Hi
I too have an issue with my latest M2 Mac mini where the Phaser in Phenix
runs extremely slow in comparision to my intel Mac laptop. I had also
posted it on the phenix bulletin board but so far did not receive any
suggestions how to fix it.
By any chance if you guys have the previous email
Thanks everyone for their wonderful suggestions.
Best
F
On Wed, Jun 22, 2022 at 11:42 AM Patrick Loll wrote:
> Kevin and Guillaume said it all quite well. I just want to stress one
> thing, namely that these solutions are metastable, and will eventually
> precipitate (hours to days).
>
> In
uate protective measures (PPE, hood, etc.).
>
> Good luck,
>
> Guillaume
>
>
> On 21 Jun 2022, at 19:38, Firdous Tarique
> wrote:
>
> Hi
>
> Sorry for the off topic question but can anybody please suggest how to
> dissolve Aluminium Fluoride in water ? I k
Hi
Sorry for the off topic question but can anybody please suggest how to
dissolve Aluminium Fluoride in water ? I know it has little solubility in
water but have seen people using AF3 for their structural studies (ADP +
AF3 as ATP analogue). Is there any other solvent where they have made AF3
Emsley
wrote:
> On Thu, 2021-06-10 at 00:20 +0530, Firdous Tarique wrote:
> > Hello everyone
> >
> > Can anybody tell me the Coot shortcut key for mutate or mutate and
> refine. Is there any way to turn it on or to assign
> > a particular key if it is disabled ?
&g
Hello everyone
Can anybody tell me the Coot shortcut key for mutate or mutate and refine.
Is there any way to turn it on or to assign a particular key if it is
disabled ?
Regards
Firdous
To unsubscribe from the CCP4BB
dge Institute for Medical Research Tel: +44 1223 336500
> The Keith Peters Building Fax: +44 1223
> 336827
> Hills Road E-mail:
> rj...@cam.ac.uk
> Cambridge CB2 0XY, U.K.
> www-structmed.c
Dear CCP4 community members.
I have solved a crystal structure of a protein and am now trying to get a
structure with a ligand bound to it, but so far unsuccessful. A homologous
structure with the same ligand is present in the RCSB PDB (un published).
Is it permissible to fetch structural
Hi
Just downloaded the new CCP4-7.1. Wondering where the extension bar in Coot
0.9 has gone. Please help me to find it. I think it is hidden somewhere.
Best
Kahkashan
To unsubscribe from the CCP4BB list, click the
Hi
I am trying to incorporate novel disulfide bond by introducing Cys mutants
at the interface of a protein complex (A+B) and (C+B) whose crystal
structure are already known. The idea is to introduce novel disulfide bonds
in these individual complexes which does not dissociate and can be tried
> Guillaume
>
>
> On 16 Mar 2020, at 08:58, Firdous Tarique
> wrote:
>
> Hi
>
> I have a weird question. Is it possible to incorporate or mutate amino
> acid residues at the interface of two interacting surfaces in a multi
> subunit protein complexes hoping it
Hi
I have a weird question. Is it possible to incorporate or mutate amino acid
residues at the interface of two interacting surfaces in a multi subunit
protein complexes hoping it to form a disulfide bond making the over all
complex more stable for downstream structural studies ?
Is there any
Hello everyone
I am trying to run a molecular dynamics simulation of a protein which has a
Zn atom and few phosphorylated PTMs (Thr is phosphorylated). PTMs and Zn
play essential roles to maintain the structural integrity and therefore
cannot be removed rather I want to keep both of them for my
Hi.
I have collected multiple datasets for my crystals and now want to merge
them. Iwanted to know that between Blend and pointless, which programme is
better to merge two or more data sets?
Thanks
Kahkashan
To
Hi Paul
No, I haven't. Now I am going to.
Faisal
On Tue, Dec 24, 2019 at 1:02 PM Paul Emsley
wrote:
> On 24/12/2019 15:23, Firdous Tarique wrote:
> >
> > I recently updated my macOS to the latest Catalina and here the problem
> begins. A number of my structural
> > bio
Hi Guys
I recently updated my macOS to the latest Catalina and here the problem
begins. A number of my structural biology softwares like Coot, CCP4i2 and
CCP4 are not working. Are you facing the same problem?
Any solution please
Kahkashan
Dear members
I have got beautiful crystal hits in SaltRx screens which are not
diffracting to a good resoultion. All of them are salt based condition and
I am not able to formulate a good cryoprotectant for these crystals. I also
think that in my case the poor resolution is due to a poor
uantum refinement of a small
>> structure done as part of quantum refinement project (www.qrefine.com):
>>
>> http://scripts.iucr.org/cgi-bin/paper?S2059798317016746
>>
>> All the best,
>> Pavel
>>
>> On Fri, Aug 17, 2018 at 6:27 PM, Firdous Tarique <
Hello everyone.
I have a basic question. When a validation report of a coordinate is
generated we often come across a term known as "Too-Close Contacts".
First of all can somebody please explain me what is the shortest
interatomic distance between the two atoms which is permissible ?
Next, in
*Hello everyoneI have a structure whose quality improves a lot when
submitting it to PDB-Redo server. But when I am trying to put the output
coordinates for validation it is not taking up and comes with message that:
Structure contains Residual B values and TLS records are present but
required
Hello everyone
I am trying to clone some domains of a transmembrane protein. I have used
an online server "Phobius" for the prediction of sequences which is showing
it to be a membrane protein with cytoplasmic, non cytoplasmic and
transmembrane regions. Attached is the image of that prediction.
Hello everyone.
I am struggling with the solubility or expression of my proteins in BL21DE3
E.coli expression cells. In one of my construct I have a Sumo-His fusion at
the n-terminal of my protein. After induction what I see is the expression
of the Sumo tag only. My sequencing results are fine
Hi
I am trying to crystallize a Fe-S cluster containing protein which is
sensitive to oxygen present in the air. In the presence of air due to
'fenton reaction' the Fe-S breaks to give heterogeneous population of
different Fe-S cluster and free Fe species. I also faced lots of
difficulties in the
28 matches
Mail list logo