Hi, All,
I am new to MicroED (microcrystal electron diffraction). I know that X-ray
crystallography has phase problem, and I think MicroED has phase problem
too (it is diffraction of electron instead of x-ray). However, when I read
the Wikipedia, I could not understand the following description
ill will
> work. This is different from when you want to use the dye to do some
> quantitative work such as the Bradford assay. It would be interesting to
> know the effect of detergents on Bradford.
>
> Zhijie
>
>
>
> On Oct 4, 2018, at 9:26 PM, Alex Lee wrote:
>
> Dear
Dear All,
I am thinking that in an SDS-PAGE experiment, if protein samples are boiled
in SDS containing loading dye, and supposedly SDS interacts with proteins,
why the Coomassie Blue dyes could still interact with and stain the
proteins? I am thinking SDS is covering the proteins, making no
hael
>
> From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Alex Lee <
> alexlee198...@gmail.com>
> Reply-To: Alex Lee <alexlee198...@gmail.com>
> Date: Thursday, 19 October 2017 at 11:19
> To: "CCP4BB@JISCMAIL.AC.UK" <CCP4BB@JISCMAIL.AC
Hi All,
I tried to look for the 3-letter ligand for reducing reagent TCEP in PDB
but I could not find one. I even search with
"Tris(2-carboxyethyl)phosphine hydrochloride" in PDB but got right hit. How
do I need to to to pull the TCEP code out?
thanks. Coot works!
On Wed, Apr 19, 2017 at 10:20 AM, Vipul Panchal <panchal.vi...@igib.in>
wrote:
> I am not experienced with pymol. However if you are familiarized with
> coot, you can mutate and set rotamer. It is really simple.
>
> On 12-Apr-2017 12:15 AM, "Alex Lee&qu
MR, you should try to refine
>> the model in that SG, with only two twin domains, refining twin fraction. I
>> can guarantee that a good reviewer will have you do this (if not, then not
>> a “good reviewer.”)
>>
>>
>>
>> JPK
>>
>>
>>
>> *From:* CCP4
Or you might actually have a tetartohedral twin, but just try with the
>> higher-symmetry point group first, see what happens.
>>
>>
>>
>> JPK
>>
>>
>>
>> *From:* Alex Lee [mailto:alexlee198...@gmail.com]
>> *Sent:* Thursday, April 1
works out—I am interested in these types of
> things!
>
>
>
> JPK
>
>
>
> *From:* Alex Lee [mailto:alexlee198...@gmail.com]
> *Sent:* Thursday, April 13, 2017 9:08 PM
> *To:* Keller, Jacob <kell...@janelia.hhmi.org>
> *Cc:* CCP4BB@JISCMAIL.AC.UK
>
>
t;
>
>
>
> On 13 April 2017 at 19:52, Robbie Joosten <r.joos...@nki.nl> wrote:
>
> Hi Alex,
>
>
>
> You are not giving the number after refinement without the twin
> refinement. Nevertheless, R-free drops like this are not unheard of. You
> should check your
Dear All,
I have a protein/dna complex crystal and data collected at 3A and another
set at 2.8A, space group P32. L test shows twinning (fraction around 0.11).
The structure solved by MR and model building of the complex finish (no
solvent built yet, I do not think it's good to build solvent in
Dear All,
Is there a tool or software which can give Ramachandran information of
individual residues in a plot?
I used Coot to check for Ramachandran plots, but it shows all the residues
in a coordinate I put in Coot, not individual one. I also use "residue
info" in coot, it tells Ramachandran
Dear CCP4BB members,
I tried to use pymol command to align two proteins, I read the pymol wiki
and I could not understand the command grammars (I am not computer major
and not familiar with machine language).
For example pymol wiki says as below:
Furthermore, you may wish to restrict the
Dear All,
Sorry for the off-topic question, I'd like to do Biacore SPR assay with
N-terminal biotinylated peptide as ligand (to Biacore SA chip) and my
protein as analyte. I have a question of how to determine the concentration
of biotinylated peptide （synthetic peptide), if the peptide has no
g PARROT to impose ncs symmetry and solvent flattening, then
> beginning the rebuild cycles with these phases.
>
> This approach is provided in CCP4I2
> Eleanor
>
> On 16 December 2016 at 19:44, Alex Lee <alexlee198...@gmail.com> wrote:
>
>> Hi All,
>>
>> I am using
Hi All,
I am using CCP4i 7.0.0.025 linux version. I am wondering if Refmac5
automatically does density modification (e.g. solvent flattening, NCS,
etc..) in the refinement after I put a solution coordinate from Phaser MR
molecular replacement and the experiment data (MTZ file)? If Refmac5 does
parameters etc in iMosflm. It takes anywhere from 1 to 4 hours to
> work through, depending on how carefully you do it.
>
> HTH
>
> Harry
> --
> Dr Harry Powell
> Chairman of International Union of Crystallography Commission
> on Crystallographic Computing
> Chairman of
Dear CCP4bb members,
I am new to iMosflm data processing (I use HKL2000 but I really want to
learn iMosflm). After automatic index, cell refinement and integration in
iMosflm, I got 2 warnings.
1. Error in detector gain. BGRATIO of my data lies outside the 0.7 to 1.3
range (mine is 0.64)
ses.
>
> Greetings,
> Abhi
>
>
>
> Abhimanyu Kumar Singh, Ph.D.
> School of Biosciences
> University of Kent
> Canterbury, UK.
>
> On 27 Sep 2016 23:43, "Alex Lee" <alexlee198...@gmail.com> wrote:
>
>> Hi CCP4bb members,
>>
>> I
Hi CCP4bb members,
I have a condition for my protein crystals at "0.2M sodium thiocyanate, 25%
PEG3350, pH6.9".
I'd like to try cryoprotectant with just higher concentration of sodium
thiocyanate, but I have no google hits of the range of concentration I
should use.
I wonder anyone in this
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