>
> Dear Wim,
>
> on my M1 Macbook Air, coot 0.9.6 (latest from CCP4) works smoothly/fast.
> What is your XQuartz version? I have 2.8.1 .
>
> HTH,
> Kay
>
> On Thu, 16 Sep 2021 15:40:53 +0800, WENHE ZHONG GMAIL.COM> wrote:
>
> >Dear CCP4 community,
> &
Dear CCP4 community,
The COOT is not running smoothly on my M1 chip Macbook. For example, when
both model and the electron density map are displayed, the moving from one
residue to the next (pressing SPACE bar) is lagging/slow (>2s). This only
happened to my old computer, but I am surprised to fin
Dear members,
We are planing to purify RNA only or/and RNA-protein complex on FPLC. The
application of the purified materials is for crystallization. However, our
concern is that our FPLC has been frequently used in bacterial expressing
protein purification including purifying proteins from crude
Dear Community,
A little bit out of topic here. An enzyme we like to use in our assay is
commercially available. However, we found some unfavorable activities that
probably from the contaminants from this commercial source. We checked the
company website and found out this enzyme was purified f
to a
> surface would reduce entropy, resulting in a better kon?
> You could try ITC, you will have access to detlaH and deltaG of binding, and
> by comparing with your other molecules maybe something would come up?
>
> please correct me if I'm wrong.
>
> All
DUMAS Philippe (IGBMC)
> wrote:
>
>
> Le Jeudi 26 Avril 2018 16:50 CEST, WENHE ZHONG
> a écrit:
>
> Just to be sure: how was the nM affinity evaluated ? By in vitro
> measurements, or by obtaining an IC50 by tests on cells ?
> Of course, if you are mentioning an IC
Dear Community,
A little bit out of topic here. We are applying the structure-based approach to
design compounds that can bind our protein target. We have synthesized a series
of analogues based on the same scaffold with different substituents at one
particular site. The most potent analogue (n
Dear Community,
A little bit out-of-topic here. We have a few interesting sites would like to
mutate on proteins to test the protein stability and improve the
protein-protein interactions. Before moving forward to the site mutagenesis
experiment, we like to do some prediction first to narrow do
Dear CCP4BB members,
We would like to identify a ligand that is present in crystal structure
(according to strong positive densities at active site) but absent in
crystallization condition. We already have some candidates in mind based on our
knowledges on this protein but we need to validate f
Dear all,
I always use the SUPERPOSE tool in CCP4 to superpose molecules. This time I
want to use the RMSD values of superposed C-alpha atoms to plot a RMSD graph
(instead of using the graph automatically made by the program). However, there
are many atoms missing in the RMSD list.
In the set
Dear CCP4 friends,
I have been searching around the CCP4 mails for the discussion of soluble
protein aggregations, as I have the same problem recently. Many efforts I
have tried but without success. Here, I would like to summarise what I have
done and maybe any of you come across some ideas.
1. M
Dear members,
I have one difficult task on hand and would like to ask for your advice.
I want to superpose two enzyme structures just based on several residues
(e.g. 5 residues) which we are interested in. But these two structures do
not have similarity for overall structures. In this case, I can
Dear CCP4 members,
Recently, I got a ligand soaking structure to clearly show a large domain
(~100 amino acids) movement compared to the no soaking structure. Although
there are some reported examples of this enzyme to suggest the flexibility
of this large domain which is relevant to substrate bin
Dear members,
Just have a silly question past my mind: is there any program in CCP4 can
be used to analyze coordinate file (.pdb format) to have a very
general/overall discription about the structure? --such as the total number
of protein residues/water/ligand, the total atoms of protein/water/lig
Dear memebers,
Thank you all firsit for the helps on my previous post about sequence
alignment. They are really useful!
Apologize for the off-topic question again. I usually use DSSP method to
calculate the secondary structures on my sovled structures. I saw a nice
schematic representation for s
Dear members,
Apologize for this off-topic question. I am looking for a protein sequence
alignment tool which is capable to generate a particular output file
similar to the attached format (please see the attached picture). I have
been looking at some popular programs but none of them can show the
Dear members,
I would like to have your ideas if there is any way to identify a rotation
centre of domain in two different states using CCP4 or other program.
The situation is: the domain of the protein will rotate between two
different states (depending on substrate binding) around 8 degree, and
Dear all,
I am using the Molecular Suporpose tool under Coordinate Utilities list in
CCP4 to superpose two similar structures. I ticked the "Output all
distances to a file" option, selected "Superpose specified atoms/residues",
fit "CA atoms of Residues" to the other one. I wanted to see the RMS
n
Dear all,
I would like to show the visible metal-residue interaction during the Morph
movie. Anyone knows how to do that in Chimera? Thank you.
King regards,
Wenhe
Hi All,
Recently I did some soaking experiments for crystals. Most of them did not
change their space group (I222). But one of them seems to be a little bit
different (I222 ---> I121).
The following is the pointless data: (the data was processed by Mosflm under
space group I222)
Laue Group
Hi all,
Sorry for a little bit out of topic question. Morph Serve is the only online
server I know to make movie for protein motion. But what I want to do is to
make a movie to show one single side chain flip. It seems Morph could not do
this. Does anyone know a way to do that? Thank you.
King r
21 matches
Mail list logo
