Structure under MOSBRI umbrella: CD, ITC, DSC, MST (labeled,
non-labeled), BLI, nanoDSF, DLS, mass photometry, SPR, SAXS,
FT-IR, fluorimetry, UV-Vis, optical tweezers
See you at the instruments!
Best regards,
Jan Stransky,
on behalf of CMS, MoB-IBT team
From:* CCP4 bulletin board on behalf of Jan
Stransky
*Sent:* 18 August 2022 10:37
*To:* CCP4BB@JISCMAIL.AC.UK
*Subject:* [ccp4bb] Polymer ligand (Jefffamin) modeling in low
resolution maps
Dear all,
we have a structure at not the greatest resolution (~2.6A) of which
crystal was grown in
Dear all,
we have a structure at not the greatest resolution (~2.6A) of which
crystal was grown in crystallization condition with Jeffamin. In the
maps, we see typical PEG-like sausages. Jeffamin is basically a PEG
decorated with some methyl groups and it is terminated with amine groups.
No
Hi all,
while validating X-ray structure using Molprobity (web service), we got
systematic outlier flags on CE1-NE2 distance in histidines. The distance
is 1.36A.
I have tested it also using high resolution lysozyme structure, I have
laying around. There the distance refines as 1.31A and Mol
-capabilities-at-cms/
Best regards,
Jan Stransky
P.S. You can now follow news from Centre of Molecular Structure at
Twitter, @CmsIbt (https://twitter.com/CmsIbt)
--
Jan Stránský, PhD.
Institute of Biotechnology, AS CR
Centre of Molecular Structure
Průmyslová 595
252 50 Vestec
Czech Republic
Email
Dear all,
I am wondering, if anyone has experience with implementing stereo 3D
setup with currently available hardware. NVIDIA 3D vision seems to be
pretty much dead.
The primary usage would be model building in Coot, but also potentially
Pymol analysis.
The biggest issue is an access to control
Hi,
there is a guide here, but you should get the proper script for Pymol
from the Consurf server.
http://www.protein.osaka-u.ac.jp/rcsfp/supracryst/suzuki/jpxtal/Katsutani/en/consurf.php
Jan
On 6/22/19 10:24 PM, khaja faisal tarique wrote:
> Hi everyone,
>
> I was wondering can anyone suggest me
I can comfirm, it is my favourite feature of i2.
I would like to see it automated (or -able using CLI) for flawless
backup recovery.
Cheers,
Jan
On 16/04/2019 14:22, Christian Roth wrote:
> yes one can
>
> Cheers
> Christian
>
> On Tue, Apr 16, 2019 at 1:19 PM Eleanor Dodson
> <176a9d5ebad7
We have tried PS VR, and it works even with coot. It has some obvious
drawbacks with toolbars, so it is not perfect for model building, unless
you have good set of keybindings configured and perfect muscle memory. I
could also imagine to configure a gamepad, but we are not there yet.
Jan
On 3/11/
This can be done at Diamond I23 beamline.
https://doi.org/10.1016/j.nimb.2016.12.005
Best regards,
Jan
Dne 16.02.2019 v 18:49 Patrick Loll napsal(a):
> S has about 0.56 anomalous electrons at 8 keV, whereas P has about
> 0.44. This is a small difference between two weak signals—unlikely to
> gi
trasbourg
>>>> 15, rue René Descartes
>>>> F-67084 STRASBOURG cedex
>>>> +33.3.8841.7109
>>>> E-mails: p.be...@ibmc-cnrs.unistra.fr
>>>> <mailto:p.be...@ibmc-cnrs.unistra.fr>, philippe_be...@yahoo.fr
>>>> <mailto:philipp
; sillier than one does usually, but it works, costs nothing, needs no
> updates and i'm told that it's even good for your eye muscles!
>
> best,
>
> jon
>
>
>
> *Von:*CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *Im Auftrag von
> *Jan Strans
Dear all,
I started looking into the never ending story of stereo in
crystallography... As with our standardized linux setup we probably are
not willing to move to X.org-world, if was wondering, if anybody was
succesful to make stereo working in Windows 10. I did read some NVIDIA
forum, and it see
Dear Charles,
is there a plan to release new base package of CCP4 which would contain
all updates, so we don't have to go through the already quite lengthy
update process with new installations?
Best regards,
Jan
On 07/05/2018 03:15 PM, Ballard, Charles (STFC,RAL,CSE) wrote:
> For those of you not
Hi,
seeing a "blue" map might at lower sigma levels might give some more
insight. However, there are some caveats in doing so, like solvent
flattening during the refinement. Phenix has options to calculate some
fancy maps, which might give you some more "tips": Feature Enhanced Map,
and Polde
You could try Xenon derivation chamber.
DOI: 10.1107/S0907444902011010
Cheers,
Jan
On 29/11/17 13:05, Eleanor Dodson wrote:
> That depends on the quality of your data and your model!
>
> I play with refinement and rebuilding - check indicators v
> resolution., etc etc (I look at the v plot from
So, thanks to pointing by Paul, I have found the keybinding definition
in "python/template_key_bindings.py" on coot's github. It is called
"Step scrollable map number" with suggested key "M"
Jan
On 07/12/2017 10:33 AM, Jan Stransky wrote:
Hi,
I believe,
Hi,
I believe, I have seen somewhere a keybinding, which cycle through maps
attached to scroll wheel (basicaly moving the radio button "Scroll" in
Display Manager). However, I can't find anywhere what key does that...
Any ideas? Or do you know a coot function which does that?
Best regards,
,
Robbie
-Original Message-
From: Jan Stransky [mailto:jan.stransky.c...@gmail.com]
Sent: Wednesday, May 03, 2017 13:05
To: Robbie Joosten
Subject: Re: [ccp4bb] HETATM record after Refmac
Dear Robbie,
It is refmac from current CCP4 release. It is run from i2.
This is in the log: CCP4
Dear ccp4ers,
is there way to retain HETATM keyword for ligands when running refmac?
It apparently changes HETATM to ATOM which spoils some nice ligand
features in Coot...
Best regards,
Jan
t the data
are there in temp directory.
Any ideas? Developers, any idea how to help you track down the bug? Is
it possible to import resulting data back, including database entry?
Jan
On 02/13/2017 03:21 PM, Jan Stransky wrote:
Good to know, it works indeed.
Just worth noting, that the remote w
k just the
test button is broken. I did put in the explicit path of the ssh
private key : /Users/stuart/.ssh/id_rsa rather than $HOME.
Best wishes,
Stuart
On 13 February 2017 at 12:20, Jan Stransky
mailto:jan.stransky.c...@gmail.com>> wrote:
Dear all.
I am wondering, if somebody
Dear all.
I am wondering, if somebody was able to make "Run on server" in i2 working.
My setup:
In sever group list: server_hostname
CCP4 distro directory: /path/to/ccp4-7.0 (or do I need add /bin?)
Temp direstory: /tmp/$USER (default)
Key file: $HOME/.ssh/id_rsa (SSH key-file system is work
I had some cases, when path INTEGRATE.HKL -> Aimless gave data, from
which it was not possible to solve structure by Phaser. It looked like
structure solved, but then I got 45-50% Rwork/free. There were no
problems with XDS_ASCCI.HKL -> Aimless (Not scale, just merge) path.
Jan
On 11/24/2016 0
hows an ID contradicting to that in header.
I've been able to replicate the error by opening a PDB file downloaded
from PDBe and changing the HEADER line to show a different PDB ID. Is
that your case?
Thanks for your interest,
Jon
On 12 January 2015 at 15:59, Jan Stransky <mai
Dear all,
I am experiencing some troubles with running Privateer. It seems to fail
to read a PDB file. The Error message:
Reading xxx.pdb... MMDBfile: read_file error: xxx.pdb :3
terminate called after throwing an instance of 'clipper::Message_fatal'
Aborted
Any ideas?
Best regards,
Jan
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