Dear CCP4 scientists,
This is a joint collaborative project between Israel and the University of
Hamburg on the "mechanisms governing virulence and antibacterial properties of
protein fibrils in infectious and aggregation disease"s.
The research methods include single particle cryoEM
Hi George,
The following commands use to work for me.
=
# on computer terminal
gzip ~/Desktop/pore_loops/myProt.mrc
# compress .mrc file into .gz file; it will generate a file named
myProt.mrc.gz
load the pdb into PyMOL
# on PyMOL terminal
hide all
show cartoon
set
I wanted to ask if anyone has a good reference or tutorial link for displaying
and working with cryo-EM map files in pymol.
Thanks,
George
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Immediate update :
If you use VcXserv, you need to start it with all default option, and
generate a config file.
Then change in the file wgl to False.
Restart computer (yes)
And start VcXserv with the modified config.
If you simply deactivate native openGl via the gui nothing is working
anymore
The performance are massively improved in WSL2 versus WSL1, so maybe it's
why you had bad memory of it ?
WSL2 is currently only available in insider fast ring, but will be for
everyone with next major update (v2004) in few weeks.
The main problem is, while you can use the right toolbar by simply
On 19/03/2020 12:43, Clement Degut wrote:
I have been recently trying to use ccp4 in windows subsystem for Linux 2 (Ubuntu distribution), everything i
tried run perfectly smoothly, including graphical interfaces.
I am pleasantly surprised - when I tried that (some time ago) the graphics
Dear Colleagues,
I would like to add my voice to those advocating making available raw
diffraction images and point out another resource for raw data deposition,
https://cxidb.org, particularly for the case of emerging methods such as
serial crystallography.
Cheers,
Filipe
On Thu, 19 Mar 2020
Hi
> While those text files would be heavy, they'd be still lighter than raw
> images and the whole useless white space they carry with them between
> reflections.
At the risk of extending this thread into a different direction, the "white
space (the images) carry with them between
This last, very important point made by Graeme gives me the chance to plug
a satellite workshop at the IUCr Congress (end of August, so fingers
crossed that this will go ahead) on "MX raw image data formats, metadata
and validation". This is organized by Herbert Bernstein, Loes
Kroon-Batenburg,
Dear all
The wwPDB OneDep system allows depositors to provide DOIs of raw
diffraction images during deposition to the PDB and once again
encourages depositors to provide a DOI for raw images when they have
submitted.
Out of the 9665 X-ray entries that were released in 2019 we have DOI's
for
19-Mar-2020
Dear Loes, Peter, Clemens & Gerard,
I concur that it is crucial to preserve the original diffraction data and make
it available to anyone who would like to use it.
As an example, please see the very recent paper by
Nachon et al (2020). "A second look at the crystal structures of
Dear Julien,
On Thu, Mar 19, 2020 at 08:47:20AM +, Julien Cappèle wrote:
> Though I agree with you Clemens that raw images are amazing to work
> with as you can use any software you are confortable with, we cannot
> forget that depositing several TB of data for each lab would be bad
> for
Dear all,
On Thu, 19 Mar 2020, Winter, Graeme (DLSLtd,RAL,LSCI) wrote:
Date: Thu, 19 Mar 2020 09:08:21
From: "Winter, Graeme (DLSLtd,RAL,LSCI)"
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures
No matter how much data we produce, the
Dear Gerard,
This is a great idea. Of course I am very much in favour of making available
raw diffraction images, and such a virtual workshop could demonstrate the
usefulness of reprocessing raw diffraction data and structural refinements. I
am not at all afraid that archiving of raw data that
Hi Folks,
Quick note on "Like a super raw image diet-plan for the incoming summer” - the
bslz4 compression used with Eiger works really well, and the data are pretty
close to entropy limit in terms of size - which means if you measure your data
carefully (i.e. low background etc.) you can
Hi everyone,
There are some very interesting ideas.
Though I agree with you Clement that raw images are amazing to work with as you
can use any software you are confortable with, we cannot forget that depositing
several TB of data for each lab would be bad for ecological reason. And because
Hi Clemens,
this is curious. You are right that there's a direct link to the raw data
on 6vs4, but there isn't one on http://www.rcsb.org/structure/6H56. I'll
contact RCSB to see where the problem lies.
All best.
Andreas
On Thu, Mar 19, 2020 at 8:34 AM Clemens Vonrhein
wrote:
> Hi
Dear Petr,
On Thu, Mar 19, 2020 at 06:45:31AM +, Petr Kolenko wrote:
> For those of you who are in touch with these data, would deposition
> of unmerged intensities in P1 in the whole detector range instead of
> complete dataset be good enough to „correctly“ re-evaluete the
> structure? Or is
Hi Andreas,
On Thu, Mar 19, 2020 at 07:06:32AM +0100, Andreas Förster wrote:
> - The link to the raw data can be found inside the mmCIF file under
> _pdbx_related_exp_data_set.data_reference. Whether it's also shown on one
> of the PDB sites is up to the designers of these sides. I cannot find
For those of you who are in touch with these data, would deposition of unmerged
intensities in P1 in the whole detector range instead of complete dataset be
good enough to „correctly“ re-evaluete the structure? Or is there a doubt that
even this approach would not lead to optimal structure?
My
As someone who's done this (for one structure of minor significance), I
would like to make a few comments:
- I highly encourage deposition of raw data. Why would you not? Now that
many labs are shut is the time to do it for all these datasets hiding
somewhere on abandoned hard disk. These
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