Dear Jordi,
For this purpose, I would use AIMLESS (you can specify a list of
unmerged data sets) or xia2.multiplex. Output log files should indicate
which data sets or images to discard - then the merging can be re-run
without them.
Best regards,
Martin
On 21/06/2024 16:15, Jordi Benach
Martin,Thankyou.Unfortunately I have no explanation to offer onhttps://proteindiffraction.org/;>proteindiffraction.org
currently.Greetings,JohnEmeritus Professor John R Helliwell DScOn 13 Jun 2024, at 10:41, Martin
Malý martin.maly...@email.cz wrote:
Dear John,
Thank
Dear John,
Thank you for the link. It would be great if
https://proteindiffraction.org/ (IRRMC) was rescued. I preferred this
website but they stopped receiving new data sets - or at least they do
not reply to my emails for more than a year. I am worried that the
website will disappear and
Dear Devbrat,
I am now playing with a similar problem but I don't have a simple
solution for you as I'm also quite stuck. You can check these software
tools which involve some scripting in Python (NumPy, SciPy) and C++:
EMDA (for cryoEM maps, included in CCP-EM)
https://gitlab.com/ccpem/emda
Dear Marco,
Please don't you mind to export your refmac5 job and send it to me so I
can have a look? I will keep it confidential. In the following coot job,
do you open the structure model in PDB or mmCIF format?
You can also export a PDB or a mmCIF file from the refmac5 job -
similarly as
Dear Jon,
If I understand your question right, I would use Gemmi for this purpose:
https://gemmi.readthedocs.io/en/latest/mol.html
https://gemmi.readthedocs.io/en/latest/analysis.html
It's not in GUI, it involves scripting in Python. It's a very powerful
tool and capable of working with both
Dear Tom,
I am using basically the same setup (Linux Mint 21.3 Xfce based on
Ubuntu 22.04, CCP4 8.0.019 including Coot 0.9.8.93). Everything works
well on my computer. I did not have any issues with Coot even in CCP4
8.0.017. I am sorry I don't know the reason of the error...
Cheers,
Martin
Dear Gerlind,
The MolProbity analysis is included in the 'Multimeric validation' task
and also in the refinement task in CCP4i2 - just be sure to have the
current version 8.0.019.
In Phenix GUI, I can still find such a task: Crystals -> Validation and
map-based comparison -> Comprehensive
Dear Marian,
This issue regarding validation report in refmac task has been fixed in
the latest update 8.0.019. Please let us know if the problem persists.
Best wishes,
Martin
On 05/04/2024 13:19, Jon Agirre wrote:
Dear Marian,
Thanks for your report. I'm sorry you're having to deal with this
Dear Dennis,
As Elke wrote, some parameters were changed... I'm not sure but I think
that now definitions are even more sensitive to be specified
hierarchically. I would try to this:
phenix.refine model.pdb data.mtz params.def
where params.def are:
data_manager {
fmodel {
xray_data {
Dear Marius,
could the 'refinement exclude' keyword for refmac5 help?
refinement exclude all from [residue] [chain] to [residue] [chain]
Best regards,
Martin
On Tue, 2024-03-05 at 14:06 +0100, Ilme Schlichting wrote:
> Dear Marius,
>
> Thomas discussed this issue in great detail in the
Dear Harry,
You can try to read your PDB file and save it as mmCIF using gemmi:
https://gemmi.readthedocs.io/en/latest/mol.html#reading
https://gemmi.readthedocs.io/en/latest/mol.html#id3
Best wishes,
Martin
On Fri, 2024-02-23 at 11:32 +, Harry Powell wrote:
> Hi folks
>
> I am in the
Dear all,
I have sometimes similar issues on my Ubuntu 22.04. Nevertheless, this
command works well for me every time:
sudo /opt/ccp4/ccp4-8.0/bin/ccp4um
i.e. calling the update manager using its full path and with admin
permissions.
Best wishes,
Martin
On Tue, 2024-01-30 at 13:01 +, David
Dear all,
I am sorry for a late reply. R-values should not exceed 0.42 which
happened in your case for shells 1.91-1.83 and 1.83-1.77. It is because
theoretically (under some assumptions), a perfect model gives an R
value of 0.42 against random data (Evans & Murshudov
2013
Dear Dhiraj,
What is the script? What is the error? Please send them to us. We may
be able to fix the script - it is not easy to help without knowing the
script and error.
Cheers,
Martin
On Thu, 2023-12-14 at 21:41 +, Srivastava, Dhiraj wrote:
> Hi All
> sorry for off topic
Dear Shenyuan Xu,
I dealt with a similar problem recently. In my particular case, a
combination of the correction with STARANISO and a subsequent molecular
replacement with the MoRDa pipeline helped me a lot. MoRDa was able to
suggest how to place individual protein domains separately in the
Dear colleagues,
Firstly, I would like to thank Clemens, Claus, Ian and Gerard for the
very interesting analysis and remarks!
Similarly to Frank, I am wondering "whether any refinement program
properly extracts the high-resolution signal when there's anisotropy".
Poor completeness in high
Dear Matt,
thank you for asking. I am bit confused how you set up the PAIREF run.
In paired refinement, data are added step by step - going to higher
resolution, i.e. lower d_hkl. So the merged data in the PAIREF input
should not be cut to much. The data statistics look from DIALS quite
knowledge. Does anyone has a clue?
In the mean time, we are reading the other literature provided by you, of
course.
Best regards,
Martin
Od: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> za uživatele Martin Malý
<malym...@fjfi.cvut.cz>
Odesláno: 6. listo
,
Martin Maly
Od: Ilme Schlichting <ilme.schlicht...@mpimf-heidelberg.mpg.de>
Odesláno: 6. listopadu 2017 12:38:17
Komu: Martin Malý
Předmět: Re: [ccp4bb] Radiation damage to the FAD in enzyme structure
Hello,
Are you sure you had full occupancy to begin wit
Dear colleagues,
I am investigating a structure of a FAD-dependent enzyme. The electron density
map suggests radiation damage to the FAD. It apparently is different from
simple change of the redox state and "butterfly"-like structure. We did not
find in literature possible products of
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