Sent: Friday, January 10, 2025 8:16 AM
To: Mooers, Blaine H.M. (HSC) ; CCP4BB@JISCMAIL.AC.UK
Subject: [EXTERNAL] Re: [ccp4bb] Issues with MacOS 15.2
Dear all,
Thanks all for your generous suggestions. It turns out install XQuarts and
grants it full access perfectly solved the issue.
Again
lletin board on behalf of Mooers, Blaine
H.M. (HSC)
Sent: Friday, January 10, 2025 2:09:34 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Issues with MacOS 15.2
Hi Jiazhi,
Thank you for the post.
I, too, have a new m4 Mac with OS 15.2 Sequoia.
I had installed ccp4-9 two days ago, bu
04-5419
Central Time Zone (follows Daylight Savings Time)
office: (405) 271-8300 lab: (405) 271-8313
From: CCP4 bulletin board on behalf of Arnaud Basle
<b39969b3d1dc-dmarc-requ...@jiscmail.ac.uk>
Sent: Friday, January 10, 2025 6:42 AM
To: CCP4BB@JISCMAIL.AC.UK
Su
ore team
UKRI Science and Technology Facilities Council
Rutherford Appleton Laboratory
Harwell Campus
Didcot, Oxfordshire
OX11 0QX
UK
From: CCP4 bulletin board on behalf of Tang, Jiazhi
Date: Thursday, 9 January 2025 at 17:20
To: ccp4bb
Subject: [ccp4bb] Issues with MacOS 15.2
Dear all,
I got
Hi Jiazhi,
Good luck with you new adventures!
You may want to contact specifically the CCP4 core team and they should be able
to help.
They may not have seen you email on the ccp4BB as we were at the study weekend
the past 3 days.
You can contact me off list if you don't manage to get a conta
Hi,
The latest version of DIALS may be able to read this format. If you can
send me an image off-list I would be happy to check. Once in DIALS, it also
may be possible to export the dataset in CBF format.
Best wishes
David
On Tue, 10 Oct 2023, 06:28 Vyankatesh Rajmane,
wrote:
> Dear all,
> We
Vyankatesh,
Follow Kay's suggestion and check. I was trying to say same thing in chat.
On our instrument, we can process images too in xds.
Best of luck
- Ameya
On Tue, 10 Oct 2023, 8:50 pm Kay Diederichs,
wrote:
> If you export the images in XDS format, then you get .pck files that
> MOSFL
If you export the images in XDS format, then you get .pck files that MOSFLM
certainly can read, plus a XDS.INP with the geometry parameters.
Hope this helps,
Kay
On Tue, 10 Oct 2023 10:47:51 +0530, Vyankatesh Rajmane
wrote:
>Dear all,
>We have collected diffraction data on a Rigaku FR-X machi
Hi
If you’re not in a hurry, I should be able to take a look and see what needs to
be done (I’m a little busy right now, but I do know more than a ittle about
Mosflm and image formats). Otherwise I’d contact Mathias Meyer directly at
Rigaku Oxford Diffraction, who should be able to point you in
Dear all,
We have collected diffraction data on a Rigaku FR-X machine with a
HyPix-6000HE detector. The images are in .rod_img format. We are trying to
export the data in iMosflm compatible format using the options available in
CrysAlisPro RED software provided by Rigaku. But the images generated s
HI Zoe
If, from a terminal with CCP4 configured, you type
dials.image_viewer (path-to-hdf5-master-file)
Where (path-to-hdf5-master-file) is your file location, does it work?
All the i2 message says is “something went wrong” which is not super helpful
As a general rule, I also usually recommend
Hi everyone,
I am currently trying to view images with dials through CCP4i2 (on mac)
I have so far tried using the DUI but when importing files, nothing seems to
happen… there are no error codes appearing as such but no images/experimental
data is imported. I have tried this on both .cbf and .h5
To: "CCP4BB@JISCMAIL.AC.UK"
Subject: [ccp4bb] Fwd: [ccp4bb] Issues with Coot and PyMOL on MacOS Ventura 13.2
-- Forwarded message -
From: Nicholas Clark mailto:ndcla...@buffalo.edu>>
Date: Mon, Feb 6, 2023 at 6:44 AM
Subject: Re: [ccp4bb] Issues with Coot an
-- Forwarded message -
From: Nicholas Clark
Date: Mon, Feb 6, 2023 at 6:44 AM
Subject: Re: [ccp4bb] Issues with Coot and PyMOL on MacOS Ventura 13.2
To: Julia Griese
Julia,
I have the same issue with PyMOL. After it opens the blank session, if you
return to the file explorer
Hi all,
I’ve recently upgraded to MacOS Ventura (yes, I regret giving in to my
computer’s nagging) and am now encountering some issues with Coot and PyMOL.
The issues persist after updating to version 13.2.
Regarding Coot version 0.9.8.7: The rotate/translate zone function does not
work proper
Dear Charles,
Since my institution migrated from lotus notes to MS Outlook many (not
all) ccp4bb mails get into quarantine and I have to liberate them
manually from the list. This might be the reason why ccp4bb
black-flagged my e-mail address this morning (first time since almost 30
years). O
Dear All
Jisc, who we use to run the ccp4bb have been having issues delivering to some
(a lot) of e-mail addresses. So far 1400 addresses have been unsubscribed, and
another 2000 are being monitored. I have turned for automatic removal (I
think) and asked that the status of the list be return
Hello all!
I am trying to run blend on some datasets, and it keeps getting stuck at:
> Input command lines <
I have tried running it using ccp4-7.0 and ccp4-7.1 on terminal. I run:
blend -aDO .
I have also tried creating a .dat file with complete path to each INTEGRATE.HKL
and it still
>
> My scripting is not great so I wondered if anyone could hep me with a short
> script to recursively look for ‘refine.mtz’ within subdirectories from the
> top-level ‘model-building’ directory and then run CAD to change the column
> names from 2FOFCWT-iso-fill and PH2FOFCWT_iso-fill to 2FOFCW
Hi Charlie - that's quite a technical question, so I suggest you ask the
question on the xchembb (use The Google to find it), in case someone has
that script to hand.
(But if you need to do any scripting, chances are you'll need to spend a
few days on the Google anyway, even if someone can sen
Dear All,
Having some difficulty running PANDDA with a large batch of structures with
significantly anisotropic data:
1. We have to use Autoproc / Staraniso processing for all datasets.
2. The default Dimple (Refmac) pipeline gives weird maps with large areas of
-ve density for no apparen
Hi Saurabh
It looks like the “tdom” package (which is used by iMosflm to parse the XML
output from Mosflm in order to produce all the graphics) is missing from the
tcltk used by iMosflm in the ccp4 distribution.
CCP4 central should be able to help (see this web-page:
https://www.ccp4.ac.uk/?pa
Hi,
I am running CTF estimation on RELION 3.1. Nearly the end of CTF estimation,
there is an error msg said ' $< line too long'. This error crushed all system
command, and technician told me to fix it by removing history file. I removed
history file, the system had been recovered. But once CT
.@fredhutch.org> / 206-667-4066
>
> From: CCP4 bulletin board CCP4BB@JISCMAIL.AC.UK>> on behalf of "Werther, Rachel A" <
> rwert...@fredhutch.org<mailto:rwert...@fredhutch.org>>
> Reply-To: "Werther, Rachel A" rwert...@fredhutch.org>>
> Date
m: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>>
on behalf of "Werther, Rachel A"
mailto:rwert...@fredhutch.org>>
Reply-To: "Werther, Rachel A"
mailto:rwert...@fredhutch.org>>
Date: Tuesday, October 15, 2019 at 5:01 PM
To: "CCP4BB@JISCMAIL.AC.UK&
...@fredhutch.org<mailto:rwert...@fredhutch.org> / 206-667-4066
From: CCP4 bulletin board on behalf of "Werther, Rachel
A"
Reply-To: "Werther, Rachel A"
Date: Tuesday, October 15, 2019 at 5:01 PM
To: "CCP4BB@JISCMAIL.AC.UK"
Subject: [ccp4bb] Issues in new Mac ve
Which ones?
All of the binaries in $CBIN I have say "Mach-O 64-bit executable x86_64” So
that is unlikely the issue.
I haven’t installed Catalina yet, as I only have one computer that is new
enough. But one of the changes is they have locked down much of the file
system, and are urging i
Hello,
this is the warning that our IT people gave us :
*"Do not *install the MAcOS upgrade to the new system CATALINA
This system version will apparently NOT allow 32-bit applications to
run, which are still many ,
see https://support.apple.com/en-us/HT208436
Try to go back to the former
Hi Rachel,
Did you try to reinstall XQuartz ?
https://www.xquartz.org/
> Le 16 oct. 2019 à 01:50, Werther, Rachel A a écrit :
>
> Hello All,
>
> I downloaded the latest Mac Update, 10.15 Catalina, and then Coot wouldn’t
> open on my computer.
>
> Phenix opened as usual. I use the GUI, and
Hello All,
I downloaded the latest Mac Update, 10.15 Catalina, and then Coot wouldn’t open
on my computer.
Phenix opened as usual. I use the GUI, and the button that says “Open in COOT”
was not greyed out, but would not launch the window. When I tried to open it
directly from Finder, it also
9
E-mails: p.be...@ibmc-cnrs.unistra.fr, philippe_be...@yahoo.fr
URLs: http://www-ibmc.u-strasbg.fr/ , http://www-ibmc.u-strasbg.fr/spip-arn/
En date de : Mar 2.7.19, Reddiravikumar Kumar a écrit :
Objet: [ccp4bb] Issues with stero in Wincoot
Dear all,
We are trying to install stereo in Wincoot in windows 10 pro,
64 bit computer. We have installed nvidia quadro K4000 graphics driver in
our system. The stereo is working well with Pymol, but keep crashing on
Wincoot. Can you anyone experienced the same issue and how can I f
Descriptions are now available online:
http://www.ccp4.ac.uk/updates/
If your update manager does not start, look at No 3 and 4 - they may
relate to your case.
Best wishes
Andrey
Dear all,
I am trying to fit Cd in a protein structure using Phenix. However, the
refinement returns me a result with DC (2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE)
in the validation report and gives me the missing atoms accordingly. When I
open the same structure in Coot, it shows me the ion Cd. Also,
Thank you Kay!
Speaking as a beamline scientist I agree that the instrument should be
set up right and things like the distance, beam center, and various
angles should be known.
However, also speaking as a beamline scientist I feel I should point out
that EVERY instrument goes through at lea
Dear all,
a new BUILT of XDS is available for academic users at
http://xds.mpimf-heidelberg.mpg.de . This reverts to the old distance
refinement behavior with its larger radius of convergence, and is relevant for
processing data from beamlines where the header distance is not accurate.
Thanks
Dear Keitaro,
I have come to the exact same conclusions, and the next version of XDS will
revert to the old refinement behavior.
As a preview, I've uploaded a fixed Linux binary (not the whole package, just
xds_par) to
ftp://turn5.biologie.uni-konstanz.de/pub/xds/xds_par.refi_cell_position_t
Dear Kay,
I also tested this using a publicly available data of thaumatin
https://zenodo.org/record/10271
(resolution ~1.4 Å, wavelength= 0.97625 Å).
The camera distance from header is 265.27 mm. I tested this original
distance and some shifts (+1, +2, +4, ..., +32 mm) with different
versions of X
: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Issues with latest XDS (20171218)
I agree that accurate and complete image header information is useful, but not
universal. How about a routine similar to
dials.discover_better_experimental_model?
W.
On Wed, Jan 24, 2018 at 10:12 AM, Engin Özkan
mailto:eoz
==
>>PD Dr. Oliver H. Weiergräber
>>Institute of Complex Systems
>>ICS-6: Structural Biochemistry
>>Tel.: +49 2461 61-2028
>>Fax: +49 2461 61-9540
>>
>>
>>
>>
>> ____
>> From: CCP4 bulletin board [CCP
_
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Clemens Vonrhein
[vonrh...@globalphasing.com]
Sent: Wednesday, January 24, 2018 2:39 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Issues with latest XDS (20171218)
Dear Oliver,
yes, there are other changes to the
Dear Georg,
On Wed, 24 Jan 2018 14:38:09 +0100, Georg Mlynek
wrote:
>Dear Kay, thank you ver much for the (as always) detailed and nicely
>explained answer.
>
>However this brings up some questions for me:
>
>1. Could you please tell me how the "correct high-resolution cutoff"
>will effect the
behalf of Clemens Vonrhein
[vonrh...@globalphasing.com]
Sent: Wednesday, January 24, 2018 2:39 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Issues with latest XDS (20171218)
Dear Oliver,
yes, there are other changes to the parameter refinement procedure
within XDS as far as I understand.
;
> From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Kay Diederichs
> [kay.diederi...@uni-konstanz.de]
> Sent: Tuesday, January 23, 2018 9:16 PM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Issues with latest XDS (20171218)
&
Dear Kay, thank you ver much for the (as always) detailed and nicely
explained answer.
However this brings up some questions for me:
1. Could you please tell me how the "correct high-resolution cutoff"
will effect the data processing in the INTEGRATE CORRECT step.
In other words what will be
-9540
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Kay Diederichs
[kay.diederi...@uni-konstanz.de]
Sent: Tuesday, January 23, 2018 9:16 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] I
Dear Oliver,
sorry for the trouble!
A default should be correct in the majority of situations, but it's impossible
to have it work for _all_ situations. The XDS default for REFINE(IDXREF) was
changed (i.e. POSITION was removed) to improve the indexing for weak and lousy
data, _and_ because the
Dear all,
After upgrading XDS from build date 20170601 to 20171218, I am experiencing
severe degradation of apparent data quality reported by CORRECT for certain
data sets. Following first indications of issues with a slightly problematic
candidate, I went back to a previously very well-behaved
r your help!
>
> Best wishes,
>
> Laura
> --
> *From:* CCP4 bulletin board on behalf of Phil
> Evans
> *Sent:* 22 November 2016 12:45:35
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* Re: [ccp4bb] Issues with Coot & XQuartz
>
> I can run
: [ccp4bb] Issues with Coot & XQuartz
I can run coot locally (though not remotely) on Quartz 2.7.11 (OS X Yosemite
10.10.5)
Phil
> On 22 Nov 2016, at 12:39, Martin Montgomery wrote:
>
> Hi,
>
> We have had these problems with coot and xquartz versions greater than 2.7.8.
&
I can run coot locally (though not remotely) on Quartz 2.7.11 (OS X Yosemite
10.10.5)
Phil
> On 22 Nov 2016, at 12:39, Martin Montgomery wrote:
>
> Hi,
>
> We have had these problems with coot and xquartz versions greater than 2.7.8.
> This affects coot running locally on OSX and via ssh -XY
Hi,
We have had these problems with coot and xquartz versions greater than 2.7.8.
This affects coot running locally on OSX and via ssh -XY from the mac to our
linux workstations. You should still be able to download the xquartz-2.7.8
package (https://www.xquartz.org/releases/XQuartz-2.7.8.htm
And to enale openGL/glx enter in a local terminal of the mac:
defaults write org.macosforge.xquartz.X11 enable_iglx 1
Mit freundlichen Grüßen
Joachim Reichelt
> Am 22.11.2016 um 13:32 schrieb Phil Evans :
>
> Something we [re]discovered at a recent workshop is that after installing
> Quar
Something we [re]discovered at a recent workshop is that after installing
Quartz you need to reboot (I believe to start the X11 launch daemon). Could
this be the problem?
Phil
> On 22 Nov 2016, at 11:28, Laura Croenen wrote:
>
> Hello all,
>
> I recently downloaded the CCP4 package on Mac (O
Hello all,
I recently downloaded the CCP4 package on Mac (OS X Yosemite 10.10.2). With
this I am using the latest update of XQuartz. Some aspects of the package
(ccp4i2, QtMG) are working fine, but others, inc. Coot, are not working at all.
When I try to open Coot, it appears to start opening (
Hi All,
Thanks for all the help in fixing the refmac TLS refinement issue.
The new refmac (5.5.0093) is working well so far.
Best,
Seema Mittal
On May 22, 2009, at 8:56 AM, Ronan Keegan wrote:
Hi Seema and Ben,
Garib has produced a fix for the TLS problem and put the update on
his re
The issue is:
While running tls and restrained refinement, the program doesn't
perform the given no. of tls refinements. For e.g., if you ask it
to perform 10 TLS and 5 restrained refinement rounds, it'll run
may be 2 or 3 rounds of TLS and then jump to restrained refinement
rounds and fi
Not sure if this is your problem, but I had a different issue with
using this version of refmac5 from the OSX binaries off the CCP4
website. I upgraded to the latest version off of Garbs website and
everything seems to be back normal or a least consistent across
various platforms.
Leona
I might be wrong but it seems Garib has implemented some sort of line
minimization for the tls part which causes the observed behavior. Garib?
Roberto
On 21 May 2009, at 00:39, Dima Klenchin
wrote:
The issue is:
While running tls and restrained refinement, the program doesn't
perform
The issue is:
While running tls and restrained refinement, the program doesn't perform
the given no. of tls refinements. For e.g., if you ask it to perform 10
TLS and 5 restrained refinement rounds, it'll run may be 2 or 3 rounds of
TLS and then jump to restrained refinement rounds and finish
Hi All,
We recently upgraded to ccp4suite 6.1.1 version and have been
experiencing some issues while running refmac_5.5.0088 (for tls
refinement) through this ccp4 interface. We use these softwares
through sbgrid. I would really appreciate any help to troubleshoot
this issue.
The issue
James Foadi
Sent: Tuesday, 5 May, 2009 12:37:17
Subject: Re: [ccp4bb] issues with idiffdisp
Hi,
I use it routinely with no problem OUTSIDE the gui.
Cheers,
Boaz
- Original Message -
From: James Foadi
Date: Tuesday, May 5, 2009 14:02
Subject: [ccp4bb] issues
I have tried starting "idiffdisp"" from ccp4i, but got a wish window open and a
message saying:
"Impossible to load Diffraction Image library
/home/james/build/ccp4-6.1.1/lib/libDiffractionImage.so!! ..."
The file is there, though:
> ls -l $CCP4_LIB
. . . . . . . . .
. . .
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