mporting 1 or no jobs for each project, although each project has more than
> 8 projects and some have 40 jobs. Is there any way to address this?
>
> Kind regards,
> Otsile
>
> -Original Message-
> From: Stuart McNicholas
> Sent: 19 November 2024 08:28
> To:
OK.
So could we see:
/Users/xalbert/Armando/0_1_Current/SOS3_Alejandra/Bsk5486x12/Refine_new/CCP4_JOBS/job_8/log.txt
?
That should be Coot's log file.
Stuart
On Tue, 19 Nov 2024 at 09:34, Armando Albert wrote:
>
> Yes, it does
> Armando
>
> > El 19 nov 2024, a las 1
Dear Armando,
Many apologies. Does coot run outside of ccp4i2?
i.e. does the following in a Terminal work OK:
/Applications/ccp4-9/start
coot
?
If it does we'll have to try some other tests. If it does not work, is
XQuartz installed?
Best wishes,
Stuart
On Tue, 19 Nov 2024 at 08:25, Armand
the backup files.
If this does not work, thy the other methods. And please get back in
touch with us if you cannot fix it.
Best wishes,
Stuart McNicholas
On Sat, 16 Nov 2024 at 16:46, Otsile Mojanaga
<d0bf4738f9f3-dmarc-requ...@jiscmail.ac.uk> wrote:
>
> Dear all
>
> I updated
/python3.9/site-packages/ccp4i2/core/CCP4I2Runner.py
Please let me know if these do or not fix the problem.
Best wishes,
Stuart
On Fri, 30 Aug 2024 at 08:26, Stuart McNicholas
wrote:
>
> Dear Xin,
> It appears that the command line arguments are not being parsed
> properly. I am looki
Dear Xin,
It appears that the command line arguments are not being parsed
properly. I am looking into this right now. I hope to have a fix for
you very shortly.
Best wishes,
Stuart
On Fri, 30 Aug 2024 at 06:30, zx2...@connect.hku.hk
wrote:
>
> Hi all,
>
> I am experiencing some issues with i2r
Dear Maria,
Could you please try deleting the file
/home/msa/CCP4I2_PROJECTS/TRT84A11C/DATABASE.db.xml ?
I think that this file is corrupted (empty) and that this is causing
the problems.
Best wishes,
Stuart McNicholas
On Wed, 24 Jul 2024 at 12:22, Marian Oliva wrote:
>
> Dear all,
>
Dear Stefano,
I wonder if the problem is simply displaying any ccp4i2 reports on
the new computer, rather than just the imported ones. Have you tried
creating a completely new project and seeing if anything works in
that? There are some potential things to think about in the log file.
Best wishe
I got i2run to work with this data by:
* Importing the data with "Import merged"
* Importing the 2 sequences one at a time with 2 import sequence jobs
* Running a 'Define AU contents' job with both sequences added to the
contents.
* Creating a Crank2 job, then clicking the "Show i2 run command" to
Dear Fred,
Many apologies for your difficulties. My first thought is that perhaps
CCP4MG's lighting settings are completely messed up. This can be tested by
removing completely the folder:
$HOME/.CCP4MG2
If this does not work, then further investigation will be required.
Also, in CCP4 we are w
Dear Matt,
What version of CCP4MG are you using? I thought I had fixed this in the
version that is in recent CCP4 8.0, but apologies if this is still causing
problems.
Best wishes,
Stuart
On Thu, 25 May 2023 at 21:54, Matt McLeod wrote:
> Hi all,
>
> I am having a weird issue where the CCP4M
I think this is the page Boaz is referring to:
https://www.ccp4.ac.uk/download/doc/known_issues_linux.html
The "Missing libraries" section might help you.
Best wishes,
Stuart McNicholas
On Sat, 10 Dec 2022 at 19:54, Boaz Shaanan wrote:
> Hi,
> Did you check the 'is
Does "Contents one unit cell", then "Extend unit cell" do this?
Stuart
On Wed, 2 Jun 2021 at 14:14, Stefano Trapani wrote:
>
> Yes, that is the way I usually do, but it can be cumbersome.
>
> It would be easier if I could first superpose two molecules from the two
> crystals, and then decide in
Dear Stefano,
It might be possible to do what you want in a roundabout way:
i) Apply matrix to molecule: Molecule Icon -> Transform coordinates ->
Enter transformation
ii) Save the molecule: Molecule Icon -> File save/restore -> Save to file.
iii) Load in the saved molecule
iv) For the new file:
Drawing style (right menu in display table) -> Worm scaled by -> Worm
scaled by NMR variability
in ccp4mg?
This changes the size of the worm but not the colour.
On Thu, 27 May 2021 at 09:56, Harry Powell - CCP4BB
<193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
>
> Anyway, thanks to all th
se, since we ar enow in teh 21st Century, maybe we should make
> these problems go away, if necessaryby dropping those elements of the suite
> that can’t handle international, modeern scientists ?
>
>
> Sent from my iPad
>
> On 18 Nov 2020, at 09:20, Stuart McNicholas
> wrot
> Sent from my iPad
>
> On 17 Nov 2020, at 13:13, Stuart McNicholas <
> 19a0c5f649e5-dmarc-requ...@jiscmail.ac.uk> wrote:
>
>
>
> ⚠ External sender. Take care when opening links or attachments. Do not
> provide your login details.
> Dear Kevin,
>Glad y
Dear Kevin,
Glad you worked it out. Sorry I missed earlier messages. This is another
common Windows problem - not just spaces either, but anything not ASCII
alphanumeric is likely to cause problems.
Stuart
On Tue, 17 Nov 2020 at 12:54, Kevin Cowtan <
2ba34e97fcaf-dmarc-requ...@jiscmail.ac.
Dear Kevin,
It sometimes helps (for reasons unknown) to run i2 as an administrator
once on Windows. Having said that, there may well be a pointless bug or
compiler error which only manifests on some CPUs/Windows version, etc. But
I'd try the run as admin idea first, if it's possible. If it's not
Dear Sam,
We have heard reports that running as Administrator the first time fixes
some issues on Windows. It might be worth testing this before anything else.
Best wishes,
Stuart
On Thu, 1 Oct 2020 at 11:53, Horrell, Sam (DLSLtd,RAL,LSCI) <
sam.horr...@diamond.ac.uk> wrote:
> Hello CCP4bb,
Apologies, it did work for me, I think. I just hadn't set my username.
On Tue, 9 Jun 2020 at 09:45, Stuart McNicholas
wrote:
> My idea seemingly hasn't worked for me. I'll keep trying.
>
> On Tue, 9 Jun 2020 at 09:17, Stuart McNicholas <
> stuart.mcnicho...@york.a
My idea seemingly hasn't worked for me. I'll keep trying.
On Tue, 9 Jun 2020 at 09:17, Stuart McNicholas
wrote:
> Dear Michael,
>I think that the port number is hardwired in CCP4i2 on line 439 of
> $CCP4/share/ccp4i2/core/CCP4JobServer.py
>
> trans
ort number for what is suitable
for you.
If this works, then I will make the port number an option in the program.
If not, then I will try something else.
Best wishes,
Stuart McNicholas
On Mon, 8 Jun 2020 at 17:40, Michael Weyand
wrote:
> Dear CCP4I2 experts,
>
> I'm trying to su
Dear Sam,
Apologies for your problem. I have tested myself on Mac and do not see
the problem, however I will try on Linux and Windows as well.
However, this menu not functioning may not mean that you cannot saves. Do
"Save mol to CCP4i2.." and "Save to CCP4i2" appear in Coot's File menu? If
so
Paul is completely correct. Just remember to click the "Apply" button after
changing "Application" font size.
Best wishes,
Stuart
On Thu, 21 May 2020 at 01:22, Paul Emsley wrote:
> On 21/05/2020 01:00, Khushboo Patel wrote:
> > Hi Everyone,
> >
> > This is rather a silly question but the font
Dear Francois,
This does indeed look very odd. It looks as though you cannot make a
directory in your home directory. Could you try typing the following in a
terminal please:
i) mkdir /home/hoh-asus/.CCP4I2/
ii) mkdir /home/hoh-asus/.CCP4I2/logs/
iii) ccp4i2
and see if you get any errors in an
Dear Sam,
Please try:
Edit->preferences
The default tab on the preferences widget should be "Task interface". This
has font size options, after picking a bigger number, click Apply.
This may not fix all problems, but should make things better.
Best wishes,
Stuart
On Wed, 1 Apr 2020 at 14:
this a
new computer onto which you've installed CCP4MG? I guess write permissions
may vary in the various cases.
Best wishes,
Stuart
On Wed, 13 Nov 2019 at 12:06, Jon Agirre wrote:
> He mentions 'render' - perhaps he means he's used the Render menu option?
>
>
On Wed, 13 Nov 2019 at 08:56, Stuart McNicholas <
stuart.mcnicho...@york.ac.uk> wrote:
> Dear Jerome,
>It is entirely possible that this is a Catalina problem. I do not have
> a Catalina machine and hence have not tested CCP4MG on Catalina. I will
> install Catalina on on
Dear Jerome,
It is entirely possible that this is a Catalina problem. I do not have a
Catalina machine and hence have not tested CCP4MG on Catalina. I will
install Catalina on one of my computers right away and see if I get the
same problem. It may also depend on what graphics chip you have in y
rm $HOME/.CCP4I2/db/database.sqlite-shm $HOME/.CCP4I2/db/database.sqlite-wal
Then try restarting CCP4i2.
Please let me know if this works or not.
Best wishes,
Stuart McNicholas
On Thu, 29 Aug 2019 at 08:42, Jan Gebauer wrote:
> Dear all,
>
> I recently switched most of my work to the
Dear Charles and Kevin,
If I install CCP4 myself on Windows, refmac works fine from the CCP4
console. This was with CCP4 installed in the default C: location. I did not
try from within Coot, however ...
... when trying to run refmac from Coot on a couple of OS X machines
nothing happens, no error
Dear Gerlind,
With thanks to Phil Evans and Huw Jenkins there are a couple of
suggestions that I've seen passed around:
Phil found this on Stack Exchange:
"I met this problem before and it's very annoying. Finally, I realized that
because the size and resolution of additional monitor are differe
of ccp4mg outside of the CCP4 suite.
This will not have the MrBUMP/CCP4i2 integration, but should have all other
features. The latest version of this can be got from:
http://www.ccp4.ac.uk/MG/nightly/
Best wishes,
Stuart McNicholas
On 9 January 2018 at 19:28, Whitley, Matthew J wrote:
&
Dear Johannes,
Many apologies, this behaviour should certainly not be expected. The
cause could be quite difficult to determine, I shall start by installing a
Ubuntu virtualbox myself.
Best wishes,
Stuart
On 4 July 2017 at 13:46, Johannes Cramer wrote:
> Dear CCP4 bb,
>
> I would like to use
Dear Pratibha,
It sounds to me to be most likely caused by some preference to be set
which is incompatible with your computer. I do not know why this would be,
but we can try to see if this really is the problem. You can try removing
all preferences.
On Linux and Mac:
rm -fr ~/.CCP4MG2/
On
I set DYLD_LIBRARY_PATH on the command line to point to location of the svn
libraries.
On 16 February 2017 at 10:09, Tristan Croll wrote:
> Hi all,
>
> While using the ccp4-jhbuild system to rebuild specific components on the
> Mac, I'm running into the bug detailed at https://bugs.launchpad.net
Dear Jan,
I see the same error message when doing "Test server group". However,
when I actually run a job, all seems OK. I think 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 Februa
This is described in *Acta Cryst.* (2007). D*63*, 50-57 (J. Gruber, A.
Zawaira, R. Saunders, C. P. Barrett and M. E. M. Noble).
On 10 December 2014 at 13:02, Tim Green wrote:
> CCP4MG can also generate electrostatic surfaces, which can then be
> rendered and exported for publication. As a cavea
Dear All,
The CCP4MG team would like to announce version 2.8.0 of the program (the
Christmas 2013 release).
The program may be downloaded from
http://www.ccp4.ac.uk/MG/download/
Highlights of this release include:
- Reworked picture wizards and default program parameters to give more
comp
Dear all,
Version 2.7.3 of CCP4MG is now available for download from:
http://www.ccp4.ac.uk/MG/download/
This is a minor bug fix release over the recent 2.7.2
The complete list of changes is give below.
Best wishes,
CCP4MG team.
Changes from 2.7.2:
o Fix Geometry causing crash on Windows/
Dear all,
Version 2.7.2 of CCP4MG is now available for download from:
http://www.ccp4.ac.uk/MG/download/
This version fixes two critical problems on Windows (failure to create
movies and complete failure to work at all with many Intel graphics
chips) and one critical problem on Linux (crash/
the issue. Many
apologies. I will attempt to get a version with a software renderer
working as soon as possible.
Stuart McNicholas
Dear all,
Version 2.7 of CCP4MG is now available for download from:
http://www.ccp4.ac.uk/MG/download/
The complete list of changes is give below.
Best wishes,
CCP4MG team.
* OpenGL (graphics window use of hardware):
Shadows. (Display->Lighting->Shadows check-box).
Occlus
On 15/11/2012 13:57, SANCHEZ BARRENA, MARIA JOSE wrote:
Dear all,
it seems that none of the tricks from Mark or Tim or Stuart´s ccp4mg
"making bond" strategy works out... In all cases, the bond is made when
drawing in "think/fat band" style... However, when representing in
ribbon style, the link
on
one of the atoms you wish to connect and select Add/delete bond -> first
atom. Then right click on secon atom, select Add/delete bond -> (name of
first atom). This should draw a bond between them.
Best wishes,
Stuart McNicholas
On 6 Jul 2012, at 15:10, Regina Kettering wrote:
> The model is a theoretical model of Q766C3 (nepenthesin 1), link to the
> download below:
>
> http://swissmodel.expasy.org/?pid=smf02&source=repository&tid=file_model&mid=7d1184184e0086123cd94070ab861eb2_1
>
This is a very silly bug in CCP4MG
add
scripting ability in the future.
Best wishes,
Stuart McNicholas
irus. How
you do that depends on which anti-virus program you have. Then you need to
search the web to find out how to deal with false positives. If you know what
your anti-virus program is, I might be able to help you with fixing the problem.
Best wishes,
Stuart McNicholas
On 17/05/12 11:44, Jan Dohnalek wrote:
Dear all,
in Fedora 15 I am having troubles to get the .plt outputs drawn.
The complaint is
Using CCP4 programs from /protein/ccp4-6.2/ccp4-6.2.0/bin
xplot84driver: error while loading shared libraries: libXaw.so.7:
cannot open shared object file: No such f
On 17/08/11 10:49, Phil Evans wrote:
Roll on the loggraph replacement!
Next month ?
Dear All,
Version 2.5.0 of the CCP4 Molecular Graphics Program
(CCP4MG) has just been placed on the downloads page:
http://www.ccp4.ac.uk/MG/download/
This version includes many bug fixes and improvements over 2.4.3, including:
### General bug fixes
* Fix very serious Vista/Windows 7 crash
Dear All,
Version 2.4.3 of the CCP4 Molecular Graphics Program
(CCP4MG) has just been placed on the downloads page:
Please note, the change of download location.
http://www.ccp4.ac.uk/MG/download/
This release is largely a bug fix release over 2.4.2, it features:
* Fixed crashes when gene
Dear All,
Version 2.4.2 of the CCP4 Molecular Graphics Program
(CCP4MG) has just been placed on the downloads page:
http://www.ysbl.york.ac.uk/~ccp4mg/download2/
This release features:
* A sequence viewer (Tools->Sequence viewer..), including:
o Multiple sequence alignment
see the same problems.
Best Wishes,
Stuart McNicholas (CCP4MG programmer)
Warren DeLano wrote:
Stuart, Robert, & Others,
I believe Stuart is confusing the Samsumg 2233rz frame-sequential stereo 3D display with the Zalman M220W interlaced stereo 3D solution.
Due to lack of driver support, as far as I know, the Samsung isn't yet supported by any OpenGL-based software
have
it working. I believe Pymol has supported this for some time.
Best Wishes,
Stuart McNicholas
Donnie Berkholz wrote:
On 14:57 Tue 28 Apr , Stuart McNicholas wrote:
I clicked the source code link and it didn't send me anywhere. Is the
source code going to show up at some point, or will that wait until the
rewrite is entirely complete?
My apologies, this is now avai
Wishes,
Stuart McNicholas
William G. Scott wrote:
Hi Citizens:
Today I decided to try ccp4Mg, to see what I have been missing. I
downloaded the CCP4 website precompiled version.
OS X intel iMac.
When the program starts up, a window appears, and it is flickering at a
rapid frequency. I closed it
tab to add whatever colour you like. I believe
the current release requires you to name the colour before apply will
work. This will be addressed in next release.
Best Wishes,
Stuart McNicholas
On 9 Jan 2008, at 10:34, Eleanor Dodson wrote:
Bong angels are probably ideal already!
There is really no such animal as an ideal bondlength or angle -
they depend to some extent on the atomic environment.
Not to a complete extent?
Stuart
://chemistry.ucsc.edu/~wgscott
CCP4MG can also read Gaussian cube files. Someday the ability to
calculate a map from basis function definition, wave function data,
density matrix, etc. will appear.
Best Wishes,
Stuart McNicholas
execute
binary file
Is any one have this kind of experience?
please give the suggesstions.
This is slightly wierd. What output do the commands:
file /home/thomas/ccp4mg-1.0/bin/pythondist/bin/python
ldd /home/thomas/ccp4mg-1.0/bin/pythondist/bin/python
give?
Best Wishes,
Stuart McNicholas
can specify
atom selections. These can be anything, so in one selection specify one
of your residues and in the other column the other residue. You can do
this by using eg. the "..of residue ranges.." option and selecting just
one residue.
Best Wishes,
Stuart McNicholas
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