[ccp4bb] CCP4MG Release 2.8.0

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

Re: [ccp4bb] Drawing plt and libXaw lib

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

Re: [ccp4bb] Problems with CCP4MG

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

Re: [ccp4bb] Accessing CCP4MG applications via python scripts

, Stuart McNicholas

Re: [ccp4bb] Problems with CCP4MG

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=smf02source=repositorytid=file_modelmid=7d1184184e0086123cd94070ab861eb2_1 This is a very silly bug in CCP4MG, you

Re: [ccp4bb] ccp4mg question

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

Re: [ccp4bb] ccp4mg question

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 is

[ccp4bb] CCP4MG version 2.7

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).

Re: [ccp4bb] python.exe stops working

. Many apologies. I will attempt to get a version with a software renderer working as soon as possible. Stuart McNicholas

[ccp4bb] CCP4MG Version 2.7.2

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

[ccp4bb] CCP4MG Version 2.7.3

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

Re: [ccp4bb] ccp4MG- selecting h-bonds

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

Re: [ccp4bb] Problem in installation of the ccp4mg on the FC6

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

Re: [ccp4bb] display a map from a quantum chemical calculation

://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

Re: [ccp4bb] ideal bond length and bong angel

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

Re: [ccp4bb] ccp4mg question

. 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

[ccp4bb] CCP4MG Version 2.4.2

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

[ccp4bb] CCP4MG Version 2.4.3

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

[ccp4bb] CCP4MG Version 2.5.0

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

Re: [ccp4bb] BLT wish

On 17/08/11 10:49, Phil Evans wrote: Roll on the loggraph replacement! Next month ?

Re: [ccp4bb] ccp4mg and OS X

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

Re: [ccp4bb] ccp4mg and OS X

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 available

Re: [ccp4bb] 3D LCD and glasses

it working. I believe Pymol has supported this for some time. Best Wishes, Stuart McNicholas

Re: [ccp4bb] 3D LCD and glasses

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

Re: [ccp4bb] pdb2pqr generation

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 tpgr...@liverpool.ac.uk wrote: CCP4MG can also generate electrostatic surfaces, which can then be rendered and exported for

Re: [ccp4bb] jhbuild system on Mac

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

Re: [ccp4bb] Run on remote server

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

Re: [ccp4bb] ccp4i2 crashes on start

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

Re: [ccp4bb] problem with CCP4MG representation styles

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

Re: [ccp4bb] CCP4MG error after installation

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 <mjw...@pi

Re: [ccp4bb] off-screen display window

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

Re: [ccp4bb] Can anyone run refmac from the WINDOWS command prompt?

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

Re: [ccp4bb] Rescuing CCP4i2 projects after a loss of CCP4 installation

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

Re: [ccp4bb] CCP4MG cannot save images in Mac OS

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 one of

Re: [ccp4bb] CCP4MG cannot save images in Mac OS

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

Re: [ccp4bb] CCP4MG cannot save images in Mac OS

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 201

Re: [ccp4bb] CCP4i2 Text size

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

Re: [ccp4bb] ccp4i2 issue

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

Re: [ccp4bb] QTMG font too small

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

Re: [ccp4bb] File System Problems

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,

Re: [ccp4bb] Coot CCP4i2 extensions

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

Re: [ccp4bb] CCP4I2: non standard ssh port for remote jobs

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 > > transport = par

Re: [ccp4bb] CCP4I2: non standard ssh port for remote jobs

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.ac.uk> wrote:

Re: [ccp4bb] CCP4I2: non standard ssh port for remote jobs

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 submit

Re: [ccp4bb] Pointless error in ccp4i2 import merged data...

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 yo

Re: [ccp4bb] Pointless error in ccp4i2 import merged data...

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

Re: [ccp4bb] Pointless error in ccp4i2 import merged data...

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

Re: [ccp4bb] Pointless error in ccp4i2 import merged data...

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 <

Re: [ccp4bb] superpose crystal objects in CCP4MG or other software

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

Re: [ccp4bb] {Disarmed} AW: [ccp4bb] superpose crystal objects in CCP4MG or other software

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

Re: [ccp4bb] Analysis of NMR ensembles

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

Re: [ccp4bb] issue with running ccp4i2

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 'issues

Re: [ccp4bb] Render artifacts with CCP4MG

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

Re: [ccp4bb] i2run crank2 problem

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"

Re: [ccp4bb] problem running ccp4mg: ugly and useless graphics

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

Re: [ccp4bb] problem transferring ccp4i2 projects from one computer to another

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