[ccp4bb] Problems displaying CCP4i2 remotely on Mac with CCP4 8.0
Hi, We have a team who run all their CCP4 jobs on a central server, displaying the CCP4i or CCP4i2 GUI remotely on a Mac laptop or desktop using XQuartz and ssh. With the update to CCP4 8.0, CCP4i2 now crashes. The issue appears to be rendering the GUI via ssh on X11. There are a variety of errors, including QQuickWidget: Failed to make context current QOpenGLShader: could not create shader and Failed to create OpenGL context for format QSurfaceFormat(... This is not the problem often experienced with remote X11 sessions of iGLX not being permitted - coot from 8.0 runs, as do other GL applications. As far as I can tell, this is because the GUI uses features of GL2.0+. Indirect GLX only supports GL up to 1.4. If anyone has this working, any help they can give would be greatly appreciated. Chris -- Chris Richardson | Scientific Computing - Division of Structural Biology The Institute of Cancer Research | 237 Fulham Road, London SW3 6JB T +442071535445 | E chris.richard...@icr.ac.uk<mailto:chris.richard...@icr.ac.uk> | W www.icr.ac.uk<http://www.icr.ac.uk/> | Twitter @ICR_London<https://twitter.com/ICR_London> Facebook www.facebook.com/theinstituteofcancerresearch<http://www.facebook.com/theinstituteofcancerresearch> Making the discoveries that defeat cancer [ICR Logo]<http://www.icr.ac.uk/> The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] [Off-Topic] 3D Vision stereo with Ubuntu 18.04
Thanks to everyone who gave helpful suggestions; I now have stereo working on
Ubuntu 18.04.
To help anyone who comes across this in the CCP4 archives in the future, it was
necessary to:
1) Install lightdm and set it as the default display manager. Other display
managers that don't do compositing may also work.
2) Install a suitable desktop environment (I used gnome flashback metacity in
the end, but XFCE also works).
3) Edit the Xorg configuration (which is now a series of files in
/usr/share/X11/xorg.conf.d) to include "Stereo" "10", and "Composite" "Disable".
The step I was missing was the first one. In Ubuntu 16.04, stereo worked
without having to do this.
Thanks again,
Chris
--
Dr Chris Richardson :: Sysadmin, structural biology, icr.ac.uk
On 08/11/2019, 12:19, "CCP4 bulletin board on behalf of Chris Richardson"
wrote:
Apologies for the only slightly relevant question.
Does anyone know the correct incantations to get nVidia 3D Vision glasses
and emitter working with Ubuntu 18.04?
None of the tricks that work with 16.04 are helping with the new release.
In particular, disabling composite in the extensions makes the display blank
while X11 restarts itself every few seconds.
Thanks in advance,
Chris
--
Dr Chris Richardson :: Sysadmin, structural biology, icr.ac.uk
The Institute of Cancer Research: Royal Cancer Hospital, a charitable
Company Limited by Guarantee, Registered in England under Company No. 534147
with its Registered Office at 123 Old Brompton Road, London SW7 3RP.
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the message is received by anyone other than the addressee, please return the
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Registered Office at 123 Old Brompton Road, London SW7 3RP.
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[ccp4bb] [Off-Topic] 3D Vision stereo with Ubuntu 18.04
Apologies for the only slightly relevant question. Does anyone know the correct incantations to get nVidia 3D Vision glasses and emitter working with Ubuntu 18.04? None of the tricks that work with 16.04 are helping with the new release. In particular, disabling composite in the extensions makes the display blank while X11 restarts itself every few seconds. Thanks in advance, Chris -- Dr Chris Richardson :: Sysadmin, structural biology, icr.ac.uk The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] Stereo graphics systems
Apologies for revisiting this oft-discussed subject. nVidia no longer support their 3D Vision system, and appear to have stopped manufacturing it. Does anyone have suggestions for an alternative? Not all of our scientists use it, but those who find it valuable would be sad to lose it. To clarify, I'm seeking a desktop solution as we don't have the space for 3D projectors. If there is nothing else out there, I may have to start searching eBay for second hand IR emitters. Regards, Chris -- Dr Chris Richardson :: Sysadmin, structural biology, icr.ac.uk The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] PanDDA error revisiting old run
One of our group has been using the newly updated PanDDA (0.2.12 in ccp4
7.0.058) to look at some data previously processed with PanDDA. It dies with
an error on unpickling a pickle file (see errors below).
My guess is that changes have left it unable to read some pickle files from
previous versions. I’ve tried running pandda.analyse on the tutorial data and
it completes without errors.
Can anyone shed some light on this?
TIA,
Chris
---%<---
PanDDA is running on Ubuntu 16.0.4 LTS with CCP4 7.0.058. The command was:
pandda.analyse data_dirs="/work//foop/"
out_dir="//pandda/pandda_analyse" min_build_datasets=30
max_new_datasets=500 grid_spacing=0.5 cpus=8 events.order_by=cluster_size
pdb_style='pandda_in_*.pdb' mtz_style='pandda_in_*_map_coeffs.mtz'
recalculate_statistical_maps=no existing_datasets=reprocess
reference.pdb="/work//pandda/pandda_analyse/reference/reference.pdb"
reference.mtz="/work//pandda/pandda_analyse/reference/reference.mtz"
The error is:
<…>
Checking for existing analyses
->>>
Looking for pickled files from previous runs in: pickled_data
-> Loading reference grid
Unpickling File: pickled_data/grid.pickle
-> Loading reference dataset
Unpickling File: pickled_data/reference_dataset.pickle
Runtime: 00 hours:00 minutes:00 seconds
## <~~~>
###
### PanDDA exited with an error
###
## <~~~>
###
->>>
Traceback (most recent call last):
File
"/common/app/ccp4/7.0.0/ccp4-7.0/lib/python2.7/site-packages/panddas-0.2.12-py2.7.egg/pandda/analyse/__init__.py",
line 1081, in run
pandda_analyse_main(pandda=pandda)
File
"/common/app/ccp4/7.0.0/ccp4-7.0/lib/python2.7/site-packages/panddas-0.2.12-py2.7.egg/pandda/analyse/__init__.py",
line 1020, in pandda_analyse_main
pandda.run_analysis_init()
File
"/common/app/ccp4/7.0.0/ccp4-7.0/lib/python2.7/site-packages/panddas-0.2.12-py2.7.egg/pandda/analyse/classes.py",
line 771, in run_analysis_init
self.load_pickled_objects()
File
"/common/app/ccp4/7.0.0/ccp4-7.0/lib/python2.7/site-packages/panddas-0.2.12-py2.7.egg/pandda/analyse/classes.py",
line 821, in load_pickled_objects
self.datasets.set_reference(dataset=self.unpickle(self.pickle_handler.get_file('reference_dataset')))
File
"/common/app/ccp4/7.0.0/ccp4-7.0/lib/python2.7/site-packages/panddas-0.2.12-py2.7.egg/giant/manager.py",
line 82, in unpickle
return easy_pickle.load(pickle_file)
File
"/common/app/ccp4/7.0.0/ccp4-7.0/lib/py2/site-packages/cctbx_project/libtbx/easy_pickle.py",
line 80, in load
return cPickle.loads(_open(file_name, "rb").read())
AttributeError: 'module' object has no attribute 'ElectronDensityMap'
->>>
## <~~~>
###
### PanDDA exited with an error
###
## <~~~>
###
--
Dr Chris Richardson :: Sysadmin, structural biology, icr.ac.uk
The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company
Limited by Guarantee, Registered in England under Company No. 534147 with its
Registered Office at 123 Old Brompton Road, London SW7 3RP.
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message is received by anyone other than the addressee, please return the
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Re: [ccp4bb] Coot 'Edit Chi Angles' on Mac misbehaving
Many thanks for explaining where it is going awry. Looking at GLU.cif in the monomer library that is part of the CCP4 distribution, it contains the following lines: GLN chi1 N CA CB CG 180.000 15.000 3 GLN chi2 CA CB CG CD 180.000 15.000 3 GLN chi3 CB CG CD OE10.000 30.000 2 In the monomer library you link, it has: GLU chi1 N CA CB CG 180.000 15.000 3 GLU chi2 CA CB CG CD 180.000 15.000 3 GLU chi3 CB CG CD OE20.000 30.000 2 Which makes more sense. Thanks again, Chris From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Huw Jenkins <h.t.jenk...@me.com> Sent: 26 April 2018 09:47 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Coot 'Edit Chi Angles' on Mac misbehaving > On 26 Apr 2018, at 09:19, Chris Richardson <chris.richard...@icr.ac.uk> wrote: > > I've just compiled Coot on the same Mac using Fink, and the dialogue for this > version of Coot shows CA <--> CB, CB <--> CG, and CG <--> CD angles for the > same residue. >From a quick look at the Fink coot.info it appears to get the monomer library >from here: http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/refmac/Dictionary/refmac_dictionary_v5.41.tar.gz Setting $CLIBD_MON to point to this and the 'Edit Chi Angles' dialogue for CCP4 distributed Coot 0.8.9.1 shows CA <--> CB, CB <--> CG and CG <--> CD of Glu 14 A from the RNase tutorial model. Huw The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.
[ccp4bb] Coot 'Edit Chi Angles' on Mac misbehaving
?We have an issue with the 'Edit Chi Angles' dialogue in Coot on Macs using the version of Coot bundled with CCP4. For some residues - such as Glu - the dialogue only shows the C <--> CA angle. If you tick the 'Add Chi Angles for Hydrogens' box, it adds CA <--> N. I've just compiled Coot on the same Mac using Fink, and the dialogue for this version of Coot shows CA <--> CB, CB <--> CG, and CG <--> CD angles for the same residue. The CCP4 version which misbehaves is 0.8.9.1; the working Fink version is 0.8.9. Both are running on OS X 10.11.6. Has anyone else experienced this? Any suggestions as to how to fix this? Regards, Chris The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.
[ccp4bb] Fluidigm TOPAZ system looking for new home
We have a Fluidigm TOPAZ free interface diffusion crystallisation system that we no longer use. If it can't find a new home it will be disposed of. We're offering it free of charge to any interested UK organisation on the condition that the recipient pays for its transport. It's currently in central London. The TOPAZ system automates nanoscale crystallisation trials. We have the FID Crystallizer and associated laptop (assuming we can unchain it from the lab bench). The system also requires TOPAZ Screening Chips and associated reagents. Although Fluidigm has ended new system sales for the Topaz, it continues to manufacture and supply consumables. For further information, look at: http://www.fluidigm.com/topaz-system.html Note that this is *not* the system we are offering. We have the previous model, which can be seen on this page from the Internet Archive: http://web.archive.org/web/20060326075010/http://www.fluidigm.com/topazinstruments.htm If you're interested, please email nora.cro...@icr.ac.uk. Chris -- Dr Chris Richardson :: Sysadmin, structural biology, icr.ac.uk The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.
[ccp4bb] Cryo-Xe-Siter looking for new home
We have an MSC Cryo-Xe-Siter that won't fit in our refurbished X-ray laboratory. If it can't find a new home it will be disposed of. We're offering it free of charge to any interested UK organisations on the condition that the recipient pays for its transport. It's currently in central London. The Cryo-Xe-Siter is used for preparing xenon derivates of protein crystals. A quick web search reveals a review in Nature Structural Molecular Biology from 1998. http://www.nature.com/nsmb/journal/v5/n12/full/nsb1298_1107.html If you're interested, please email nora.cro...@icr.ac.uk. If we don't have any interest before this Friday it will be scrapped. Chris -- Dr Chris Richardson :: Sysadmin, structural biology, icr.ac.uk The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.
Re: [ccp4bb] GeForce Graphics cards
On the subject of nVidia graphics cards, linux and stereo, I feel I ought to mention the Asus VG278H. This is a 120Hz 27 1920x1080 monitor with a built-in nVidia 3D vision emitter, which comes bundled with a pair of 3D vision glasses. The great thing about the built-in emitter is that it takes stereo synch from the DVI cable even under Linux. This removes the need for a Quadro card with a 3-pin mini-DIN connector or 3-pin adapter. Here in the UK our cheapest supplier was selling it for £380 ex. VAT. There is little information about using it with Linux on the web, but as I understand it you still need a Quadro card. I got it running with little trouble using a Quadro 2000, Ubuntu 12.04 LTS and the latest nVidia drivers. It may be possible to use cheaper Quadro cards. The picture and stereo quality is excellent when compared to our existing stereo systems. Chris -- Dr Chris Richardson :: Sysadmin, structural biology, icr.ac.ukhttp://icr.ac.uk/ The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.
Re: [ccp4bb] Mac mini advice (rapidly veering off topic)
In the great internet tradition I'll chip in with my opinion even though it doesn't differ substantially from those already stated earlier in the thread. I'm responsible for a mixed bag of Windows, Linux and Mac boxen used for crystallography and structural electron microscopy. In terms of setting up the infrastructure and getting things working, Linux wins by a mile. It's easy to buy cheap, powerful machines as desktops or servers. There's a wealth of resources to help the sysadmin. The ubiquity of Linux means that if you're trying to do something, there's almost always someone who has done it already and posted about it on a forum or blog. In terms of getting people to use the machines, OS X wins hands down. Putting people in front of linux machines requires more hand-holding on my part, especially for people who are inexperienced or even afraid of computers. This is becoming more of an issue: gone are the days when most crystallographers had a favourite shell and were happy editing scripts. Linux has come on in leaps and bounds but it's still not quite user-friendly enough; even something as simple as copying and pasting still doesn't have a uniform implementation. People familiar with commercial software struggle with the open source equivalents. I won't cover Windows as I have an irrational hatred of it. Having said all that, I too am worried about the way Apple is going. They haven't released a proper Mac Pro upgrade in ages, and seem to be concentrating on making iMacs as wafer thing as possible at the expense of other practical considerations. Their move to using the App Store for everything has concentrated on individual users and hasn't included support for corporate IT. Support for NFS and other UNIXy under-the-hood features is changed or dropped seemingly on a whim with no real documentation. Their habit of making every change or new release a big surprise makes it difficult to plan for the future. I'm glad I've got that off my chest. Now I can do something productive. Chris -- Dr Chris Richardson :: Sysadmin, structural biology, icr.ac.uk The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.
Re: [ccp4bb] Mac mini advice
On 23 Jan 2013, at 14:05, Bosch, Juergen wrote: I assume nobody of you is running an actual Osx server ? I mean the upgrade to a full server version of the commonly distributed normal Osx releases ? At the moment we have two OS X servers. One runs open directory for user authentication. The other is an AFP server for network home directories. They are elderly Xeon-based XServes and will be retired as soon as possible. We're getting rid of the authentication server because of unrelated changes to the way user authentication will be handled. We're getting rid of the file server because it's old and needs replacing. It will, however, be replaced by a Linux server. In my opinion, Apple's abandonment of its rack-mountable server line shows a lack of commitment to servers. The Promise RAID storage they resell is considerably more expensive than the equivalent from our Windows/Linux supplier. Finally, the other Mac admins in my organisation haven't been saying nice things about mountain lion server. If you look at forums like AFP548.com it's apparent that many other people are moving away from OS X server. Moving to OS X servers does simplify some aspects of administration. In the past, there was the added bonus that it was easy to get Linux and Windows machines to talk to a Mac server. Creeping changes made by Apple since OS X server 10.4 mean that this is less true. In particular, the horrible way Apple sets up SMB make its use a nightmare with other modern operating systems. Chris -- Dr Chris Richardson :: Sysadmin, structural biology, icr.ac.uk The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.
[ccp4bb] CCP4 package and update managers: relocating installations
Dear CCP4, While we're talking about the package and update managers, I have a question. Is there any way to install the CCP4 suite in a non-standard location under OS X and still use the package manager and update facilities? With a large number of Macs it's much easier for me to have CCP4 living in a single, network-mounted directory than on each machine. Under Linux, the package manager and updater allow me to put things where I like. Under OS X the package manager wants to put things in /Applications and I can't edit that, despite it being in a GUI element that looks like an input field. Regards, Chris -- Dr Chris Richardson :: Sysadmin, structural biology, icr.ac.uk The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.
Re: [ccp4bb] [COOT] CCP4 6.3.0 released
On 17 Jul 2012, at 22:34, William G. Scott wrote: On Jul 17, 2012, at 6:25 AM, Felix Frolow wrote: I will wait for fink version if it will be one… :-\ Does anyone use or want this anymore? Apologies for reanimating this long-dead discussion, but did you reach a conclusion about putting ccp4 6.3.0 in fink? I'd rather use the dmg installer (choosing alternative install locations seems a little wonky) but will bite the bullet if it's not going to be finkified. Thanks, once again, for all your hard work on fink over the years. Chris -- Dr Chris Richardson :: Sysadmin, structural biology, icr.ac.uk The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.
[ccp4bb] cTruncate fails after Scala - clipper::Message_fatal
Dear all, We have a problem where cTruncate generates an error message when trying to process data from Scala as part of a Scale and Merge Intensities task in the GUI. Scala appears to run ok. cTruncate produces *** * Information from CCP4Interface script *** The program run with command: /sw/share/xtal/ccp4-6.2.0/bin/ctruncate -hklin /tmp/foop/Scala_1_1_mtz.tmp -hklout /tmp/foop/Scala_1_3_mtz_MPS1-1624-118.tmp -colin /*/*/\[IMEAN,SIGIMEAN\] -colano /*/*/\[I(+),SIGI(+),I(-),SIGI(-)\] -colout MPS1-1624-118 has failed with error message CCP4MTZfile - internal error terminate called after throwing an instance of 'clipper::Message_fatal' *** #CCP4I TERMINATION STATUS 0 CCP4MTZfile - internal error terminate called after throwing an instance of 'clipper::Message_fatal' We're running CCP4 6.2.0 compiled by 32-bit fink on OS X 10.6.8. The GUI task runs to completion with other input MTZ files that I have tried. If I run the ctruncate command in a shell, it generates the same error. Dr Stephen Carr posted a similar query back in March 2011, but didn't get any replies on the bb. Does anyone know what's going on here? Regards, Chris -- Dr Chris Richardson :: Sysadmin, structural biology, icr.ac.uk The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.
Re: [ccp4bb] Permissions and ownerships in ccp4 6.2.0
While we're on the subject of issues with the ccp4 6.20 distribution, I've had a problem with the Mac OS X package installer. It seems to be missing the ccp4i executable. Launching the application gives the following error: 19/07/2011 13:04:02 [0x0-0x269269].com.yourcompany.ccp4[17160] /Applications/ccp4-6.2.0/ccp4.app/Contents/Resources/ccp4.sh: line 202: /Applications/ccp4-6.2.0/bin/ccp4i: No such file or directory I've searched what gets installed in /Applications/ccp4-6.20 and there is no ccp4i. The package installer also has the aforementioned issues with script permissions. Regards, Chris -- Dr Chris Richardson :: Sysadmin, structural biology, icr.ac.uk The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.
Re: [ccp4bb] rosetta/ubuntu
On 8 Jul 2011, at 14:21, Harry Xu wrote: I want to try mr_rosetta for my project, but I had problem installing rosetta on my computer. My computer is running ubuntu 11.04 with gcc 4.5. Compiling of rosetta 3.2 failed with the message: KeyError: Unknown version number 4.5 for compiler 'gcc' . There's a good summary of the problem and a proposed solution here: http://morganbye.net/blog/2011/05/rosetta-32-ubuntu-1104 I haven't tried this myself, but I've done something similar to get it working with Intel compilers on an SGI ICE cluster. Basically, Rosetta uses SCons to compile itself. SCons has, among its many configuration files, one that lists the compiler versions it is prepared to use and any compiler-specific options that go with them. gcc 4.5 is relatively new and not in the config files included with rosetta. Editing the files and adding 4.5 as an acceptable compiler should fix the problem. Note that the author of the blog post also has a fix for a piece of code that gcc v4.5 rejects on syntactical grounds. Regards, Chris -- Dr Chris Richardson :: Sysadmin, structural biology, icr.ac.uk The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.
[ccp4bb] AMoRe fails to use model coordinates
One of our group was having trouble getting AMoRe to use model coordinates as a trial model. I've replicated this using the data from the tutorial at http://www.ccp4.ac.uk/dist/examples/tutorial/html/mr-tutorial-amore.html It fails using CCP4 6.1.13 on OS 10.6.7 (compiled from Fink) and Ubuntu 8.0.4 LTS (binary installation from ccp4.ac.uk). The tutorial uses a PDB file of model coordinates (model.pdb). As I understand it, AMoRe is supposed to generate an SF table file from this. Instead, AutoAMoRe seems to be looking for an mtz file. The logs look like this: *** * Information from CCP4Interface script *** There is no SF Table file for the map of the model coordinates Generating the file /home/foop/temp/amoretest/AmoreModel_MR_trial.tab *** File: /home/foop/temp/amoretest/AmoreModel_MR_trial.mtz Cannot be opened for reading CCP4 library signal ccp4_general:Cannot find input file (Error) raised in ccp4setenv amore: Cannot find input file Times: User: 0.0s System:0.0s Elapsed: 0:00 *** * Information from CCP4Interface script *** The program run with command: /sw/share/xtal/ccp4-6.1.13/bin/amore HKLIN /home/foop/temp/amoretest/AmoreModel_MR_trial.mtz HKLPCK0 /tmp/foop/AmoreTest_1_3_hkl.tmp TABLE1 /home/foop/temp/amoretest/AmoreModel_MR_trial.tab has failed with error message Last system error message: No such file or directory amore: Cannot find input file *** The command script generating this is: *** /tmp/foop/AmoreTest_1_4_com.tmp *** title AmoreTest sortfun - MODEL - resolution 60.0 - 3.0 labin FC=FC PHIC=PHIC ## This script run with the command ## # /sw/share/xtal/ccp4-6.1.13/bin/amore HKLIN /home/foop/temp/amoretest/AmoreModel_MR_trial.mtz HKLPCK0 /tmp/foop/AmoreTest_1_3_hkl.tmp TABLE1 /home/foop/temp/amoretest/AmoreModel_MR_trial.tab If anyone can suggest a way around this problem (other than using an alternative MR program), I'd be grateful. Regards, Chris -- Dr Chris Richardson :: Sysadmin, structural biology, icr.ac.uk The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.
Re: [ccp4bb] AMoRe fails to use model coordinates
On 27 Apr 2011, at 15:02, Edward A. Berry wrote: No, that would be the TABFUN step. You are running SORTFUN which takes your experimental data and puts in the the .tab format required by the subsequent routines. And with the HKLIN command line variable you are telling it to get data from AmoreModel_MR_trial.mtz . Does that file exist, is it readable, and path name correct? The file doesn't exist, it's a figment of the GUI's imagination. After some poking around, I've now got it to work properly. The problem seems to be that the GUI is very sensitive to the order in which you enter data. When you choose to run AMoRe, it pops up an AMoRe window and a Model Database window. If you enter data into these in the order specified in the tutorial, it will run the scripts for a model in the form of SFs from an MTZ, even though the Model Database window claims to be using a model in the form of coordinates. The trick to getting it to work seems to be: 1) Open the Model Database window. Enter your pdb filename. Don't even think about clicking Close, despite what the tutorial says. Click SaveExit, and never open the window again. If you do have to open it again, Restore Default Parameters and start from scratch. 2) Open the AMoRe window, set up the job parameters and run the job. Doing this will get it to run TABFUN on your pdb file rather than SORTFUN on a non-existent mtz file. Most of the time. Thanks to Stefano Trapani and Jorge Navaza for pointing us in the direction of the standalone AMoRe. Chris -- Dr Chris Richardson :: Sysadmin, structural biology, icr.ac.uk The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.
Re: [ccp4bb] Graphics card for Nvidia 3D vision
Andreas Eichinger a.eichin...@wzw.tum.de 03/01/11 9:24 AM We are currently setting up a new 3D workstation with a Samsung SyncMaster 2233RZ monitor and a Nvidia 3D vision glasses kit on a Redhat Enterprise Linux box. According to Nvidia, a Quadro FX 4800, Quadro FX 4600 or Quadro FX 3700 graphics card can be used for 3D on Linux if it is connected via a 3-pin mini-DIN stereo connector. Has somebody experience with such a setup? The FX 3800 will also work, but it doesn't have a mini-DIN connector. You can buy a separate riser fitted with the connector, which mounts in a spare slot next to the card and connects to it by a cable. This is made by PNY, part number 900-50762--000. In our experience, an FX 3800 and separate riser is a lot cheaper than a card with a built-in DIN connector. When you buy the 3D Vision glasses kit, check that it contains the mini-DIN to emitter cable. At one stage this was included in kits for the US market, but not in kits for Europe. This may have changed. We use the same monitor with an FX 3800 and 3D vision glasses kit on a couple of machines and are very impressed with the quality of the stereo. The glasses are a lot nicer than the old models, and it's nice being able to recharge them by USB rather than constantly swapping batteries because someone left the arms open and the glasses active overnight. Regards, Chris The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.
Re: [ccp4bb] Full-screen stereo with Coot/PyMol/etc on 3D LCD displays?
On 25 Jan 2011, at 08:35, Harry M. Greenblatt wrote: Has someone received an official answer from NVIDIA that they do *not* work? I raised this issue here back in November. Someone, whose email I cannot now find, replied off-list to say that they had been told by nVidia that 3D Vision did not work on Macs. nVidia's website is a little confused. Their 3D Vision pages say that it requires Microsoft Windows XP 32/64 bit, Vista 32/64-bit or Windows 7 32/64-bit, Linux 32/64 bit. Their Quadro FX4800 for Mac page says that Professional 3D Stereo Solutions enables robust control of stereo effect through a dedicated 3-pin mini-din connection between the graphics card and 3D stereo hardware and links to the 3D Vision pages. I spent quite a while looking at this last year and found several people who couldn't get it to work and none who could. Chris The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.
[ccp4bb] nVidia stereo problems : Mac Pro, Quadro FX 4800
(Apologies to those who have already seen this on the PyMol list) Does anyone have experience of a working Mac Pro/Quadro FX 4800/120Hz flat screen setup? I'm trying to put one together, and am getting nowhere. We have: - Mac Pro (early 2010, MacPro 5,1) running 10.6.4 - Quadro FX 4800 for Mac - nVidia drivers Retail_256.01.00f03 (latest as of 19/10/2010) - nVidia IR emitter and glasses set connected by DIN and USB cables - ViewSonic Fuhzion VX2268WM, refresh 120Hz We have working Linux setups that are the same as this (apart from the Mac Pro), and I've tested that the graphics card, monitor, glasses and emitter all work in Stereo. With the Mac, I've tried both Stereo-capable native apps (PyMol incentive product, QtMG) and X11 apps (Coot). The problem is that the emitter refuses to turn on; it just sits there flashing red. The display looks as it should for stereo. nVidia's support for Mac is effectively non-existent, so I'm hoping that someone on ccp4bb has got this working in the past and knows the correct incantations. Regards, Chris -- Dr Chris Richardson :: Sysadmin, structural biology, icr.ac.uk The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.
Re: [ccp4bb] Coot cannot read mtz or pdb files
On 4 Oct 2010, at 11:15, Leiman Petr wrote: It cannot read in MTZ files (quote: This is not an mtz file). PDB files are garbled up on reading as well. Most (but not all) connections are broken. A screenshot is attached. Is the Mac set up with an unusual language, locale or set of formats? I experienced this with an older version of Coot when one of our group fiddled with Language Text in System Preferences. They were trying to make it easier for themselves to create text files in Greek and/or Cyrillic script. The changes had the unintended consequence of breaking coot. My theory at the time was that the number separators (, and .) had reversed which was confusing an input library that was used in reading PDB and MTZ files. Setting the region back to UK or US fixed the problem, and I didn't investigate much further. Regards, Chris The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.
[ccp4bb] Web sites ports (was Regarding BMCD)
On 13 Jun 2009, at 00:12, Edward A. Berry wrote: That seems likely. I also can't reach the BMCD link, but I can reach the same host on port 80. I understand my institution has a very restrictive firewall ... My apologies for wandering off topic, but this is an irrational obsession of mine. Can people setting up web sites, web tools, and databases please *not* use anything other than port 80 (or 443 for https) for their site. In my limited experience, the benefits of running it on another port are vanishingly small. The only noticeable effect is that you reduce the number of potential users. Many scientists are stuck behind very tight firewalls, and this will only get worse as organisations become more and more paranoid about leaks of patient data and intellectual property. In the UK the situation isn't helped by the government's inability to keep personal data private; publicly funded bodies are desperate to avoid the media attention that would follow such a leak. Whether it's rational or not, in most cases this security policy is non-negotiable. If it's not on a standard port, I can't see it (unless I go home or to a coffee shop with WiFi). Chris -- Dr Chris Richardson :: sysadmin :: Structural Biology :: icr.ac.uk The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.
Re: [ccp4bb] scala on mac osx - off topic, really
On 7 May 2008, at 13:32, Andreas Förster wrote: a colleague is running ccp4 6.0.2 on a MacBook with Timid Tiger. Built-in Scala is 3.2.25. Because of a bug, he wants to upgrade Scala. Running Scala 3.3.2-beta5 or 3.2.34 (phil's binaries) fails because gcc shared libraries are missing. I ran into exactly the same problem. After wasting plenty of time trying to to get gcc4.0 and gcc43 to coexist happily, I tried another tack. I edited the ccp4.info file (in /sw/fink/10.4/unstable/main/ finkinfo/sci) to download the scala_3.2.34 source code and unpack it over the top of the rest of the source. I'm fairly sure that you're *not* supposed to do it this way, but it worked and I haven't had any complaints that the newer version of scala is broken. If you'd like me to send you the edited ccp4.info file or executable, I'd be happy to do so. I don't want to put them on ccp4, because they're so bodged that they'll probably cause more harm than good in the wild. Regards, Chris -- Dr Chris Richardson - sysadmin, Structural Biology Section, icr.ac.uk The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.
Re: [ccp4bb] arp/warp and refmac problem on os x
On 24 Apr 2008, at 3:38 PM, Ronnie Berntsson wrote: I've got a rather weird problem when trying to run arp/warp. When trying to run arp/warp (latest version 7.0.1) it complains that I should install a newer version of Refmac (5.4.0045). The version of Refmac I have installed is 5.4.0066, and thats what is being used if I run Refmac both from terminal or via CCP4i. However, when arp/warp starts to run it magically finds a refmac 5.2.something and uses that. Reinstalling arp/warp did not help, even though the install script showed that I had refmac 5.4.0066 installed... I'm running OS X 10.5.2 and have installed ccp4 and refmac via fink. All other CCP4 programs work fine and Refmac runs normally as well, it's only when it's called from arp/warp that something goes wrong.. All ideas to fix this problem are most welcome. This is an interesting feature of the Fink CCP4/Refmac installation. When you install the new refmac in Fink, you get an executable called refmac-5.4, which lives in /sw/share/xtal/ccp4-6.0.2/bin. The refmac5 that you get from the terminal lives in /sw/bin and is a symbolic link to this executable. However, in /sw/share/xtal/ccp4-6.0.2/bin there still lurks an executable refmac5, and this is version 5.2.0019. When you run ARP/wARP from the GUI, it seems that this is the executable that it uses - hence the version warnings. In our experience, this also breaks flex-wARP when run through the GUI. Whether this is just a symptom of the way I use Fink to install things, or whether it's a problem for everyone, I don't know. I have a solution to this, although it may not be the most elegant one. I move the old refmac5 out of the way, and create a new symbolic link mv /sw/share/xtal/ccp4-6.0.2/bin/refmac5 /sw/share/xtal/ ccp4-6.0.2/bin/refmac5.old ln -s /sw/share/xtal/ccp4-6.0.2/bin/refmac-5.4 /sw/share/xtal/ ccp4-6.0.2/bin/refmac5 (This is from memory, so the details may not be correct.) Hope this helps, Chris The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.
Re: [ccp4bb] Installing coot on MacOSX 10.5
An update, in case this is still a burning issue for anybody. The fink package maintainer for Ruby updated the package over the weekend. Coot now builds fine from scratch on 10.4.11. I haven't tested 10.5, but it should also be okay. On 17 Apr 2008, at 20:23, Paul Emsley wrote: The mind boggles as to why you'd need ruby to install Coot... Ruby is a dependency of SWIG (in Fink, at least). Chris -- Dr Chris Richardson - sysadmin, Structural Biology Section, icr.ac.uk The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.
