Re: [ccp4bb] imosflm in ccp4 6.1.0 in linux problems
Dear Paula, The tcltk++ binary either from the downloads pages or ftp://ftp.ccp4.ac.uk/ccp4/current/extras should work fine - if you unpack this somewhere, export CCP4I_TCLTK appropriately and add the lib directory to the LD_LIBRARY_PATH it should solve your problem. If you would like more detail please don't hesitate to get in touch. This works fine on all the 32 and 64 linux systems I have tested. Best wishes, Graeme -Original Message- From: CCP4 bulletin board on behalf of Salgado, Paula Sent: Tue 1/6/2009 11:03 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] imosflm in ccp4 6.1.0 in linux problems Hi everyone I've been trying to run the new imosflm version from ccp4i 6.1.0 gui on ubuntu 8.0.4, but keep having problems. After struggling with it to search for the correct MOSDIR directory path, it then complained it was missing several packages from wish8.4. I did manage to find some of them, but after searching the web I still can't find: treectrl 2.1 img::png 1.3 img::gif 1.3 img::jpeg 1.3 can anyone tell me where I can download them or what other solutions to get imosflm to run properly? Thanks a lot Paula
Re: [ccp4bb] Fwd: Twinning
Dear Steve, Presence of several Patterson peaks at impossible (as far as crystal packing is concerned) distances and an NCS two-fold normal to the crystallographic one suggests it could be an order-disorder (OD) structure, like the one we had in Exeter. An order-disorder twin crystal of L-2-haloacid dehalogenase from Sulfolobus tokodaii. Rye CA, Isupov MN, Lebedev AA, Littlechild JA. Acta Crystallogr D Biol Crystallogr. 2007 Aug;63(Pt 8):926-30. For that case at 1.6 A Andrey Lebedev from York had written a dedicated detwinning (demodulation) program and FreeR went down from 0.27 to 0.22. Original FreeR was nearly acceptable as only several percent of reflections were overlapping. If you feel your case appears similar to our OD-structure I would suggest you to contact Andrey, as he is collecting cases of OD-structures and probably could modify his program for your case. Best wishes Misha Isupov University of Exeter From: CCP4 bulletin board [ccp...@jiscmail.ac.uk] On Behalf Of Stephen Hare [s.h...@mail.cryst.bbk.ac.uk] Sent: 06 January 2009 16:35 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Fwd: Twinning Dear All, We are currently working on a structure of apparent P21 symmetry which has been solved by molecular replacement. The data are to 2.7Å but the Rfree will not drop below 30%. The density is clear for the model we have, however there is extra density that suggests a shift of the structure by 16Å in either direction - resulting in three possible overlapping positions for the structure. We assume this is the result of twinning. The unit cell dimensions are 102.7Å, 83.0Å, 115.3Å, 90°, 101.8°, 90°. Examining the data with phenix.xtriage also suggests pseudo translational symmetry with a separation of 16Å. A Patterson peak at 0.097, 0.000, -0.096 is approximately 30% of the origin peak, while a second peak of double the translation at 0.192, 0.000, 0.195 is 7% of the origin peak. The structure contains a dimer of dimers with an NCS 2 fold axis almost perpendicular to the crystallographic 2 fold. This NCS axis almost coincides with the diagonal between the A and C axes. A twin axis along the A C diagonal (l,-k,h) could explain the observed extra density, however this is not possible because A and C are different lengths. As a result of the NCS axis running almost perpendicular to the observed P21 axis, it is possible to merge the reflections in a larger orthorhombic unit cell - dimensions 137.1Å, 83.3Å, 169.8Å although here the Rmerge is higher and it is not possible to get a molecular replacement solution. Is it possible to define the (l,-k,h) twinning operator in our original unit cell? or have we missed the actual unit cell? Orsomething else? Steve Stephen Hare PhD Post doctoral research associate Jefferiss Research Laboratories Wright-Fleming Institute Division of Medicine Imperial College London Norfolk Place London W2 1PG UK Phone: +44 (0) 20 7594 3908 Fax: +44 (0) 20 7594 3906
[ccp4bb] nVidia Quadro FX3000 on Ubuntu 8.10
Hi, I'm trying to install a nVidia Quadro FX3000 card on a PC running Ubuntu 8.10 intrepid. I run into the following error when I install drivers I downloaded from the nVidia site: The installer fails to find a kernel interface from the nvidia ftp site and fails to compile the kernel. Any help would be greatly appreciated. Thanks and best wishes. -Chris Attached is the complete log file. Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm nvidia-installer.log Description: Binary data +++ Chris Ulens, Ph.D. Lab of Structural Neurobiology Division of Pharmacology Campus Gasthuisberg, ON1 Herestraat 49, PB 601 B-3000 Leuven Belgium +++
Re: [ccp4bb] nVidia Quadro FX3000 on Ubuntu 8.10
Chris, Try this: sudo apt-get install envyng sudo apt-get install envyng-gtk fire the envyng-gtk interface from the command line or menu and see if it finds a solution.. HTH, Partha On Wed, Jan 7, 2009 at 10:49 AM, Chris Ulens chris.ul...@med.kuleuven.be wrote: Hi, I'm trying to install a nVidia Quadro FX3000 card on a PC running Ubuntu 8.10 intrepid. I run into the following error when I install drivers I downloaded from the nVidia site: The installer fails to find a kernel interface from the nvidia ftp site and fails to compile the kernel. Any help would be greatly appreciated. Thanks and best wishes. -Chris Attached is the complete log file. Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm +++ Chris Ulens, Ph.D. Lab of Structural Neurobiology Division of Pharmacology Campus Gasthuisberg, ON1 Herestraat 49, PB 601 B-3000 Leuven Belgium +++ -- MRC National Institute for Medical Research Division of Molecular Structure The Ridgeway, NW7 1AA, UK Email: pcha...@nimr.mrc.ac.uk Phone: + 44 208 816 2515
Re: [ccp4bb] Fwd: Twinning
Hey Stephen, how about simply putting three models, separated by 16A, into your original unit cell and refining them together. You'd have to guess their fractional occupancies from the heights of the Patterson peaks (and make them add up to one, obviously). This approach (in contrast to correcting the intensities) was the consensus when I talked to Peter Zwart and Tom Terwilliger about a similar problem. As my problem still hasn't been solved (probably because of flawed data processing due to overlapping spots), I'd be very keen on hearing about your progress. http://scripts.iucr.org/cgi-bin/paper?S0907444908016648 describes both approaches to lattice-translocated crystals (correcting intensities and refining several models concurrently). http://scripts.iucr.org/cgi-bin/paper?ba5111 is the best review on the subject. All the best. Andreas Stephen Hare wrote: Dear All, We are currently working on a structure of apparent P21 symmetry which has been solved by molecular replacement. The data are to 2.7Å but the Rfree will not drop below 30%. The density is clear for the model we have, however there is extra density that suggests a shift of the structure by 16Å in either direction - resulting in three possible overlapping positions for the structure. We assume this is the result of twinning. The unit cell dimensions are 102.7Å, 83.0Å, 115.3Å, 90°, 101.8°, 90°. Examining the data with phenix.xtriage also suggests pseudo translational symmetry with a separation of 16Å. A Patterson peak at 0.097, 0.000, -0.096 is approximately 30% of the origin peak, while a second peak of double the translation at 0.192, 0.000, 0.195 is 7% of the origin peak. The structure contains a dimer of dimers with an NCS 2 fold axis almost perpendicular to the crystallographic 2 fold. This NCS axis almost coincides with the diagonal between the A and C axes. A twin axis along the A C diagonal (l,-k,h) could explain the observed extra density, however this is not possible because A and C are different lengths. As a result of the NCS axis running almost perpendicular to the observed P21 axis, it is possible to merge the reflections in a larger orthorhombic unit cell - dimensions 137.1Å, 83.3Å, 169.8Å although here the Rmerge is higher and it is not possible to get a molecular replacement solution. Is it possible to define the (l,-k,h) twinning operator in our original unit cell? or have we missed the actual unit cell? Orsomething else? Steve Stephen Hare PhD Post doctoral research associate Jefferiss Research Laboratories Wright-Fleming Institute Division of Medicine Imperial College London Norfolk Place London W2 1PG UK Phone: +44 (0) 20 7594 3908 Fax: +44 (0) 20 7594 3906 -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London
Re: [ccp4bb] imosflm in ccp4 6.1.0 in linux problems
Hi folks We have had a good look at this at Mosflm HQ now on Linux. The CCP4 TclTk++ distribution seems to work okay, and there's no need to install the ActiveTcl version to run iMosflm. It seems that if you use the CCP4 instructions on the wiki (http://ccp4wiki.org/~ccp4wiki/wiki/index.php?title=CCP4_installation ) things work okay. Bear in mind that there are now *two* include files you need to source when setting up ccp4 - both ccp4.setup (as before) and ccp4- others.setup (new). I strongly recommend downloading ipmosflm from the Mosflm website (http://www.mrc-lmb.cam.ac.uk/harry/mosflm/ver704/pre-built/index.html ), since it's built without the (unnecessary) libtermcap dependency - if you download the noX11 version you can avoid some rare bugs that only show up with iMosflm. Also, take care to heed Ronan's point about having the ccp4i project set up *before* running iMosflm from ccp4i, so that the directories are properly assigned. On 7 Jan 2009, at 08:32, Winter, G (Graeme) wrote: Dear Paula, The tcltk++ binary either from the downloads pages or ftp://ftp.ccp4.ac.uk/ccp4/current/extras should work fine - if you unpack this somewhere, export CCP4I_TCLTK appropriately and add the lib directory to the LD_LIBRARY_PATH it should solve your problem. If you would like more detail please don't hesitate to get in touch. This works fine on all the 32 and 64 linux systems I have tested. Best wishes, Graeme -Original Message- From: CCP4 bulletin board on behalf of Salgado, Paula Sent: Tue 1/6/2009 11:03 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] imosflm in ccp4 6.1.0 in linux problems Hi everyone I've been trying to run the new imosflm version from ccp4i 6.1.0 gui on ubuntu 8.0.4, but keep having problems. After struggling with it to search for the correct MOSDIR directory path, it then complained it was missing several packages from wish8.4. I did manage to find some of them, but after searching the web I still can't find: treectrl 2.1 img::png 1.3 img::gif 1.3 img::jpeg 1.3 can anyone tell me where I can download them or what other solutions to get imosflm to run properly? Thanks a lot Paula Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 0QH
Re: [ccp4bb] imosflm in ccp4 6.1.0 in linux problems
What is this ccp4-others.setup? I don't have it in my working 6.1.0 installation (built from source) Phil On 7 Jan 2009, at 11:50, Harry Powell wrote: Hi folks We have had a good look at this at Mosflm HQ now on Linux. The CCP4 TclTk++ distribution seems to work okay, and there's no need to install the ActiveTcl version to run iMosflm. It seems that if you use the CCP4 instructions on the wiki (http://ccp4wiki.org/~ccp4wiki/wiki/index.php?title=CCP4_installation ) things work okay. Bear in mind that there are now *two* include files you need to source when setting up ccp4 - both ccp4.setup (as before) and ccp4- others.setup (new). I strongly recommend downloading ipmosflm from the Mosflm website (http://www.mrc-lmb.cam.ac.uk/harry/mosflm/ver704/pre-built/index.html ), since it's built without the (unnecessary) libtermcap dependency - if you download the noX11 version you can avoid some rare bugs that only show up with iMosflm. Also, take care to heed Ronan's point about having the ccp4i project set up *before* running iMosflm from ccp4i, so that the directories are properly assigned. On 7 Jan 2009, at 08:32, Winter, G (Graeme) wrote: Dear Paula, The tcltk++ binary either from the downloads pages or ftp://ftp.ccp4.ac.uk/ccp4/current/extras should work fine - if you unpack this somewhere, export CCP4I_TCLTK appropriately and add the lib directory to the LD_LIBRARY_PATH it should solve your problem. If you would like more detail please don't hesitate to get in touch. This works fine on all the 32 and 64 linux systems I have tested. Best wishes, Graeme -Original Message- From: CCP4 bulletin board on behalf of Salgado, Paula Sent: Tue 1/6/2009 11:03 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] imosflm in ccp4 6.1.0 in linux problems Hi everyone I've been trying to run the new imosflm version from ccp4i 6.1.0 gui on ubuntu 8.0.4, but keep having problems. After struggling with it to search for the correct MOSDIR directory path, it then complained it was missing several packages from wish8.4. I did manage to find some of them, but after searching the web I still can't find: treectrl 2.1 img::png 1.3 img::gif 1.3 img::jpeg 1.3 can anyone tell me where I can download them or what other solutions to get imosflm to run properly? Thanks a lot Paula Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 0QH
Re: [ccp4bb] nVidia Quadro FX3000 on Ubuntu 8.10
This usually means that you have to install the header files for your kernel. They come in a separate package, but I don't know its name for Ubuntu. The Debian package is called linux-headers-$(uname -r) (where 'uname -r' issued at the command line returns the version of the current kernel), maybe it's the same with Ubuntu. -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A On Wed, 7 Jan 2009, Chris Ulens wrote: Hi, I'm trying to install a nVidia Quadro FX3000 card on a PC running Ubuntu 8.10 intrepid. I run into the following error when I install drivers I downloaded from the nVidia site: The installer fails to find a kernel interface from the nvidia ftp site and fails to compile the kernel. Any help would be greatly appreciated. Thanks and best wishes. -Chris Attached is the complete log file. Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm
Re: [ccp4bb] imosflm in ccp4 6.1.0 in linux problems
Hi Sorry - just noticed that ccp4-others.setup doesn't seem to be in the source distribution, just in the binary distro. My assumption is that if you build from source (or install the Mac OS X binary installation) , it's not necessary. On 7 Jan 2009, at 11:54, Phil Evans wrote: What is this ccp4-others.setup? I don't have it in my working 6.1.0 installation (built from source) Phil On 7 Jan 2009, at 11:50, Harry Powell wrote: Hi folks We have had a good look at this at Mosflm HQ now on Linux. The CCP4 TclTk++ distribution seems to work okay, and there's no need to install the ActiveTcl version to run iMosflm. It seems that if you use the CCP4 instructions on the wiki (http://ccp4wiki.org/~ccp4wiki/wiki/index.php?title=CCP4_installation ) things work okay. Bear in mind that there are now *two* include files you need to source when setting up ccp4 - both ccp4.setup (as before) and ccp4- others.setup (new). I strongly recommend downloading ipmosflm from the Mosflm website (http://www.mrc-lmb.cam.ac.uk/harry/mosflm/ver704/pre-built/index.html ), since it's built without the (unnecessary) libtermcap dependency - if you download the noX11 version you can avoid some rare bugs that only show up with iMosflm. Also, take care to heed Ronan's point about having the ccp4i project set up *before* running iMosflm from ccp4i, so that the directories are properly assigned. On 7 Jan 2009, at 08:32, Winter, G (Graeme) wrote: Dear Paula, The tcltk++ binary either from the downloads pages or ftp://ftp.ccp4.ac.uk/ccp4/current/extras should work fine - if you unpack this somewhere, export CCP4I_TCLTK appropriately and add the lib directory to the LD_LIBRARY_PATH it should solve your problem. If you would like more detail please don't hesitate to get in touch. This works fine on all the 32 and 64 linux systems I have tested. Best wishes, Graeme -Original Message- From: CCP4 bulletin board on behalf of Salgado, Paula Sent: Tue 1/6/2009 11:03 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] imosflm in ccp4 6.1.0 in linux problems Hi everyone I've been trying to run the new imosflm version from ccp4i 6.1.0 gui on ubuntu 8.0.4, but keep having problems. After struggling with it to search for the correct MOSDIR directory path, it then complained it was missing several packages from wish8.4. I did manage to find some of them, but after searching the web I still can't find: treectrl 2.1 img::png 1.3 img::gif 1.3 img::jpeg 1.3 can anyone tell me where I can download them or what other solutions to get imosflm to run properly? Thanks a lot Paula Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 0QH Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 0QH
Re: [ccp4bb] nVidia Quadro FX3000 on Ubuntu 8.10
Thanks envyng did the trick, but the emitter doesn't light up when I run pymol or coot. There's also no stereo sync on the screen. I've installed driver version 173.14.12 Thanks. -Chris On 07 Jan 2009, at 11:54, Partha Chakrabarti wrote: Chris, Try this: sudo apt-get install envyng sudo apt-get install envyng-gtk fire the envyng-gtk interface from the command line or menu and see if it finds a solution.. HTH, Partha On Wed, Jan 7, 2009 at 10:49 AM, Chris Ulens chris.ul...@med.kuleuven.be wrote: Hi, I'm trying to install a nVidia Quadro FX3000 card on a PC running Ubuntu 8.10 intrepid. I run into the following error when I install drivers I downloaded from the nVidia site: The installer fails to find a kernel interface from the nvidia ftp site and fails to compile the kernel. Any help would be greatly appreciated. Thanks and best wishes. -Chris Attached is the complete log file. Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm +++ Chris Ulens, Ph.D. Lab of Structural Neurobiology Division of Pharmacology Campus Gasthuisberg, ON1 Herestraat 49, PB 601 B-3000 Leuven Belgium +++ -- MRC National Institute for Medical Research Division of Molecular Structure The Ridgeway, NW7 1AA, UK Email: pcha...@nimr.mrc.ac.uk Phone: + 44 208 816 2515 Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm
Re: [ccp4bb] nVidia Quadro FX3000 on Ubuntu 8.10
Hi, In Ubuntu the use of Nvidia drivers is very slick, or should be. https://help.ubuntu.com/community/BinaryDriverHowto/Nvidia Go to the System menu, then: System - Administration - Hardware Drivers A window opens up which then searches for proprietary drivers, and propose that you use Nvidia accelerated driver 173, or some such version. Click the activate button, and restart X. Behind the scenes, this installs the linux-restricted-modules package, which will update your Nvidia module every time you upgrade your linux kernel, which is tiresome otherwise. There is no need for this Envy thing in Ubuntu. For stereo, you will need lines in /etc/X11/xorg.conf like: Section Device Identifier Configured Video Device Option AllowDFPStereo on Option Stereo3 Driver nvidia Screen 0 EndSection Section Extensions Option Composite off EndSection Good luck, Mark 2009/1/7 Chris Ulens chris.ul...@med.kuleuven.be Hi, I'm trying to install a nVidia Quadro FX3000 card on a PC running Ubuntu 8.10 intrepid. I run into the following error when I install drivers I downloaded from the nVidia site: The installer fails to find a kernel interface from the nvidia ftp site and fails to compile the kernel. Any help would be greatly appreciated. Thanks and best wishes. -Chris Attached is the complete log file. Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm +++ Chris Ulens, Ph.D. Lab of Structural Neurobiology Division of Pharmacology Campus Gasthuisberg, ON1 Herestraat 49, PB 601 B-3000 Leuven Belgium +++ -- Mark Brooks, IBBMC, UMR8619 - Bâtiment 430, Université de Paris-Sud, 91405 Orsay CEDEX. Tel: 0169157968 Fax: 0169853715 Skype: markabrooks
Re: [ccp4bb] imosflm in ccp4 6.1.0 in linux problems
Hi Phil, ccp4.setup sets up ccp4, ccp4-others.setup sets up everything else, like tcltk etc. This layout relates to the way the downloads pages tar up the download... Cheers, Graeme -Original Message- From: CCP4 bulletin board on behalf of Phil Evans Sent: Wed 1/7/2009 11:54 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] imosflm in ccp4 6.1.0 in linux problems What is this ccp4-others.setup? I don't have it in my working 6.1.0 installation (built from source) Phil On 7 Jan 2009, at 11:50, Harry Powell wrote: Hi folks We have had a good look at this at Mosflm HQ now on Linux. The CCP4 TclTk++ distribution seems to work okay, and there's no need to install the ActiveTcl version to run iMosflm. It seems that if you use the CCP4 instructions on the wiki (http://ccp4wiki.org/~ccp4wiki/wiki/index.php?title=CCP4_installation ) things work okay. Bear in mind that there are now *two* include files you need to source when setting up ccp4 - both ccp4.setup (as before) and ccp4- others.setup (new). I strongly recommend downloading ipmosflm from the Mosflm website (http://www.mrc-lmb.cam.ac.uk/harry/mosflm/ver704/pre-built/index.html ), since it's built without the (unnecessary) libtermcap dependency - if you download the noX11 version you can avoid some rare bugs that only show up with iMosflm. Also, take care to heed Ronan's point about having the ccp4i project set up *before* running iMosflm from ccp4i, so that the directories are properly assigned. On 7 Jan 2009, at 08:32, Winter, G (Graeme) wrote: Dear Paula, The tcltk++ binary either from the downloads pages or ftp://ftp.ccp4.ac.uk/ccp4/current/extras should work fine - if you unpack this somewhere, export CCP4I_TCLTK appropriately and add the lib directory to the LD_LIBRARY_PATH it should solve your problem. If you would like more detail please don't hesitate to get in touch. This works fine on all the 32 and 64 linux systems I have tested. Best wishes, Graeme -Original Message- From: CCP4 bulletin board on behalf of Salgado, Paula Sent: Tue 1/6/2009 11:03 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] imosflm in ccp4 6.1.0 in linux problems Hi everyone I've been trying to run the new imosflm version from ccp4i 6.1.0 gui on ubuntu 8.0.4, but keep having problems. After struggling with it to search for the correct MOSDIR directory path, it then complained it was missing several packages from wish8.4. I did manage to find some of them, but after searching the web I still can't find: treectrl 2.1 img::png 1.3 img::gif 1.3 img::jpeg 1.3 can anyone tell me where I can download them or what other solutions to get imosflm to run properly? Thanks a lot Paula Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 0QH
[ccp4bb] New ligand and link interface
Dear All Happy new year to you all!! JLigand is a java application which allows ligands to be linked on- screen and a link description to be created. JLigand 0.1 Beta is now available at http://www.ysbl.york.ac.uk/~pyoung/JLigand/JLigand.html There is a documentation how to use JLigand (under JLigand Info) It is a new software and there might be few problems. Please let us know if you have difficulty of installing or using it. Please send all your suggestion and problems to Paul Young - pyo...@ysbl.york.ac.uk or ga...@ysbl.york.ac.uk With best regards Paul and Garib
Re: [ccp4bb] imosflm in ccp4 6.1.0 in linux problems
Does sourcing the ccp4-others.setup' (which doesn't appear in the linux binary distribution which i've installed - very strange) correct the location of the BLT_LIBRARY in configure.def file stored .CCP4 in the users home directory. My configure.def file had a link to an old version of the blt libraries which was not compatible with imosflm and was causing imosflm invoked within ccp4i to crash but allowing imosflm to work when run from the command line (where it picked up the correct version of bltwish). John Harry Powell wrote: Hi Sorry - just noticed that ccp4-others.setup doesn't seem to be in the source distribution, just in the binary distro. My assumption is that if you build from source (or install the Mac OS X binary installation) , it's not necessary. On 7 Jan 2009, at 11:54, Phil Evans wrote: What is this ccp4-others.setup? I don't have it in my working 6.1.0 installation (built from source) Phil On 7 Jan 2009, at 11:50, Harry Powell wrote: Hi folks We have had a good look at this at Mosflm HQ now on Linux. The CCP4 TclTk++ distribution seems to work okay, and there's no need to install the ActiveTcl version to run iMosflm. It seems that if you use the CCP4 instructions on the wiki (http://ccp4wiki.org/~ccp4wiki/wiki/index.php?title=CCP4_installation) things work okay. Bear in mind that there are now *two* include files you need to source when setting up ccp4 - both ccp4.setup (as before) and ccp4-others.setup (new). I strongly recommend downloading ipmosflm from the Mosflm website (http://www.mrc-lmb.cam.ac.uk/harry/mosflm/ver704/pre-built/index.html), since it's built without the (unnecessary) libtermcap dependency - if you download the noX11 version you can avoid some rare bugs that only show up with iMosflm. Also, take care to heed Ronan's point about having the ccp4i project set up *before* running iMosflm from ccp4i, so that the directories are properly assigned. On 7 Jan 2009, at 08:32, Winter, G (Graeme) wrote: Dear Paula, The tcltk++ binary either from the downloads pages or ftp://ftp.ccp4.ac.uk/ccp4/current/extras should work fine - if you unpack this somewhere, export CCP4I_TCLTK appropriately and add the lib directory to the LD_LIBRARY_PATH it should solve your problem. If you would like more detail please don't hesitate to get in touch. This works fine on all the 32 and 64 linux systems I have tested. Best wishes, Graeme -Original Message- From: CCP4 bulletin board on behalf of Salgado, Paula Sent: Tue 1/6/2009 11:03 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] imosflm in ccp4 6.1.0 in linux problems Hi everyone I've been trying to run the new imosflm version from ccp4i 6.1.0 gui on ubuntu 8.0.4, but keep having problems. After struggling with it to search for the correct MOSDIR directory path, it then complained it was missing several packages from wish8.4. I did manage to find some of them, but after searching the web I still can't find: treectrl 2.1 img::png 1.3 img::gif 1.3 img::jpeg 1.3 can anyone tell me where I can download them or what other solutions to get imosflm to run properly? Thanks a lot Paula Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 0QH Harry -- John Berrisford Medical Research Council Dunn Human Nutrition Unit Wellcome Trust / MRC Building Hills Road Cambridge CB2 0XY WEB: www.mrc-dunn.cam.ac.uk Tel: +44 1223 252882
Re: [ccp4bb] nVidia Quadro FX3000 on Ubuntu 8.10
FYI, the distribution drivers work fine on our systems with the X4600 (stereo and everything). Pete Chris Ulens wrote: Hi, I'm trying to install a nVidia Quadro FX3000 card on a PC running Ubuntu 8.10 intrepid. I run into the following error when I install drivers I downloaded from the nVidia site: The installer fails to find a kernel interface from the nvidia ftp site and fails to compile the kernel. Any help would be greatly appreciated. Thanks and best wishes. -Chris Attached is the complete log file. Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm +++ Chris Ulens, Ph.D. Lab of Structural Neurobiology Division of Pharmacology Campus Gasthuisberg, ON1 Herestraat 49, PB 601 B-3000 Leuven Belgium +++
[ccp4bb] imosflm fails on suse
Hi everyone, Also got a imosflm problem - I installed the ccp4-6.1.0 before Xmas. Downloaded the binaries and installed it using the install script. (both setup-files are sourced in my .bashrc file). All programs I tried so far worked fine. But if I try to start imosflm (from the gui or the comandline) I get the following error message: MOSDIR is /home/schneider/project1/scratch Error in startup script: unknown namespace in import pattern itcl::* while executing namespace import itcl::* (file /usr/local/share/CCP4new/ccp4-6.1.0/ccp4i/imosflm/src/imosflm.tcl line 91) invoked from within source $env(IMOSFLM) (file /usr/local/share/CCP4new/ccp4-6.1.0/ccp4i/imosflm/imosflm.tcl line 111) Am using a Suse 10.3 x84_64 linux box and I have the old CCP4 version somewhere else, but not sourced (just kept it since I thought ie shar might get upset). I also installed CCP4 6.1 on a different suse linux-box (where there hadn't been CCP4 on it before) and it worked just fine? I got Tkl/tk version 8.4 installed. Any ideas? Thanks a lot for your help! Sabine -- -- Dr. Sabine Schneider Ludwig-Maximilians-University Department of Chemistry and Pharmacy Butenandtstrasse 5-13, Building F 81377 Munich Germany Phone: +49 (0)89 2180 77846 Fax: +49 (0)89 2180 77756 http://www.carellgroup.de/
Re: [ccp4bb] imosflm fails on suse
Hi Sabine, Although the GUI may still work, iMosflm needs a number of other odds and ends which should be included with tcltk++ - if you asked for these as part of the download it should work at least from the command line - are you using the same tcl/tk/blt from 6.0.2? If so the easiest thing to do is fetch the tcltk++ binary from the CCP4 ftp site and unpack it, setting the CCP4I_TCLTK and LD_LIBRARY_PATH appropriately. To have iMosflm start correctly from ccp4i you'll need the PATH to start with $CCP4I_TCLTK. If you need any further information please feel free to ask - there are also some more details here: http://ccp4wiki.org/~ccp4wiki/wiki/index.php?title=CCP4_6.1_installation Best wishes, Graeme -Original Message- From: CCP4 bulletin board on behalf of Sabine Schneider Sent: Wed 1/7/2009 4:00 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] imosflm fails on suse Hi everyone, Also got a imosflm problem - I installed the ccp4-6.1.0 before Xmas. Downloaded the binaries and installed it using the install script. (both setup-files are sourced in my .bashrc file). All programs I tried so far worked fine. But if I try to start imosflm (from the gui or the comandline) I get the following error message: MOSDIR is /home/schneider/project1/scratch Error in startup script: unknown namespace in import pattern itcl::* while executing namespace import itcl::* (file /usr/local/share/CCP4new/ccp4-6.1.0/ccp4i/imosflm/src/imosflm.tcl line 91) invoked from within source $env(IMOSFLM) (file /usr/local/share/CCP4new/ccp4-6.1.0/ccp4i/imosflm/imosflm.tcl line 111) Am using a Suse 10.3 x84_64 linux box and I have the old CCP4 version somewhere else, but not sourced (just kept it since I thought ie shar might get upset). I also installed CCP4 6.1 on a different suse linux-box (where there hadn't been CCP4 on it before) and it worked just fine? I got Tkl/tk version 8.4 installed. Any ideas? Thanks a lot for your help! Sabine -- -- Dr. Sabine Schneider Ludwig-Maximilians-University Department of Chemistry and Pharmacy Butenandtstrasse 5-13, Building F 81377 Munich Germany Phone: +49 (0)89 2180 77846 Fax: +49 (0)89 2180 77756 http://www.carellgroup.de/
[ccp4bb] POSTDOCTORAL POSITION IN X-RAY CRYSTALLOGRAPHY in La Jolla, California
POSTDOCTORAL POSITION IN X-RAY CRYSTALLOGRAPHY We are looking for a qualified and highly motivated biochemist/ protein crystallographer with 0-2 years of postdoctoral experience to work on the structural characterization of antibody-antigen complexes involved in infectious diseases and allergy. The project is a collaboration between the Division of Vaccine Discovery and Cell Biology and the candidate should show a general interest in immunology. Experience in protein expression (both bacterial and insect cell systems), purification, crystallization and structure determination is highly desired. Experience in working with antibodies is a plus. The structural biology lab is well equipped with state of the art robotics and imaging systems (Art Robbins Phoenix, Rigaku Desktop Minstrel), a xray source (Oxford Diffraction Xcalibur PX Ultra) and access to SSRL for remote data collection. The position is available immediately and funded by the NIH for at least 2-3 years. Applications, including the name an addresses of 2 references can be directly send to dzaj...@liai.org Dirk Zajonc, Ph. D. Assistant Member Division of Cellular Biology La Jolla Institute for Allergy Immunology 9420 Athena Circle La Jolla, CA 92037 e-mail: dzaj...@liai.org http://www.liai.org/pages/faculty-zajonc -- The La Jolla Institute for Allergy Immunology is located in UC San Diego's Science Research Park and is a world-class facility covering 145,000 square feet. Our space provides an open laboratory setting that encourages La Jolla Institute for Allergy Immunology's highly collaborative research environment. Specialized research rooms are suited for all aspects of molecular and cellular biology and feature larger lab areas that can support critical technologies and infrastructure. These technologies include highly sophisticated instrumentation for analysis at the atomic, genetic, protein and cellular levels - all of which are critical to advancing understanding of immune system disease.
[ccp4bb] Characterization of Protein Conformational Changes
Dear Crystallographers, I am sure that most here have dealt with the issue, when making superpositions of conformationally-different structures, of which regions to align as references and which to call mobile. Conformational changes can range from very local (e.g., unwinding of a helix) to very diffuse (e.g., subtle but significant rigid body shifts between two domains.) In the first case, it would probably make sense to do a global least-squares fitting, but in the latter, one would do better to fix one of the domains, and show the shift in the other domain. These cases, however, presuppose that one knows which type of case one is dealing with. This could be done by guesswork and trial-and-error, but does anybody know of an approach (e.g., a program) to define the most reasonable way to think about a given conformational change? Variable-size sliding-window least-squares superpositions with comparisons of local versus global rmsd's come to mind, but I do not know whether this has been implemented anywhere, and would not know readily how to set the parameters thereof either. Best Regards, Jacob Keller *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.9185 email: j-kell...@northwestern.edu ***
[ccp4bb] position available
Dear CCP4 Users, We have an opening for one federally funded post-doctoral or staff scientist position for a structural biologist to study bacterial voltage-gated sodium channels. The ideal candidate will be self-motivated, creative, organized, and experienced in crystallography. The lab is a structural biology group within the department of Pharmacology at the Vanderbilt University medical center in Nashville, TN. Nashville combines the features of a college town with those of a fairly large city. Urban amenities include restaurants, museums, theatres, music, yet the cost of living is moderate and the city is very livable. Please email questions, CVs, and references to Ben Spiller
Re: [ccp4bb] Characterization of Protein Conformational Changes
On Wed, Jan 7, 2009 at 1:54 PM, Jacob Keller j-kell...@md.northwestern.edu wrote: I am sure that most here have dealt with the issue, when making superpositions of conformationally-different structures, of which regions to align as references and which to call mobile. Conformational changes can range from very local (e.g., unwinding of a helix) to very diffuse (e.g., subtle but significant rigid body shifts between two domains.) In the first case, it would probably make sense to do a global least-squares fitting, but in the latter, one would do better to fix one of the domains, and show the shift in the other domain. These cases, however, presuppose that one knows which type of case one is dealing with. This could be done by guesswork and trial-and-error, but does anybody know of an approach (e.g., a program) to define the most reasonable way to think about a given conformational change? Variable-size sliding-window least-squares superpositions with comparisons of local versus global rmsd's come to mind, but I do not know whether this has been implemented anywhere, and would not know readily how to set the parameters thereof either. DynDom may do this, but I'm not familiar with the program. (It's in CCP4 now, I think) If you're just trying to get a reasonable superposition and don't care very much about the resulting statistics, you can usually use a much simpler method called a sieve-fit, described in these references: http://www.ncbi.nlm.nih.gov/pubmed/2067013 http://www.ncbi.nlm.nih.gov/pubmed/10734184 In practice, the procedure described in the second paper generally worked very well for the intended purpose of visualizing any arbitrary conformational change in the PDB clearly. The code that actually performs this isn't distributed as far as I know; however, it should be relatively trivial to re-implement using CCTBX or something equivalent. PyMOL's align command also does some kind of iterative optimization by throwing away outliers, but it's much less aggressive and appears to try for the best global fit, excluding loops etc. -Nat
[ccp4bb] ARP/wARP Solvent
Dear all, I tried to use ARP/wARP 7.0.1 GUI for solvent building, however it couldn't recognize my ligand library file (.cif), which works fine in refmac refinement. Apparently, the error message is: === Error: New ligand has been encountered. Stopping now Refmac_5.2.0019: New ligand has been encountered. Stopping now Your coordinate file has a ligand which has either minimum or no description in the library A new ligand description has been added to /tmp/mchu/refmac5_temp1.03957_lib.cif Even if I use the one refmac created after the error, it still can't recognize this new cif file... I also tried to run it from command line, another problem was raised. It couldn't recognize the FP label in my mtz when I used the keyword [fp F_New] [sigfp SIGF_New] [freer FreeR_flag] Error message: Label FP does not match the content of the datafile /home/mchu/ARP_wARP/solvent/L1.mtz Possible mtz labels are: F_New FC FWT DELFWT Does anyone have any idea why and how I can fix it? Thank you so much in advance! Kind regards, Matt -- -- Matthew LH Chu PhD Student School of Pharmacy and Pharmaceutical Sciences University of Manchester --
Re: [ccp4bb] Characterization of Protein Conformational Changes
This sounds like a job for a DDM (difference-distance matrix). This method can detect very subtle conformational changes between a pair of protein structures without performing a structural alignment. Once the areas of change have been identified a traditional alignment can be performed using the conformationally inert regions as a target. The program ESCET can do this and full details can be found here: http://schneider.group.ifom-ieo-campus.it/escet/index.html Alternatively DDMP could be used: http://www.csb.yale.edu/userguides/datamanip/ddmp/ddmp_descrip.html Hope that helps, Tom On Wed, Jan 7, 2009 at 2:18 PM, Nathaniel Echols nathaniel.ech...@gmail.com wrote: On Wed, Jan 7, 2009 at 1:54 PM, Jacob Keller j-kell...@md.northwestern.edu wrote: I am sure that most here have dealt with the issue, when making superpositions of conformationally-different structures, of which regions to align as references and which to call mobile. Conformational changes can range from very local (e.g., unwinding of a helix) to very diffuse (e.g., subtle but significant rigid body shifts between two domains.) In the first case, it would probably make sense to do a global least-squares fitting, but in the latter, one would do better to fix one of the domains, and show the shift in the other domain. These cases, however, presuppose that one knows which type of case one is dealing with. This could be done by guesswork and trial-and-error, but does anybody know of an approach (e.g., a program) to define the most reasonable way to think about a given conformational change? Variable-size sliding-window least-squares superpositions with comparisons of local versus global rmsd's come to mind, but I do not know whether this has been implemented anywhere, and would not know readily how to set the parameters thereof either. DynDom may do this, but I'm not familiar with the program. (It's in CCP4 now, I think) If you're just trying to get a reasonable superposition and don't care very much about the resulting statistics, you can usually use a much simpler method called a sieve-fit, described in these references: http://www.ncbi.nlm.nih.gov/pubmed/2067013 http://www.ncbi.nlm.nih.gov/pubmed/10734184 In practice, the procedure described in the second paper generally worked very well for the intended purpose of visualizing any arbitrary conformational change in the PDB clearly. The code that actually performs this isn't distributed as far as I know; however, it should be relatively trivial to re-implement using CCTBX or something equivalent. PyMOL's align command also does some kind of iterative optimization by throwing away outliers, but it's much less aggressive and appears to try for the best global fit, excluding loops etc. -Nat
Re: [ccp4bb] ultrafiltration/buffer exchange device for insect cell cultures
As an alternative to the Pellicon system, Millipore also makes PrepScale TFF cartridges (http://www.millipore.com/techpublications/tech1/ef063). Unlike the Pellicon, they are sealed units, but like the Pellicon membranes, they are true tangential-flow devices and can be reused many times (20preps or ~1year in our hands). The time required to concentrate insect-cell culture medium from 10-20L to 1L, is also on the order of hours, depending on the MWCO and the size of the cartridge. With 10L, the 2.5ft^2 3MWCO cartridge should take 1-2 hours. For 10L at 3MWCO, use the 6ft^2 cartridge. When we compared prices a number of years ago, the upfront cost was lower with the TFF. If you're going to be a long-term heavy user, it may be worth it to invest in the Pellicon. Prices may have changed... Another point: if you use a peristaltic pump like the Masterflex, keep a close eye on the tubing in the head. The back pressure can be significant at the required flow rates and can cause tubing failure. We replace the section within the pump head after each use. Dean Michael Hothorn wrote: Dear all, sorry for the non-CCP4 question. I am expressing a protein in insect cells that is targeted for secretion into the medium. After expression, I want to concentrate the medium containing my protein of interest (from 10 l to 0.3 L) and at the same time change the buffer to something that is compatible with my first ion exchange chromatography step. I would be interested to know what kind of ultrafiltration devices can be used for this purpose, and whether some of you could suggest a quick, reliable and efficient system that we could purchase for our lab. Thanks! Michael -- Dean R. Madden, Ph.D. Department of Biochemistry Dartmouth Medical School 7200 Vail Building, Rm 408A Hanover, NH 03755-3844 USA tel: +1 (603) 650-1164 fax: +1 (603) 650-1128 e-mail: dean.mad...@dartmouth.edu
[ccp4bb] error in startup of ccp4i 6.1
Dear all,
I have installed precompiled ccp4 61 (Redhat from download manager) on Centos5
box, X86_64.
Running ccp4i gives:
[guen...@hypatia ~]$ ccp4i
Top level CCP4 directory is /usr/local/software/CCP4/61/ccp4-6.1.0
Using CCP4 programs from /usr/local/software/CCP4/61/ccp4-6.1.0/bin
Error in startup script: wrong # args: should be dbccp4i_open_project project
args
while executing
dbccp4i_open_project
(eval body line 1)
invoked from within
eval dbccp4i_open_project $project $args
(procedure DbLoadFile line 12)
invoked from within
DbLoadFile $project
(procedure DbOpenDatabase line 13)
invoked from within
DbOpenDatabase $project
(procedure DbOpen line 30)
invoked from within
DbOpen -init
(procedure DbInitialise line 19)
invoked from within
DbInitialise
(procedure taskbrowser line 38)
invoked from within
$system(RUN_MODE)
(default arm line 9)
invoked from within
switch $system(RUN_MODE) \
script {
# Run a script ($CCP4I/scripts/project.script) with parameters from def file
source [file join $env(CCP4I_...
(file /usr/local/software/CCP4/61/ccp4-6.1.0/ccp4i/bin/ccp4i.tcl line 163)
invoked from within
source [file join $env(CCP4I_TOP) bin ccp4i.tcl]
(file /usr/local/software/CCP4/61/ccp4-6.1.0/ccp4i/bin/ccp4i line 5)
-
If I run ccp4i as root everyting is fine.
Moreover on another Centos5 box with similar architecture there are no problems
usin the same installation files.
Albert Guskov has reported the same error on Mac OS X.
He edited the configure.def file changing the value fro
USE_DBCCP4I_ON_STARTUP from 1 to 0.
Did not work in my case.
Any ideas?
Thanks a lot in advance,
Guenter
*
Fachbereich Biologie
Sektion Naturwissenschaften
Universitaet Konstanz
http://www.biologie.uni-konstanz.de/fritz
Universitaetsstrasse 10
Postfach M665
D-78457 Konstanz
e-mail: guenter.fr...@uni-konstanz.de
Tel. Office: +49-(0)7531 88 3205
Tel. Lab : +49-(0)7531 88 3687
Fax: +49-(0)7531 88 2966
Re: [ccp4bb] Characterization of Protein Conformational Changes
You can abuse/mis-use the TLSMD server from Ethan to analyse domain movements and draw your conclusions accordingly, see here http://skuld.bmsc.washington.edu/~tlsmd/ Jürgen On 7 Jan 2009, at 16:54, Jacob Keller wrote: Dear Crystallographers, I am sure that most here have dealt with the issue, when making superpositions of conformationally-different structures, of which regions to align as references and which to call mobile. Conformational changes can range from very local (e.g., unwinding of a helix) to very diffuse (e.g., subtle but significant rigid body shifts between two domains.) In the first case, it would probably make sense to do a global least-squares fitting, but in the latter, one would do better to fix one of the domains, and show the shift in the other domain. These cases, however, presuppose that one knows which type of case one is dealing with. This could be done by guesswork and trial-and-error, but does anybody know of an approach (e.g., a program) to define the most reasonable way to think about a given conformational change? Variable-size sliding-window least- squares superpositions with comparisons of local versus global rmsd's come to mind, but I do not know whether this has been implemented anywhere, and would not know readily how to set the parameters thereof either. Best Regards, Jacob Keller *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.9185 email: j-kell...@northwestern.edu *** - Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Biochemistry and Molecular Biology, W8708 615 North Wolfe Street Baltimore, MD 21205 Phone: +1-410-614-4742
[ccp4bb] Affordable 3D LCD Arriving Soon
I came across an article about Samsung's $400 3D LCD monitor coming out in April so I thought I'd pass it on for those who may be interested. http://www.engadget.com/2009/01/07/samsung-officially-introduces-2233rz-the-22-inch-3d-panel-for-g/ I'm pretty sure their 3D implementation is different than the current shutter-glasses active 3D. Hopefully it will be supported by coot and other 3D programs.
[ccp4bb] 2D
Sorry for the non ccp4 related post. Can anyone point me in the direction of a good method, reference or link for improving 2D xtals? They are hexagonal 2D plates, and some have a tendency to stack. Cheers. =v=
Re: [ccp4bb] ARP/wARP Solvent
Dear Matt, have you tried the 'input a user-defined library file' check box under 'refmac parameters' in the gui? Else try the keyword 'extralibrary' when using the 'auto_solvent.sh' script from the command line. Both options define a string 'LIB_IN mylib.cif' that is passed on to refmac. When using the auto_solvent.sh script, please omit the '[' and ']' characters. Type e.g.: auto_solvent.sh datafile L1.mtz protein L1.pdb fp F_New sigfp SIGF_New extralibrary refmac5_templ.03957_lib.cif I hope this will help. Regards, Gerrit. Matthew Chu wrote: Dear all, I tried to use ARP/wARP 7.0.1 GUI for solvent building, however it couldn't recognize my ligand library file (.cif), which works fine in refmac refinement. Apparently, the error message is: === Error: New ligand has been encountered. Stopping now Refmac_5.2.0019: New ligand has been encountered. Stopping now Your coordinate file has a ligand which has either minimum or no description in the library A new ligand description has been added to /tmp/mchu/refmac5_temp1.03957_lib.cif Even if I use the one refmac created after the error, it still can't recognize this new cif file... I also tried to run it from command line, another problem was raised. It couldn't recognize the FP label in my mtz when I used the keyword [fp F_New] [sigfp SIGF_New] [freer FreeR_flag] Error message: Label FP does not match the content of the datafile /home/mchu/ARP_wARP/solvent/L1.mtz Possible mtz labels are: F_New FC FWT DELFWT Does anyone have any idea why and how I can fix it? Thank you so much in advance! Kind regards, Matt
Re: [ccp4bb] 2D
It mostly means little intermolecular contacts in one direction because of charge repulsion, shape incomplementarity etc etc. One thing to try is screen for additives that can help to make more contacts between the layers or, screen for new crystal forms using microseed matrix screening! - J. - Vin Purp wrote: Sorry for the non ccp4 related post. Can anyone point me in the direction of a good method, reference or link for improving 2D xtals? They are hexagonal 2D plates, and some have a tendency to stack. Cheers. =v= -- Dr. Jeroen R. Mesters Gruppenleiter Strukturelle Neurobiologie und Kristallogenese Institut für Biochemie, Universität zu Lübeck Zentrum für Medizinische Struktur- und Zellbiologie Ratzeburger Allee 160, D-23538 Lübeck Tel: +49-451-5004065, Fax: +49-451-5004068 Http://www.biochem.uni-luebeck.de Http://www.iobcr.org Http://www.selfish-brain.org Http://www.opticryst.org -- If you can look into the seeds of time and say which grain will grow and which will not - speak then to me (Macbeth) --
