[ccp4bb] Solved: Re: [ccp4bb] refmac5: FIND_CONTACT_WITH_BRICKING failed
Hi, I compiled refmac5/ ccp4 libraries with the intel fortran compiler and the aforementioned problems did not occur anymore. So it looks like the gcc 4.2.1 that comes with SuSE 10.3 is broken (again...), which is also what somebody from our group pointed me out to. Tim -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A On Mon, 5 Nov 2007, Tim Gruene wrote: --[PinePGP]--[begin]-- Good morning, I compiled the latest Version of refmac5 (5.3.0040) and installed the latest library. When I want to read in a glycerol with coot and also when running buccaneer, refmac bails out with the above error message Too many symmetry related atoms check symmetry and cell FIND_CONTACT_WITH_BRICKING failed ccp4 is version 6.0.2, gcc/gfortran 4.2.1 from SuSE 10.3 Has anyone seen this error message before and knows a remedy? The only hints from google told me to install the latest version of remfac5... Thanks a lot, Tim -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A --[PinePGP]--- gpg: Signature made Mon Nov 5 10:19:18 2007 CET using DSA key ID A46BEE1A gpg: Good signature from "Tim Gruene (Universitaet Goettingen) <[EMAIL PROTECTED]>" gpg: aka "Tim Gruene <[EMAIL PROTECTED]>" gpg: aka "Tim Gruene (Private email address) <[EMAIL PROTECTED]>" gpg: aka "Tim Grune <[EMAIL PROTECTED]>" gpg: aka "Tim Gruene (address in rare use) <[EMAIL PROTECTED]>" gpg: aka "Tim Grune (Australian Synchrotron, 2007 -) <[EMAIL PROTECTED]>" --[PinePGP][end]--
Re: [ccp4bb] converting structure factor files to mtz files
Dear Bjoern, this is a problem with several newer mmcif files in the PDB. There are many items in the cif-file which are not in the CCP4 library. This is a bit annoying when you want to convert large numbers of mmcifs to mtzs for whatever reason, but I guess the only solution is to wait until the CCP4 guys have updated their dictionaries. Cheers, Manfred. * * *Dr. Manfred S. Weiss * * * * Team Leader * * * * EMBL Hamburg OutstationFon: +49-40-89902-170 * * c/o DESY, Notkestr. 85 Fax: +49-40-89902-149 * * D-22603 Hamburg Email: [EMAIL PROTECTED] * * GERMANY Web: www.embl-hamburg.de/~msweiss/ * * * On Tue, 6 Nov 2007, [ISO-8859-1] Bj?rn Kauppi wrote: > Hi, > I also have problems running cif2mtz using ccp4i (5.99) interface with > several mmCIF files downloaded from the pdb (e.g., 2pip, ) on my linux box. > Problems with the _refln.pdbx_F_plus etc cards it seems: > Files without anomalous data work. > > --snip from log file: > Line 58: data name "_refln.pdbx_F_plus" not present in dictionary > > Line 59: data name "_refln.pdbx_F_plus_sigma" not present in dictionary > > Line 60: data name "_refln.pdbx_F_minus" not present in dictionary > > Line 61: data name "_refln.pdbx_F_minus_sigma" not present in dictionary > > Line 62: data name "_refln.pdbx_anom_difference" not present in > dictionary > > Line 63: data name "_refln.pdbx_anom_difference_sigma" not present in > dictionary > > Line 64: data name "_refln.pdbx_I_plus" not present in dictionary > > Line 65: data name "_refln.pdbx_I_plus_sigma" not present in dictionary > > Line 66: data name "_refln.pdbx_I_minus" not present in dictionary > > Line 67: data name "_refln.pdbx_I_minus_sigma" not present in dictionary > > --- CIF opened read-only for input --- > The file contains the following data blocks: > data_r2piusf (at line 1) > > > CCIF signal CCIF_CATNOTCOMPLETE (severity: Warning) > (Raised in new_context) > Could not open context on category 'refln'; item '_refln.pdbx_F_plus' not > defined in dictionary! > > > cif2mtz: Error in ccp4ccif_setup_context: Unexpected context type for > category REFLN > Times: User: 0.6s System:0.0s Elapsed: 0:00 > > > > > > Bj?rn Kauppi > > > -Original Message- > > From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of > > Martyn Winn > > Sent: den 1 november 2007 10:14 > > To: CCP4BB@JISCMAIL.AC.UK > > Subject: Re: [ccp4bb] converting structure factor files to mtz files > > > > The first 3 cif columns are not the problem. cif2mtz will happily skip > > these along with any other items it doesn't explicitly deal with. > > > > The problem is simply the extra columns F(+) etc, yes? > > > > This bug has been seen on Windows. The same job should work fine on > > Linux or Macs. Or you should be able to simply delete these spurious > > columns with cad, sftools, etc > > I'm sure this will be easier than playing with Fortran formatting > > > > The bug is somewhere in the depths of the cif library, and we don't have > > a fix yet. > > > > HTH > > Martyn > > > > On Wed, 2007-10-31 at 19:49 -0400, Zheng Zhou wrote: > > > Hi, > > > > > > Could anyone give a quick hint for the Fortran format for the > > > following structure factor mmCIF file? or Is there any easy program or > > > better way to convert it? I think I need to skip first 3 columns. > > > > > > Thanks in advance. > > > > > > Joe > > > > > > loop_ > > > _refln.crystal_id > > > _refln.wavelength_id > > > _refln.scale_group_code > > > _refln.index_h > > > _refln.index_k > > > _refln.index_l > > > _refln.F_meas_au > > > _refln.F_meas_sigma_au > > > _refln.status > > > 1 1 1200 617.50 5.41 o > > > 1 1 1400 773.50 6.92 o > > > 1 1 1600 62.30 3.19 o > > > > > > I am trying to view the electron density of a published structure. I > > > downloaded the file from pdb and used cif2mtz in ccp4. I think the > > > following output mtz is wrong. > > > > > > * Column Labels : > > > > > > H K L FREE FP SIGFP F(+) SIGF(+) F(-) SIGF(-) DP SIGDP I(+) SIGI(+) > > > I(-) SIGI(-) > > > > > > * Column Types : > > > > > > H H H I F Q G L G L D Q K M K M > > > > > > * Associated datasets : > > > > > > 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 > > > > > > * Cell Dimensions : (obsolete - refer to dataset cell dimensions > > > above) > > > > > >
Re: [ccp4bb] converting structure factor files to mtz files
Hi, I also have problems running cif2mtz using ccp4i (5.99) interface with several mmCIF files downloaded from the pdb (e.g., 2pip, ) on my linux box. Problems with the _refln.pdbx_F_plus etc cards it seems: Files without anomalous data work. --snip from log file: Line 58:data name "_refln.pdbx_F_plus" not present in dictionary Line 59:data name "_refln.pdbx_F_plus_sigma" not present in dictionary Line 60:data name "_refln.pdbx_F_minus" not present in dictionary Line 61:data name "_refln.pdbx_F_minus_sigma" not present in dictionary Line 62:data name "_refln.pdbx_anom_difference" not present in dictionary Line 63:data name "_refln.pdbx_anom_difference_sigma" not present in dictionary Line 64:data name "_refln.pdbx_I_plus" not present in dictionary Line 65:data name "_refln.pdbx_I_plus_sigma" not present in dictionary Line 66:data name "_refln.pdbx_I_minus" not present in dictionary Line 67:data name "_refln.pdbx_I_minus_sigma" not present in dictionary --- CIF opened read-only for input --- The file contains the following data blocks: data_r2piusf (at line 1) CCIF signal CCIF_CATNOTCOMPLETE (severity: Warning) (Raised in new_context) Could not open context on category 'refln'; item '_refln.pdbx_F_plus' not defined in dictionary! cif2mtz: Error in ccp4ccif_setup_context: Unexpected context type for category REFLN Times: User: 0.6s System:0.0s Elapsed: 0:00 Björn Kauppi > -Original Message- > From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of > Martyn Winn > Sent: den 1 november 2007 10:14 > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] converting structure factor files to mtz files > > The first 3 cif columns are not the problem. cif2mtz will happily skip > these along with any other items it doesn't explicitly deal with. > > The problem is simply the extra columns F(+) etc, yes? > > This bug has been seen on Windows. The same job should work fine on > Linux or Macs. Or you should be able to simply delete these spurious > columns with cad, sftools, etc > I'm sure this will be easier than playing with Fortran formatting > > The bug is somewhere in the depths of the cif library, and we don't have > a fix yet. > > HTH > Martyn > > On Wed, 2007-10-31 at 19:49 -0400, Zheng Zhou wrote: > > Hi, > > > > Could anyone give a quick hint for the Fortran format for the > > following structure factor mmCIF file? or Is there any easy program or > > better way to convert it? I think I need to skip first 3 columns. > > > > Thanks in advance. > > > > Joe > > > > loop_ > > _refln.crystal_id > > _refln.wavelength_id > > _refln.scale_group_code > > _refln.index_h > > _refln.index_k > > _refln.index_l > > _refln.F_meas_au > > _refln.F_meas_sigma_au > > _refln.status > > 1 1 1200 617.50 5.41 o > > 1 1 1400 773.50 6.92 o > > 1 1 1600 62.30 3.19 o > > > > I am trying to view the electron density of a published structure. I > > downloaded the file from pdb and used cif2mtz in ccp4. I think the > > following output mtz is wrong. > > > > * Column Labels : > > > > H K L FREE FP SIGFP F(+) SIGF(+) F(-) SIGF(-) DP SIGDP I(+) SIGI(+) > > I(-) SIGI(-) > > > > * Column Types : > > > > H H H I F Q G L G L D Q K M K M > > > > * Associated datasets : > > > > 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 > > > > * Cell Dimensions : (obsolete - refer to dataset cell dimensions > > above) > > > >88.0800 86.3600 80.7700 90. 95.7100 90. > > > > * Resolution Range : > > > > 0.000450.29217 ( 47.298 - 1.850 A ) > > > > * Sort Order : > > > > 1 2 3 0 0 > > > > * Space group = 'C 1 2 1' (number 5) > > > > > > > > OVERALL FILE STATISTICS for resolution range 0.000 - 0.292 > > === > > > > > > Col SortMinMaxNum % Mean Mean Resolution > > Type Column > > num order Missing complete abs. LowHigh > > label > > > >1 ASC-47 47 0 100.00 -1.4 17.9 47.28 > > 1.85 H H > >2 NONE 0 46 0 100.00 17.2 17.2 47.28 1.85 > > H K > >3 NONE 0 43 0 100.00 16.4 16.4 47.28 1.85 > > H L > >4 NONE0.0 19.0 0 100.00 9.52 9.52 47.28 > > 1.85 I FREE > >5 NONE0.0 1566.050 99.90 162.85 162.85 47.28 1.85 > > F FP > >6 NONE0.082.150 99.90 9.49 9.49 47.28 1.85 > > Q SIGFP > >7 BOTH ? ? 513730.00 ?? -999.00 0.00 > > G F(+) > >8 BOTH ? ? 513730.00 ?? -999.00 0.00 > > L SIGF(+) > >9 BOTH ? ? 513730.00 ?? - 999.00 > > 0.00 G F(-) > > 10 BOTH ? ? 513730.00 ?? -999.00 0.00 > > L SIGF(-) > > 11
Re: [ccp4bb] Apple OS 10.5 and X11
Hi, I just installed Leopard, using a clean install (no upgrade), and here are a few reflections on it so far. Installation goes very smoothly, clean install on ~40 minutes on my MacBook 2 Ghz (~30 minutes for an upgrade on an iMac 2.4 GHz). Fink installation of 0.27.8 via bootstrapping goes without any problems. Installed Coot version 0.4-pre-1 via fink, and it seems to run ok. Have some issues with X11 not wanting to let me have the window on my second screen, but that is something with X11 rather than Coot. Probably is the same as the broken support for fullscreen.. http://lists.apple.com/archives/X11-users/2007/Oct/msg00065.html . Installed CCP4 6.0.2 from binary installation using the dmg from the ccp4 homepage. Installation proceeded without problem. CCP4 also seems to run fine, although I must confess that I haven't had much time to run through much of the programs. I'll spend some time thoroughly testing the build later this week. Cheers, Ronnie On Nov 5, 2007, at 7:03 PM, R.M. Garavito wrote: After Bill Scott's and Juergen Bosch's comments about upgrading to Leopard 10.5, it has been quiet. As I am upgrading some "non- essential" machines up to 10.5, I just wanted to check if there is more info out there. Despite horror stories on the discussion site, upgrading 1 G4 PB, an Intel MacBook Pro, an Intel MacBook, and an Intel Mac Mini went without a hitch, either as an upgrade or "archive and install". I was motivated by the Time Machine option for automatic backups. But I will be rebuilding one of the machines with CCP4 and other programs for testing, as well as some NFS disk cross-mounting. However, as Bill alluded to, X11 in Leopard has some problems (http://lists.apple.com/archives/X11-users/2007/Oct/msg00065.html ) and X11 users are reinstalling the Tiger version (http://aaroniba.net/articles/x11-leopard.html ). I found that just backing up the /etc/X11/ directory, the /usr/ X11R6 directory, and the Tiger /Applications/Utilities/X11.app before the installation avoids the problem. Just edit /etc/X11/ xinit/xinitrc to replace "exec quartz-wm" with "exec /usr/X11R6/bin/ quartz-wm". That worked fine for me, but it does have the annoying "double X11 icon in Dock" problem mentioned by Ben Byer in his method of installing both Tiger X11 and Leopard X11 (http://lists.apple.com/archives/x11-users/2007/Nov/msg5.html ). One last hint that was really useful is that the installation DVD can be transferred to a small (20-80 Gb) FireWire disk: "This is what I did: Used an empty (blank) external FW drive, created 2 partitions (one 10GB the other with the remainder), then using Disk Utility Restore selected the Leopard install DVD as the source and my 10GB partition as the destination. Be advised this took a while!! When finished, I selected the 10GB partition as Startup Disk and installed Leopard from the external FW drive. I have installed Leopard on two machines using my external FW install disk. I formated the external FW drive with Apple Partition Map NOT GUID." On my G4 PowerBook, it only took 20 min to load it onto an ancient 20Gb FW disk, but doing this prevents a major complaint about upgrading to Leopard: variable readability of the dual-layered install DVD between machines. People have also complained about the poor quality of some of the DVDs (scratches, smudges, etc.). Finally, you don't have to go through the DVD verification every time you install. Thanks for any new information, Michael R. Michael Garavito, Ph.D. Professor of Biochemistry & Molecular Biology 513 Biochemistry Bldg. Michigan State University East Lansing, MI 48824-1319 Office: (517) 355-9724 Lab: (517) 353-9125 FAX: (517) 353-9334Email: [EMAIL PROTECTED] Ronnie Berntsson -- Ph.D. Student Department of Biochemistry Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials University of Groningen Nijenborgh 4, 9747 AG Groningen, The Netherlands telephone: +31 50 363 4195 telefax: +31 50 363 4165 e-mail: [EMAIL PROTECTED] homepage: http://www.rug.nl/gbb/research/researchgroups/enzymology/index
Re: [ccp4bb] converting structure factor files to mtz files
You need to update to CCP4 6.0.2, these items are now recognised. We try to keep up with the latest cif definitions, but there is a lag. The documentation for cif2mtz lists the column labels recognised. These are only labels, so if the worst comes to the worst, you can edit these in the cif file to something that cif2mtz recognises (as long as it is the same type of column!!) HTH Martyn -Original Message- From: Björn Kauppi [mailto:[EMAIL PROTECTED] Sent: Tue 11/6/2007 10:16 AM To: Winn, MD (Martyn); CCP4BB@JISCMAIL.AC.UK Subject: RE: [ccp4bb] converting structure factor files to mtz files Hi, I also have problems running cif2mtz using ccp4i (5.99) interface with several mmCIF files downloaded from the pdb (e.g., 2pip, ) on my linux box. Problems with the _refln.pdbx_F_plus etc cards it seems: Files without anomalous data work. --snip from log file: Line 58:data name "_refln.pdbx_F_plus" not present in dictionary Line 59:data name "_refln.pdbx_F_plus_sigma" not present in dictionary Line 60:data name "_refln.pdbx_F_minus" not present in dictionary Line 61:data name "_refln.pdbx_F_minus_sigma" not present in dictionary Line 62:data name "_refln.pdbx_anom_difference" not present in dictionary Line 63:data name "_refln.pdbx_anom_difference_sigma" not present in dictionary Line 64:data name "_refln.pdbx_I_plus" not present in dictionary Line 65:data name "_refln.pdbx_I_plus_sigma" not present in dictionary Line 66:data name "_refln.pdbx_I_minus" not present in dictionary Line 67:data name "_refln.pdbx_I_minus_sigma" not present in dictionary --- CIF opened read-only for input --- The file contains the following data blocks: data_r2piusf (at line 1) CCIF signal CCIF_CATNOTCOMPLETE (severity: Warning) (Raised in new_context) Could not open context on category 'refln'; item '_refln.pdbx_F_plus' not defined in dictionary! cif2mtz: Error in ccp4ccif_setup_context: Unexpected context type for category REFLN Times: User: 0.6s System:0.0s Elapsed: 0:00 Björn Kauppi > -Original Message- > From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of > Martyn Winn > Sent: den 1 november 2007 10:14 > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] converting structure factor files to mtz files > > The first 3 cif columns are not the problem. cif2mtz will happily skip > these along with any other items it doesn't explicitly deal with. > > The problem is simply the extra columns F(+) etc, yes? > > This bug has been seen on Windows. The same job should work fine on > Linux or Macs. Or you should be able to simply delete these spurious > columns with cad, sftools, etc > I'm sure this will be easier than playing with Fortran formatting > > The bug is somewhere in the depths of the cif library, and we don't have > a fix yet. > > HTH > Martyn > > On Wed, 2007-10-31 at 19:49 -0400, Zheng Zhou wrote: > > Hi, > > > > Could anyone give a quick hint for the Fortran format for the > > following structure factor mmCIF file? or Is there any easy program or > > better way to convert it? I think I need to skip first 3 columns. > > > > Thanks in advance. > > > > Joe > > > > loop_ > > _refln.crystal_id > > _refln.wavelength_id > > _refln.scale_group_code > > _refln.index_h > > _refln.index_k > > _refln.index_l > > _refln.F_meas_au > > _refln.F_meas_sigma_au > > _refln.status > > 1 1 1200 617.50 5.41 o > > 1 1 1400 773.50 6.92 o > > 1 1 1600 62.30 3.19 o > > > > I am trying to view the electron density of a published structure. I > > downloaded the file from pdb and used cif2mtz in ccp4. I think the > > following output mtz is wrong. > > > > * Column Labels : > > > > H K L FREE FP SIGFP F(+) SIGF(+) F(-) SIGF(-) DP SIGDP I(+) SIGI(+) > > I(-) SIGI(-) > > > > * Column Types : > > > > H H H I F Q G L G L D Q K M K M > > > > * Associated datasets : > > > > 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 > > > > * Cell Dimensions : (obsolete - refer to dataset cell dimensions > > above) > > > >88.0800 86.3600 80.7700 90. 95.7100 90. > > > > * Resolution Range : > > > > 0.000450.29217 ( 47.298 - 1.850 A ) > > > > * Sort Order : > > > > 1 2 3 0 0 > > > > * Space group = 'C 1 2 1' (number 5) > > > > > > > > OVERALL FILE STATISTICS for resolution range 0.000 - 0.292 > > === > > > > > > Col SortMinMaxNum % Mean Mean Resolution > > Type Column > > num order Missing complete abs. LowHigh > > label > > > >1 ASC-47 47 0 100.00 -1.4 17.9 47.28 > > 1.85 H H > >2 NONE 0 46 0 100.00 17.2 17.2 47.28 1.85 > > H K > >3 NONE 0 43 0 100.00 16.4 16.4 47.28 1.85 > > H L > >4 NO
Re: [ccp4bb] libccp4map.so
Hi Ian What system are you running on? I might be able to provide you with something that works if it's Linux. And, are you also missing $CBIN/ccp4mapwish? There is an issue with mapslicer when compiling, if the tclconfig.sh and tkconfig.sh files are missing (which seems to be the case when the system provides Tcl/Tk rather than you having to build it yourself) then the CCP4 configure isn't able to acquire the options needed to build the library. Best wishes Peter Iain Kerr wrote: Sorry, to clarify the library is missing from my system (wasn't compiled during CCP4 installation)..I need a copy to add to $CLIB. Thanks, Iain Iain Kerr wrote: Does anyone know where I can find a copy of "libccp4map.so" for Mapslicer please ? Thanks, Iain -- ___ Peter J Briggs, [EMAIL PROTECTED] Tel: +44 1925 603826 CCP4, [EMAIL PROTECTED] Fax: +44 1925 603825 http://www.ccp4.ac.uk/ Daresbury Laboratory, Daresbury, Warrington WA4 4AD
[ccp4bb] [Protein-crystallography] November 2007 issue of the IUCr Computing Commission Newsletter on-line (fwd)
Forwarded from bionet.xtallography --dvd -- Forwarded message -- Date: Mon, 05 Nov 2007 16:22:11 -0800 From: "[EMAIL PROTECTED]" <[EMAIL PROTECTED]> To: [EMAIL PROTECTED] Newsgroups: bionet.xtallography Subject: [Protein-crystallography] November 2007 issue of the IUCr Computing Commission Newsletter on-line The November 2007 Seventh issue of the IUCr Computing Commission Newsletter is available as an Adobe Acrobat PDF file via: http://www.iucr.org/iucr-top/comm/ccom/newsletters/2007nov/ Besides having articles of general interest, this edition has the theme: 'Crystallographic Computing at Oak Ridge National Laboratory: 1954 to 1968' by William Busing Related to this is an addendum file of historical Oak Ridge National Laboratory software reports within an Adobe Acrobat PDF file The list of articles in this edition is given below. == == Crystallographic Computing at Oak Ridge National Laboratory: # Crystallographic Computing at Oak Ridge National Laboratory: 1954 to 1968 - William R. Busing # Early Stereoscopic Drawings generated by ORTEP-I for two crystallographic meetings: 1965 and 1966 - Carroll K. Johnson * Stereoscopic Drawings prepared for the joint ACA and MSA meeting, Gatlinburg, Tennesee, USA, June 27 - July 2, 1965. * Stereoscopic Drawings of Myoglobin, Vitamin B-12 coenzyme, and poly-L-alanine. Prepared for the Second Biophysical Congress, Vienna, Austria, September 5-9, 1966. == == Other Articles : # What you can expect from Jana2006 - Vaclav Petricek and Michal Dusek # Report from the GSAS-II Workshop: May 10-11, 2007 - Brian H. Toby and Robert B. Von Dreele # cctbx news - Luc J. Bourhis, Ralf W. Grosse-Kunstleve and Paul D. Adams # Rietveld refinement of structural distortion-mode amplitudes - Branton J. Campbell, John S. O. Evans, Francesca Perselli and Harold T. Stokes # MAX3D - Visualization of Reciprocal Space Volumes - Jim Britten and Weiguang Guan == == Newsletter 8 Addendum: Following historical software reports courtesy of ORNL : # A crystallographic least squares refinement program for the IBM 704, ORNL-CF-59-4-37, Oak Ridge, TN : Oak Ridge National Laboratory, 1959. - W. R. Busing and H. A. Levy # A crystallographic function and error program for the IBM 704, ORNL-CF-59-12-3, Oak Ridge, TN : Oak Ridge National Laboratory, 1959. - W. R. Busing and H. A. Levy # OR ABS : a FORTRAN program for calculating single crystal absorption corrections, ORNL-TM-229, Oak Ridge, TN : Oak Ridge National Laboratory, 1962. - D. J. Wehe, W. R. Busing and H. A. Levy # OR GLS : a general fortran least squares program, ORNL-TM-271, Oak Ridge, TN : Oak Ridge National Laboratory, 1962. - W. R. Busing and H. A. Levy # OR FLS, A Fortran crystallographic least-squares program, ORNL- TM-305, Oak Ridge, TN : Oak Ridge National Laboratory, 1962. - W. R. Busing, K. O. Martin, and H. A. Levy # OR FFE, a FORTRAN crystallographic function and error program, ORNL-TM-306, Oak Ridge, TN : Oak Ridge National Laboratory, 1964. - W. R. Busing, K. O. Martin, and H. A. Levy # OR TEP : A Fortran thermal-ellipsoid plot program for crystal structure illustrations, ORNL-3794, Oak Ridge, TN : Oak Ridge National Laboratory, 1965. - Carroll K. Johnson # OR TEP-II : a FORTRAN Thermal-Ellipsoid Plot Program for crystal structure illustration, ORNL-5138, Oak Ridge, TN : Oak Ridge National Laboratory, 1976. - Carroll K. Johnson == == Call for Contributions to the Next CompComm Newsletter The ninth issue of the Compcomm Newsletter is expected to appear around August of 2009 (2008 being an IUCr congress year) with the primary theme to be determined. If no-one is else is co-opted, the newsletter will be edited by Lachlan Cranswick. Contributions would be also greatly appreciated on matters of general interest to the crystallographic computing community, e.g. meeting reports, future meetings, developments in software, algorithms, coding, historical articles, programming languages, techniques and other news. http://www.iucr.org/iucr-top/comm/ccom/newsletters/ == == Previous Issues of the IUCr Computing Commission newsletter are online: 2006 * Compcomm Newsletter No. 7, November 2006 - 7th issue with the theme of "Understanding Crystal Structures". Editors -
[ccp4bb] Dissolving s-adenosylhomocysteine
Hi all, I am in the process of obtaining crystals in complex with s-adenosylhomocysteine but this compound doesn't dissolve in normal pH. The final concentration needs to be in mM range so the stock ideally needs to be at least 50mM. I know SAH is quite soluble in DMSO but is there anyway to get it in aqueous solution without organic solvent or strong acid? Thank you very much in advance. Ray
Re: [ccp4bb] Dissolving s-adenosylhomocysteine
I solved a structure in the presence of SAM, which is the same as SAH but with a donor methyl group, and saw clear density for SAH, and not SAM, so it seems that the SAM was either spontaneously de-methylated in solution, or the protein which bound the SAM spontaneously demethylated it. In any case, I remember having solubility issues with the SAH, but the SAM was fine. If you are not particular which molecule you have (SAM vs. SAH), you might try the SAM. Alternatively, you might just add SAH powder to the crystal mother liquor, to get a saturated solution. JPK *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.467.4049 cel: 773.608.9185 email: [EMAIL PROTECTED] *** - Original Message - From: "Ray Changrui Lu" <[EMAIL PROTECTED]> To: Sent: Tuesday, November 06, 2007 12:48 PM Subject: [ccp4bb] Dissolving s-adenosylhomocysteine Hi all, I am in the process of obtaining crystals in complex with s-adenosylhomocysteine but this compound doesn't dissolve in normal pH. The final concentration needs to be in mM range so the stock ideally needs to be at least 50mM. I know SAH is quite soluble in DMSO but is there anyway to get it in aqueous solution without organic solvent or strong acid? Thank you very much in advance. Ray
Re: [ccp4bb] Dissolving s-adenosylhomocysteine
Hi Ray, I've got a similar concern and contacted SIGMA for advice. I got the following response: "We test routinely solubility in water (100 mg/ml). A clear to slightly hazy light yellow solution is yielded. This material is 80-90% pure when prepared, but is very unstable. As much as 10% purity loss per day at 25 °C has been noted. Further it reacts with water. Solution Stability according to Data for Biochemical Research, 3rd ed., p. 2 (1987): S-adenosylmethionine is relatively stable in acid solutions and very unstable under alkaline conditions. Stock solutions should be stable when stored at -20° C at pH 2.5-4.0 for one month.The solutions should be warmed up just before use. In addition, solutions after 24 hours at 30°C decomposed 10% at pH 6.6, 32% at pH 7.8 and 70% at pH 8.8." The above is for SAM I'm still waiting for a response regarding SAH. Ralf -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Ray Changrui Lu Sent: Wednesday, November 07, 2007 2:48 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Dissolving s-adenosylhomocysteine Hi all, I am in the process of obtaining crystals in complex with s-adenosylhomocysteine but this compound doesn't dissolve in normal pH. The final concentration needs to be in mM range so the stock ideally needs to be at least 50mM. I know SAH is quite soluble in DMSO but is there anyway to get it in aqueous solution without organic solvent or strong acid? Thank you very much in advance. Ray
[ccp4bb] elusive DNA density
Dear all, I've been working on a series of DNA-protein complex structures. In my recently acquired data sets, I got almost no density for DNA if I do molecular replacement or rigid body fitting with the protein structure, although I am 100% sure I have DNA in the structure by indepenent means. If I use models with DNA, I could find some DNA density with those data sets, but as I refine the structure, the density became very poor. The resolutions for those data sets are between 2.0-2.4 A. Also, if I use the scaled data from synchrotron rather than the re-scaled data at home, I got better DNA density, although for re-scaling, I used site parameters that I copied done from synchrotron. The only differences between those two sets of scaled data are: (1) the original scaled data take into account all reflections, including high resolution data with low completeness/redundancy, which are cut in the re-scaling; (2) error models were changed so chi squares for each bin are 0.8-1.2 for re-scaling. My (very naive) questions are: (1) Does the DNA density I saw in the cases where I use models with DNA for MR/rigid body fitting only reflect model bias? (2) are simulated annealing or cycles of coordinate/B factor refinement enough to get rid of model bias? (3) Does weak DNA density have to do with data processing? Thanks very much for any suggestion, Melody Lin
Re: [ccp4bb] elusive DNA density
Hi, >(1) Does the DNA density I saw in the cases where I use models with DNA for >MR/rigid body fitting only reflect model bias? If your DNA density is becoming poor as your refine, it is quite likely that the initial DNA density you are observing after MR is model bias due to inclusion of a DNA model with the protein search molecule. If your protein is small compared to DNA ligand, or your DNA comprises more of the asu content that the protein, you could try doing MR with only DNA search model. If you then get the same solution, that would imply that the DNA density is real. If you have confirmed the presence of DNA in the crystals by silver staining gel, and assuming the crystals were washed well to avoid any DNA sticking to the crystals, etc., then loss of DNA density may indicate that the DNA is not well ordered. >(2) are simulated annealing or cycles of coordinate/B factor refinement enough >to get rid of model bias? Your observation of DNA density becoming poor and/or disappearing probably answers your question.however, it is difficult to get rid of model bias. Best way to do it is to remove DNA portion from the search model. You may also try composite omit maps and simulated annealing omit maps in CNS which basically calculate maps by removing portions of the model, or prime and switch phasing using RESOLVE to reduce model bias. >(3) Does weak DNA density have to do with data processing? Unlikely, especially if density for your protein is very good. 2.4-2.6A should be quite good to see good DNA density. You might see some differences based on what you mention about including even weak and incomplete high resolution data, but should not result in your overall observation of DNA density becoming poor after refinement. If you are very sure you have DNA in the crystal as protein-DNA complex and you are unable to see DNA density, you might consider alterations in the DNA sequence used in the crystallizations to get a more rigid DNA duplex (assuming you are working with dsDNA), getting more GC bp into it. And also consider introducing Cys mutations into the protein to get a thiol cross-linked protein-DNA complex. Regards, Debanu. -- Debanu Das, SSRL. -Original Message- From: CCP4 bulletin board on behalf of Melody Lin Sent: Tue 11/6/2007 7:36 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] elusive DNA density Dear all, I've been working on a series of DNA-protein complex structures. In my recently acquired data sets, I got almost no density for DNA if I do molecular replacement or rigid body fitting with the protein structure, although I am 100% sure I have DNA in the structure by indepenent means. If I use models with DNA, I could find some DNA density with those data sets, but as I refine the structure, the density became very poor. The resolutions for those data sets are between 2.0-2.4 A. Also, if I use the scaled data from synchrotron rather than the re-scaled data at home, I got better DNA density, although for re-scaling, I used site parameters that I copied done from synchrotron. The only differences between those two sets of scaled data are: (1) the original scaled data take into account all reflections, including high resolution data with low completeness/redundancy, which are cut in the re-scaling; (2) error models were changed so chi squares for each bin are 0.8-1.2 for re-scaling. My (very naive) questions are: (1) Does the DNA density I saw in the cases where I use models with DNA for MR/rigid body fitting only reflect model bias? (2) are simulated annealing or cycles of coordinate/B factor refinement enough to get rid of model bias? (3) Does weak DNA density have to do with data processing? Thanks very much for any suggestion, Melody Lin
