Re: [ccp4bb] Merging Data from Multiple Crystals
Dear Alex BLEND will be released soon through the CCP4 Updates. In the meantime, the easiest way to try it out is to install one of the nightly builds from here: http://www.ccp4.ac.uk/dev/nightly/. The usual warnings apply. What you obtain that way may not be (fully) tested, and may differ slightly from what is finally released. Your comments are welcome. I hope this helps. Cheers, -- David On 29 March 2014 13:38, Andreas Förster wrote: > Contact James Foadi. > > http://diamond.ac.uk/Beamlines/Mx/I24/Staff/Foadi.html > > > Andreas > > > > > On 29/03/2014 1:21, Alexander Batyuk wrote: > >> Dear Tassos, >> >> Do you know by chance whether BLEND is available? >> >> Best wishes, >> >> Alex >> >> >>
Re: [ccp4bb] Merging Data from Multiple Crystals
Contact James Foadi. http://diamond.ac.uk/Beamlines/Mx/I24/Staff/Foadi.html Andreas On 29/03/2014 1:21, Alexander Batyuk wrote: Dear Tassos, Do you know by chance whether BLEND is available? Best wishes, Alex
Re: [ccp4bb] Merging Data from Multiple Crystals
Dear Tassos, Do you know by chance whether BLEND is available? Best wishes, Alex On 27 Mar 2014, at 16:06, Tassos Papageorgiou wrote: > Hi, > > You may also try BLEND to choose the optimal data sets before scaling and > merging > > Foadi J, Aller P, Alguel Y, Cameron A, Axford D, Owen RL, Armour W, Waterman > DG, Iwata S & Evans G (2013) Clustering procedures for the optimal selection > of data sets from multiple crystals in macromolecular crystallography. Acta > Crystallogr D Biol Crystallogr 69: 1617–1632 > > Tassos Papageorgiou > > Jarrod Mousa wrote: >> Hi, >> I am trying to solve the structure of a membrane protein. The protein has 12 >> helices and I have a good molecular replacement model that seems to work for >> about half of the structure. I used chainsaw to convert the amino acid >> residues to that of my protein sequence, and the density fits the structure >> well on one side of the protein, but on the other side (about 5 helices), >> there doesn't seem to be any density for the side chains. Has anyone had >> experience with this? The completeness is high ~99% for 3.2 angstroms. The >> data was collected from fairly small crystals ~ 20um. >> Thanks. -- Alex Batyuk The Plueckthun Lab www.bioc.uzh.ch/plueckthun
[ccp4bb] AW: [ccp4bb] Merging Data from Multiple Crystals
Hi Jarrod, I think these 5 helices are either slightly misplaced, or somewhat disordered. How does the main-chain density look like? Do you see a discrete main-chain, or is the main-chain blurred and does the helix look like a blurred cylinder? If the main-chain is clear, I would take off all side chains, run some refinement and look if you could recognize some side chains. They may have shifted a few residues from what you think they are based on the homology model. Another option is to take out the 5 helices and rerun MR with them, using the 7 good helices as a partial model. You could also take one helix out at a time and try to build them again from scratch. Finally, if these helices are somewhat disordered, nothing can be done except from trying to grow different crystals, e.g. by adding a (different) ligand. With 7 out of 12 helices well-defined, your structure will nevertheless be interesting. Best, Herman -Ursprüngliche Nachricht- Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Jarrod Mousa Gesendet: Donnerstag, 27. März 2014 15:15 An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] Merging Data from Multiple Crystals Hi, I am trying to solve the structure of a membrane protein. The protein has 12 helices and I have a good molecular replacement model that seems to work for about half of the structure. I used chainsaw to convert the amino acid residues to that of my protein sequence, and the density fits the structure well on one side of the protein, but on the other side (about 5 helices), there doesn't seem to be any density for the side chains. Has anyone had experience with this? The completeness is high ~99% for 3.2 angstroms. The data was collected from fairly small crystals ~ 20um. Thanks.
Re: [ccp4bb] Merging Data from Multiple Crystals
Hi, You may also try BLEND to choose the optimal data sets before scaling and merging Foadi J, Aller P, Alguel Y, Cameron A, Axford D, Owen RL, Armour W, Waterman DG, Iwata S & Evans G (2013) Clustering procedures for the optimal selection of data sets from multiple crystals in macromolecular crystallography. Acta Crystallogr D Biol Crystallogr 69: 1617–1632 Tassos Papageorgiou Jarrod Mousa wrote: Hi, I am trying to solve the structure of a membrane protein. The protein has 12 helices and I have a good molecular replacement model that seems to work for about half of the structure. I used chainsaw to convert the amino acid residues to that of my protein sequence, and the density fits the structure well on one side of the protein, but on the other side (about 5 helices), there doesn't seem to be any density for the side chains. Has anyone had experience with this? The completeness is high ~99% for 3.2 angstroms. The data was collected from fairly small crystals ~ 20um. Thanks.
Re: [ccp4bb] Merging Data from Multiple Crystals
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Jarrod, try pointless and aimless to merge the data, this should get rid of this error message. Otherwise you would have to renumber the batches, which might be tedious and also unnecessary since pointless has been around. Best, Tim On 03/27/2014 03:17 PM, Jarrod Mousa wrote: > I am also trying to merge data from multiple crystals that I > collected from. I have tried to reindex the data in CCP4 after > indexing in iimosflm, and then put these .mtz files through > sortmtz before scala, but I keep getting an error in sort mtz: > > From ccp4_lwbat: warning: attempt to add new batch with existing > batch number 1! SORTMTZ: LWBAT: error in ccp4_lwbat, see messages > above Times: User: 0.3s System:0.0s Elapsed: 0:00 > > > > *** > > > * Information from CCP4Interface script > *** > > > The program run with command: /Applications/ccp4-6.4.0/bin/sortmtz HKLOUT "/Users/bruner/Desktop/combinedfiles.mtz" > has failed with error message SORTMTZ: LWBAT: error in > ccp4_lwbat, see messages above > *** > > > > > #CCP4I TERMINATION STATUS 0 " SORTMTZ: LWBAT: error in > ccp4_lwbat, see messages above" #CCP4I TERMINATION TIME 26 Mar 2014 > 18:50:58 #CCP4I MESSAGE Task failed > > > Any help would be greatly appreciated! > - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Icedove - http://www.enigmail.net/ iD8DBQFTNDfkUxlJ7aRr7hoRAvLSAJ0de7psQe68MoHYq1ZMPGEJTtvwGgCfTj6X tu1A/xsYbi+30ZwDbRPEO5g= =4k8U -END PGP SIGNATURE-
[ccp4bb] Merging Data from Multiple Crystals
I am also trying to merge data from multiple crystals that I collected from. I have tried to reindex the data in CCP4 after indexing in iimosflm, and then put these .mtz files through sortmtz before scala, but I keep getting an error in sort mtz: From ccp4_lwbat: warning: attempt to add new batch with existing batch number 1! SORTMTZ: LWBAT: error in ccp4_lwbat, see messages above Times: User: 0.3s System:0.0s Elapsed: 0:00 *** * Information from CCP4Interface script *** The program run with command: /Applications/ccp4-6.4.0/bin/sortmtz HKLOUT "/Users/bruner/Desktop/combinedfiles.mtz" has failed with error message SORTMTZ: LWBAT: error in ccp4_lwbat, see messages above *** #CCP4I TERMINATION STATUS 0 " SORTMTZ: LWBAT: error in ccp4_lwbat, see messages above" #CCP4I TERMINATION TIME 26 Mar 2014 18:50:58 #CCP4I MESSAGE Task failed Any help would be greatly appreciated!
[ccp4bb] Merging Data from Multiple Crystals
Hi, I am trying to solve the structure of a membrane protein. The protein has 12 helices and I have a good molecular replacement model that seems to work for about half of the structure. I used chainsaw to convert the amino acid residues to that of my protein sequence, and the density fits the structure well on one side of the protein, but on the other side (about 5 helices), there doesn't seem to be any density for the side chains. Has anyone had experience with this? The completeness is high ~99% for 3.2 angstroms. The data was collected from fairly small crystals ~ 20um. Thanks.
