[ccp4bb] serial MR / refinement
Dear all, I am looking for a way to automate molecular replacement and refinement runs. From ligand / fragment screening trials we have many datasets of the same protein with various resolutions (2.8 – 1.2Å). The apo-structure is known and well refined. The cell constants are fairly similar but not in all cases identical, hence I would prefer a MR run prior to the refinement. I am sure this can somehow be realised with some shell-script but maybe there is some more sophisticated way of realising this? I would also be happy for partial solutions or general advise to the problem. Best regards Eike
[ccp4bb] DNA interaction 2D plot software
Hello everyone, I would like to display the interactions of a protein dsDNA complex in a simplified 2D plot, similar to what LIGPLOT does for protein ligand interactions. In many articles you find interactions displayed in such a way but as far as I know those are hand-made. In my experience LIGPLOT itself is suboptimal if there are too many interactions to display Thanks a lot in advance for your suggestions. Eike
[ccp4bb] Coot 0.7 Saving Dialog opens behind main window
Dear Coot-users, I am running Coot-0.7 on OSX 10.6.8. Installation from the 'Scott'-package was no problem at all it runs very smoothly. However, whenever I want to save the coordinates the saving dialog open -behind- the main window. To be more precise: the coordinate molecule selector opens in front of it but the -file name selector- opens behind the main window. This is over the time a bit frustrating when you have to minimize/move the main window every time you want to save your structure. Does it happen to others as well, or is this specific to my system? If its possible, how could it be changed to open in front of the main window? Best regards Eike
[ccp4bb] partial specific volume
Hello everyone, I am working on protein RNA complex and would like to verify the oligomeric state from the crystal structure by analytical ultracentrifugation (AUC). To fit data from AUC we need a good estimate of the partial specific volume of the complex, therefore I wanted to retrieve this value from my pdb coordinates, in either of the oligomeric states. My idea was to calculate the volume of the complex: - I had a look at rwcontents but this gave me only the volume of the cell and not of the protein itself - AreaImol does not report the volume (?) - I also had a look at SURFACE/VOLUME but found it quiet cryptic. Are there other ways to calculate the volume of a protein/complex from pdb-coordinates, maybe an alternative to SURFACE/VOLUME? Or is there some software that directly reports the partial specific volume? Many thanks in advance Eike
[ccp4bb] Off topic: PyRosetta unrecognized aa Ur
Hello everybody, This is slightly off-topic but I still hope there might be somebody in the crowd with (Py)Rosetta experience. I successfully tried protein_protein docking before, but now I am trying to dock a RNA into a protein using PyRosetta v.1.1, which, as you can imagine, fails in a new an unusual way ;) I used the dna_dock.py script provided. When I run the script it finishes with following error message: ERROR: unrecognized aa Ur ERROR:: Exit from: src/core/io/pdb/file_data.cc line: 629 Traceback (most recent call last): File rna_dock.py, line 6, in module pose_from_pdb(p, rnadock.pdb) RuntimeError: unidentifiable C++ exception Obviously PyRosetta doesn't recognize the RNA specific residues and is still in DNA-mode. Looking fot hints in the internet took me to this website (http://www.rosettacommons.org/manuals/archive/rosetta3.2.1_user_guide/RNA_p rotein_changes.html), I followed the instructions changing files and pathes but still I receive the same error message. Below I posted the respective changes that I made according to the recommendations in /PyRosetta/rosetta_database/chemical/residue_type_sets/fa_standard: My residue_types.txt ## Nucleic Acid Types #residue_types/nucleic/ADE.params #residue_types/nucleic/THY.params #residue_types/nucleic/CYT.params #residue_types/nucleic/GUA.params residue_types/nucleic/RAD.params residue_types/nucleic/RCY.params residue_types/nucleic/RGU.params residue_types/nucleic/URA.params #residue_types/nucleic/GNP.params #residue_types/nucleic/GDP.params #residue_types/nucleic/GTP.params My patches.txt: patches/CtermProteinFull.txt patches/Cterm_amidation.txt patches/NtermProteinFull.txt #patches/LowerDNA.txt #patches/UpperDNA.txt patches/LowerRNA.txt patches/UpperRNA.txt patches/SpecialRotamer.txt patches/protein_cutpoint_upper.txt patches/protein_cutpoint_lower.txt patches/VirtualBB.txt patches/ShoveBB.txt patches/VirtualDNAPhosphate.txt patches/VirtualNterm.txt patches/RepulsiveOnly_fa.txt patches/VirtualProteinResidue.txt Do you have any ideas what could have gone wrong or what else I need to do in order to make it work? Many thanks in advance and best regards Eike
Re: [ccp4bb] ROSETTA for MR model generation
Hello Kornelius, In 2 or 3 cases I successfully used a homology model for molecular replacement using a model generated from the PHYRE server http://www.sbg.bio.ic.ac.uk/~phyre/. I know it is not the same as ROSETTA but if there is some sequence homology you might be lucky... Best regards Eike Am 25.08.10 10:13 schrieb Kornelius Zeth unter kornelius.z...@tuebingen.mpg.de: Dear all, I was wondering if anybody has used the ROSETTA software to generate a MR model that could subsequently being used successfully for a MR solution case. The sequence of the protein we work with is relatively small, ~ 85 residues. Crystallization is not very reproducible. Resolution is 1.9 A. Crystals are extremely rare. I would be grateful for any hints and will send a summary of all personally sent comments to the list. Thank you and have a nice day Kornelius -- Kornelius Zeth Max Planck Institute for Developmental Biology Dept. Protein Evolution Spemannstr. 35 72076 Tuebingen, Germany kornelius.z...@tuebingen.mpg.de Tel -49 7071 601 323 Fax -49 7071 601 349
Re: [ccp4bb] Butandiol as cryopotectant
Hello Dave, I have good experience with concentrations between 10% and 15% 2,3-butanediol. My typical starting concentration is 12.5%. Good luck. Eike Am 23.03.10 08:27 schrieb David Briggs unter drdavidcbri...@gmail.com: 2,3-BD users, What sort of concentrations are you using? Dave -- Delivered via an Android. On Mar 22, 2010 11:45 PM, Steve Tuske tu...@cabm.rutgers.edu wrote: Hi Ulrike, 2,3-butanediol has worked very nicely as a cryoprotectant. In my hands it mostly seems to decrease mosaicity. I was able to switch from a three-step soaking protocol with glycerol and glucose to a quick (30 second to one minute) soak with 2,3-BD. It's a winner. Steve I Hello Ulrike, in our lab 2,3-Butanediol has had a good reputation. Tim On Mon, Mar 22...
[ccp4bb] Postdoc Position at University of Goettingen
Hello Everyone, I am posting this in behalf of Ralf Ficner, please do not reply to me but directly contact Ralf Ficner (see below). Kind regards Eike The Department of Structural Biology at the Georg-August-University Goettingen, Germany, seeks to recruit an outstanding postdoctoral scientist in structural biology with a research focus directed towards the structure and dynamics of macromolecular complexes. The advertised position is suitable for candidates with strong expertise in X-ray crystallography or computational structural biology. An initial contract of 2 years will be offered to the successful candidate. This can be renewed up to 5 years. The position includes the opportunity to build up an independent junior research group. The University Goettingen strives to increase its proportion of female staff and specifically encourages qualified women to apply. Disabled persons with corresponding aptitude for the position will be favoured. Please send your application by Email to Prof. Dr. Ralf Ficner (rfic...@uni-goettingen.de), Department of Molecular Structural Biology, GZMB, University Goettingen, Germany. Closing date for applications: August 5, 2009.
Re: [ccp4bb] environ.def / default.def
Hello again, sourcing environ.def or ccp4.setup-bash did not help to make it work. Sourcing default.def results in -- bash: memory: command not found bash: !FITING_NR=50: command not found bash: !TRAING_NR=50: command not found bash: !ROTING_MI=60: command not found bash: !ROTING_MC=290: command not found bash: !TABLING_MI=150: command not found bash: !TABLING_MR=540: command not found --- debugging info: --- echo $CCP4 /usr/local/software/ccp4/ccp4-6.0.2 echo $CCP4I_TOP /usr/local/software/ccp4/ccp4-6.0.2/ccp4i echo $PATH /usr/local/software/ccp4/ccp4-6.0.2/src/phaser/phaser-2.1.1/build/intel-linux/bin /usr/local/software/ccp4/ccp4-6.0.2/ccp4i/bin /usr/local/software/ccp4/ccp4-6.0.2/etc /home/eschulz1/bin /usr/local/bin /usr/bin:/bin /usr/bin/X11 /usr/X11R6/bin /opt/kde3/bin /usr/lib/jvm/jre/bin /usr/lib/mit/bin /usr/lib/mit/sbin /usr/local/software/XDS-linux_ifc_Intel+AMD /usr/local/software/coot-Linux-i386-redhat-8.0/bin /usr/local/software/ccp4/ccp4-6.0.2/bin /usr/local/software/ccp4/ccp4-6.0.2/include -- I hope this helps you ... Thanks again an best regards Eike On Fri, 2008-05-16 at 20:37 -0700, William Scott wrote: Probably. You should source either the first or the second file depending on your shell (the first for bash, the second for tcsh/csh). That might be the cause of your subsequent problem. For purposes of debugging, can you send us output for the following three commands: echo $PATH echo $CCP4 echo $CCP4I_TOP On Fri, May 16, 2008 5:22 pm, Eike Schulz wrote: Hello again, thanks to some people for their fast and helpfully very detailed advice: Including source /usr/local/software/ccp4/ccp4-6.0.2/include/ccp4.setup-bash source /usr/local/software/ccp4/ccp4-6.0.2/include/ccp4.setup into my .bashrc did indeed solve the problem with MTZDUMP when executed from the shell. Further thanks for some other corrections. But unfortunately the error persists when I try to run refmac from the ccp4i GUI - it complains not to be able to extract data from an .mtz file. Did I miss anything important? Kind regards Eike On Fri, 2008-05-16 at 14:37 -0700, William Scott wrote: On Fri, May 16, 2008 1:06 pm, Eike Schulz wrote: Hello everybody, setenv CCP4_MASTER /usr/local/software/ccp4 setenv CCP4 $CCP4_MASTER/ccp4-6.0.2 For bash, zsh, etc, you need to start with export CCP4_MASTER=/usr/local/software/ccp4 export CCP4=$CCP4_MASTER/ccp4-6.0.2 setenv is specific to (t)csh. export is specific to the sh-like shells. --- ... and the .bashrc contains following entries: --- PATH=$PATH:/usr/local/software/ccp4/ccp4-6.0.2/bin/ PATH=$PATH:/usr/local/software/ccp4/ccp4-6.0.2/include/ /usr/local/software/ccp4/ccp4-6.0.2/include/ccp4.setup-bash --- I think that last line would need to be source /usr/local/software/ccp4/ccp4-6.0.2/include/ccp4.setup-bash and you shouldn't need this line: PATH=$PATH:/usr/local/software/ccp4/ccp4-6.0.2/include/ and you should get rid of the trailing slash on this line: PATH=$PATH:/usr/local/software/ccp4/ccp4-6.0.2/bin/ to make it PATH=$PATH:/usr/local/software/ccp4/ccp4-6.0.2/bin but if ccp4.setup-bash works, you shouldn't need to explicitly set any PATH, including the one you missed (for ccp4i). William G. Scott Contact info: http://chemistry.ucsc.edu/~wgscott/ William G. Scott Contact info: http://chemistry.ucsc.edu/~wgscott/
Re: [ccp4bb] environ.def / default.def
Hello Bill, thanks a lot for making such big effort. It is a real pity but the syntax does not work properly. However, I am more or less convinced now that the whole thing is a bash / (t)csh related problem. It might be the easiest way just to switch to a different sh flavour as login shell. I hope that will settle the issue. Regardless of the success I learned a lot thanks to you and many others. The link you provided seems to be a good compilation of necessary unix knowledge - I will try to circulate it among my colleagues. Thanks again and all the best. Eike On Sat, 2008-05-17 at 08:13 -0700, William Scott wrote: Hi Eric: You shouldn't have to source or do anything with the def files. There seems to be some problems with the ccp4.setup-bash from what I have seen. If it gets sourced more than once, spaces get introduced into the PATH variable, which creates havoc. The file also locally defines setenv to try to use the csh syntax, which may or may not be problematic. I've made one that should avoid these problems and I tried to set it up to what looks like you need for your system. So, please try the following: 1. Eliminate all the directives to source any setup and def files from your shell startup dot files. 2. Put this file somewhere and source it. HTH, Bill PS: The zsh and tcsh shells are both more user-friendly than bash, so you might find those easier (what I sent you should work with zsh, although I have a much better one that makes use of zsh customizable completions and so forth). Here's some more info on unix shells: http://xanana.ucsc.edu/xtal/unix.html On May 17, 2008, at 1:48 AM, Eike Schulz wrote: Hello again, sourcing environ.def or ccp4.setup-bash did not help to make it work. Sourcing default.def results in -- bash: memory: command not found bash: !FITING_NR=50: command not found bash: !TRAING_NR=50: command not found bash: !ROTING_MI=60: command not found bash: !ROTING_MC=290: command not found bash: !TABLING_MI=150: command not found bash: !TABLING_MR=540: command not found --- debugging info: --- echo $CCP4 /usr/local/software/ccp4/ccp4-6.0.2 echo $CCP4I_TOP /usr/local/software/ccp4/ccp4-6.0.2/ccp4i echo $PATH /usr/local/software/ccp4/ccp4-6.0.2/src/phaser/phaser-2.1.1/build/ intel-linux/bin /usr/local/software/ccp4/ccp4-6.0.2/ccp4i/bin /usr/local/software/ccp4/ccp4-6.0.2/etc /home/eschulz1/bin /usr/local/bin /usr/bin:/bin /usr/bin/X11 /usr/X11R6/bin /opt/kde3/bin /usr/lib/jvm/jre/bin /usr/lib/mit/bin /usr/lib/mit/sbin /usr/local/software/XDS-linux_ifc_Intel+AMD /usr/local/software/coot-Linux-i386-redhat-8.0/bin /usr/local/software/ccp4/ccp4-6.0.2/bin /usr/local/software/ccp4/ccp4-6.0.2/include -- I hope this helps you ... Thanks again an best regards Eike On Fri, 2008-05-16 at 20:37 -0700, William Scott wrote: Probably. You should source either the first or the second file depending on your shell (the first for bash, the second for tcsh/csh). That might be the cause of your subsequent problem. For purposes of debugging, can you send us output for the following three commands: echo $PATH echo $CCP4 echo $CCP4I_TOP On Fri, May 16, 2008 5:22 pm, Eike Schulz wrote: Hello again, thanks to some people for their fast and helpfully very detailed advice: Including source /usr/local/software/ccp4/ccp4-6.0.2/include/ccp4.setup-bash source /usr/local/software/ccp4/ccp4-6.0.2/include/ccp4.setup into my .bashrc did indeed solve the problem with MTZDUMP when executed from the shell. Further thanks for some other corrections. But unfortunately the error persists when I try to run refmac from the ccp4i GUI - it complains not to be able to extract data from an .mtz file. Did I miss anything important? Kind regards Eike On Fri, 2008-05-16 at 14:37 -0700, William Scott wrote: On Fri, May 16, 2008 1:06 pm, Eike Schulz wrote: Hello everybody, setenv CCP4_MASTER /usr/local/software/ccp4 setenv CCP4 $CCP4_MASTER/ccp4-6.0.2 For bash, zsh, etc, you need to start with export CCP4_MASTER=/usr/local/software/ccp4 export CCP4=$CCP4_MASTER/ccp4-6.0.2 setenv is specific to (t)csh. export is specific to the sh-like shells
[ccp4bb] environ.def / default.def
Hello everybody, once more a beginners question on some probably Linux related problem. Eventhough my ccp4 installation seemed to work fine all the way MTZDUMP and the applications which use it (namely refmac ...) unfortunatly fail with the following error: --- CCP4 library signal ccp4_general:Cannot open environ.def (Success) raised in ccp4fyp mtzdump: Cannot open environ.def mtzdump: Cannot open environ.def The folder which contains the files /usr/local/software/ccp4/ccp4-6.0.2/include/ is correctly stated in the ccp4.setup-bash ... setenv CCP4_MASTER /usr/local/software/ccp4 setenv CCP4 $CCP4_MASTER/ccp4-6.0.2 # Check for existence of CCP4_MASTER if (! test -d $CCP4_MASTER) ; then echo * WARNING ** echo The directory $CCP4_MASTER echo (assigned to CCP4_MASTER) does not exist. echo The CCP4 programs will not run correctly, and any echo installation attempt will have errors or will fail. echo * WARNING ** fi # CCP4_SCR: a per-user directory for run-time-generated scratch # files. A dedicated scratch filesystem is probably better than (/usr)/tmp # BINSORT_SCR: a scratch directory for binsort's use; normally same as CCP4_SCR setenv CCP4_SCR /tmp/$USER # check to see if this exists and if not try to make it test -d $CCP4_SCR || mkdir $CCP4_SCR test -d $CCP4_SCR || \ echo Unable to make CCP4_SCR. CCP4 progs will not run correctly. setenv BINSORT_SCR $CCP4_SCR --- ... and the .bashrc contains following entries: --- PATH=$PATH:/usr/local/software/ccp4/ccp4-6.0.2/bin/ PATH=$PATH:/usr/local/software/ccp4/ccp4-6.0.2/include/ /usr/local/software/ccp4/ccp4-6.0.2/include/ccp4.setup-bash --- All the files have the according permissions. I would greatly appreciate any help on solving this problem. Thanks a lot in advance and have a nice weekend. Eike
Re: [ccp4bb] environ.def / default.def
Hello again, thanks to some people for their fast and helpfully very detailed advice: Including source /usr/local/software/ccp4/ccp4-6.0.2/include/ccp4.setup-bash source /usr/local/software/ccp4/ccp4-6.0.2/include/ccp4.setup into my .bashrc did indeed solve the problem with MTZDUMP when executed from the shell. Further thanks for some other corrections. But unfortunately the error persists when I try to run refmac from the ccp4i GUI - it complains not to be able to extract data from an .mtz file. Did I miss anything important? Kind regards Eike On Fri, 2008-05-16 at 14:37 -0700, William Scott wrote: On Fri, May 16, 2008 1:06 pm, Eike Schulz wrote: Hello everybody, setenv CCP4_MASTER /usr/local/software/ccp4 setenv CCP4 $CCP4_MASTER/ccp4-6.0.2 For bash, zsh, etc, you need to start with export CCP4_MASTER=/usr/local/software/ccp4 export CCP4=$CCP4_MASTER/ccp4-6.0.2 setenv is specific to (t)csh. export is specific to the sh-like shells. --- ... and the .bashrc contains following entries: --- PATH=$PATH:/usr/local/software/ccp4/ccp4-6.0.2/bin/ PATH=$PATH:/usr/local/software/ccp4/ccp4-6.0.2/include/ /usr/local/software/ccp4/ccp4-6.0.2/include/ccp4.setup-bash --- I think that last line would need to be source /usr/local/software/ccp4/ccp4-6.0.2/include/ccp4.setup-bash and you shouldn't need this line: PATH=$PATH:/usr/local/software/ccp4/ccp4-6.0.2/include/ and you should get rid of the trailing slash on this line: PATH=$PATH:/usr/local/software/ccp4/ccp4-6.0.2/bin/ to make it PATH=$PATH:/usr/local/software/ccp4/ccp4-6.0.2/bin but if ccp4.setup-bash works, you shouldn't need to explicitly set any PATH, including the one you missed (for ccp4i). William G. Scott Contact info: http://chemistry.ucsc.edu/~wgscott/
[ccp4bb] glycosidic bonds for refmac library
Hello everyone, I have a couple of structures which contain oligomeric sugars in different conformations. Is there any general way of defining a glycosidic bond for the refmac library - instead of creating .cif files for every single ligand-structure ? Thank you very much in advance Eike
