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Hello, There are already some bug fixes for ChemBuild, so we have put up a new release at: http://www.ccpn.ac.uk/download/ccpnmr/chemBuild1.0beta1.tar.gz It will unpack exactly as the previous version so will just overwrite what is there if you unpack in the same place. You do not need to download the API again. Wayne On Fri, 27 Jan 2012, Tim Stevens wrote: > Hi Andy, > > Further to this, if you want to have a residue with all the right chain > linking variants, simply start from the "LinkedTemplate" in the amino acids > section of the compound library. > > Also there is some limited documentation for the program at: > > http://www.ccpn.ac.uk/documentation/ > > > T. > > >> The (newly) recommended method for this is to use ChemBuild. (After a bit >> of grief, which is why this email took so long) I've just created a version >> of this obtainable at: >> >> http://www.ccpn.ac.uk/download/ccpnmr/chemBuild1.0beta.tar.gz >> >> Note that it unpacks into ccpnmr/ccpnmr3.0. You run: >> >> ccpnmr/ccpnmr3.0/bin/chemBuild >> >> That chemBuild is a script which sets up a minimal environment and which >> assumes that your default python has Qt and PySide (on Linux you ought to >> be able to get these via the package manager). Also, if you want to use a >> non-default Python then edit the last line of the script. >> >> The release does not include the CCPN API so if you want to export a CCPN >> XML file (and it sounds like you do) then you need to also get: >> >> http://www.ccpn.ac.uk/download/ccpnmr/chemBuildApi1.0beta.tar.gz >> >> This will also unpack into ccpnmr/ccpnmr3.0. As it happens, an existing >> API (e.g. from Analysis 2.2 or 2.1) would work except that because of the >> stupidities of Python when it comes to importing code, we must have the API >> python directory be the same as the ChemBuild python directory (there's an >> arcane technical reason). >> >> We have separated out the API because it is a lot bigger than the actual >> ChemBuild code, and people might well want to use the latter without the >> former. >> >> Note that this is a semi-official release. At some point soon we will put >> out a proper one with further information. >> >> Some hints for exporting CCPN XML. You first need to give the compound a >> CCPN code. This can be set in the "Compound Info" tab at the bottom right. >> Obviously it's best to use a CCPN code that is different from existing ones >> (it can be up to 80 characters, with no white space, and the standard ones >> are 1 to 3 letters, e.g. Gly, Tyr, etc.). There is also a CCPN MolType >> that you can set. >> >> You can save the file either in the Analysis >> ccpnmr/ccpnmrX.Y/data/ccp/molecule/ChemComp directory (which is where the >> standard ChemComps live) or in your project in the >> PROJECT_DIR/ccp/molecule/ChemComp directory (which is likely not to exist >> yet) or even in ~.ccpn/data/ccp/molecule/ChemComp (I think that ought to >> work anyway, and again this directory is likely not to exist). The last >> choice might be the preferred location, it's up to you. >> >> Wayne >> >> On Wed, 25 Jan 2012, Dr Andy Herbert wrote: >> >>> Hi, >>> >>> I'm trying to add a molecule into analysis which is a small peptide that >>> contains a couple of non-standard amino acids that don't seem to be >>> already made (specifically Ne-methylated Tryptophan; and >>> N-methyl-isoleucine that has an NH2 group on the C-terminus). I can make >>> CCP-xml chemComp, or PDB representations of these, and import them into >>> analysis, but I can't then add them to my molecule. I was wondering if >>> anyone could offer suggestions as to how to do this. I'd be very grateful. > > > ------------------------------------------------------------------------------- > Dr Tim Stevens Email: [log in to unmask] > Department of Biochemistry [log in to unmask] > University of Cambridge Phone: +44 1223 766018 (office) > 80 Tennis Court Road +44 7816 338275 (mobile) > Cambridge CB2 1GA WWWeb: http://www.bio.cam.ac.uk/~tjs23 > United Kingdom http://www.ccpn.ac.uk > ------------------------------------------------------------------------------- > ------ +NH3CH(CH(CH3)OH)C(O)NHCH(CH(CH3)CH2CH3)C(O)NHCH(CH2CH2SCH3)CO2- > ------- > ------------------------------------------------------------------------------- >