[COOT] Ligands
Perhaps (most likely in fact) this has been asked and addressed in the past: is there (or will there be) a way in COOT to 'build' ligands from scratch? Currently I go through a long winded route of Sketcher... importing and pulling the coords around to fit electron density... then finally idealising the geometry. What do other people do? Thanks in advance Dean
[COOT] ligands
It looks like the new Coot no longer recognizes * for the sugar atoms in ATP, UDP, etc. Has anyone else had this problem?
Re: [COOT] Ligands
Dean Derbyshire wrote: Perhaps (most likely in fact) this has been asked and addressed in the past: is there (or will there be) a way in COOT to 'build' ligands from scratch? Currently I go through a long winded route of Sketcher... importing and pulling the coords around to fit electron density... then finally idealising the geometry. What do other people do? http://www.majorgroove.org/questions/49/how-to-add-a-ligand-to-a-model Tutorial here: http://www.biop.ox.ac.uk/coot/tutorial/ligand-fitting-tutorial.pdf Paul.
Re: [COOT] Ligands
If you can define a SMILES string for your ligand, you can get coot to build the ligand with the press of a button in a fraction of a second. If the SMILES syntax is a PITA, use this: http://www.molinspiration.com/cgi-bin/properties If you need more options, phenix.elbow also permits you to use a SMILES string input. Dean Derbyshire wrote: > Perhaps (most likely in fact) this has been asked and addressed in the > past: > is there (or will there be) a way in COOT to 'build' ligands from scratch? > > Currently I go through a long winded route of Sketcher... importing and > pulling > the coords around to fit electron density... then finally idealising the > geometry. > > What do other people do? > > Thanks in advance > > Dean >
Re: [COOT] Ligands
I don't know it. sorry.
Re: [COOT] ligands
On 21/09/11 16:10, Mike wrote: It looks like the new Coot no longer recognizes * for the sugar atoms in ATP, UDP, etc. That's right. Has anyone else had this problem? Yes. I think the solution for now is to run molprobity's remediator. A longer-term solution is for Coot - or a ccp4 program - to convert on the fly. Paul.
[COOT] ligands in alternate conformations
Hi, I'm wondering why adding alternate conformations to ligands (i.e. non amino acid residues) restricts the occupancy ratio to 50:50. I understand that ligands don't have rotamers (at least not ones that coot would know about) so I can't pick rotamers but I'd like to be able to specify the new occupancy with a little slide bar similarly to amino acid residues. Having non-1.0 occupancies complicate things further: I have a ligand with a bromine atom that has partly fallen off at the synchrotron and I refined it with occupancy = 0.5 (1.0 for all other atoms). When I split this residue coot sets the occupancies to 0.5 for every atom, except for the first half of the Br which will have 0.0. Again, I understand the logic behind this... but wouldn't it be nicer to have 0.25 for both halves of the Br so that it adds up to the original 0.5? RSR and regularize zone are also problematic for ligands in alternate conformations: unless I click on atoms that are part of the split region, RSR and regularize make the ligand explode. JED
