Re: [ccp4bb] Ligand building in real space
To answer your question... On 10/04/17 08:44, Mohamed Noor wrote: Is it possible to directly build a ligand in real space (in Coot?) and then generate a SMILES string for restraint generation. I think that you are describing a 3D editor. It is not possible to do this in Coot (Coot's molecular editor is 2D). If you want to use Coot I would do as Johannes says, use File -> Get Monomer. PG4 (first choice), PGE, PEG, PE8. These are fun to refine in Coot, they wriggle around. I think that SMILES is a bit of side-issue. I am already using Polder and omit maps that confirm these are not noise. :-) Paul.
Re: [ccp4bb] Ligand building in real space
Hey Mohamed, I am not sure, if this is what you want, but you can import different PEG molecules from coot's "File-> Get monomer". A list of different length PEGs three letter codes can be found on page 1278 of this paper: Naschberger et al., (2016) http://doi.org/10.1107/S205979831601723X. I think you must have ccp4 installed, for this to work, but I am not 100% sure. Cheers, Johannes 2017-04-10 9:44 GMT+02:00 Mohamed Noor : > Dear all > > Is it possible to directly build a ligand in real space (in Coot?) and > then generate a SMILES string for restraint generation. I have some unknown > blobs in my density where they look like PEG molecules but these do not > really fit the density (local CC of 0.7). > > I am already using Polder and omit maps that confirm these are not noise. > > Thanks. > Mohamed >
[ccp4bb] Ligand building in real space
Dear all Is it possible to directly build a ligand in real space (in Coot?) and then generate a SMILES string for restraint generation. I have some unknown blobs in my density where they look like PEG molecules but these do not really fit the density (local CC of 0.7). I am already using Polder and omit maps that confirm these are not noise. Thanks. Mohamed
