[Rdkit-discuss] problems with alignment (py3Dmol + rdkit, jupyter notebook)

dear all i am trying to align molecules read from a *sdf file (list of conformers) against another molecule (reference - a crystal structure), also read from a *sdf file and make a nice 3d picture in jupyter notebook as shown in: http://nbviewer.jupyter.org/github/greglandrum/rdkit_blog/

Re: [Rdkit-discuss] interactive py3Dmol in jupyter notebook - not all py3Dmol.view() are visible

> > On Tue, Mar 28, 2017 at 4:06 PM, gosia olejniczak < > gosia.olejnic...@gmail.com> wrote: > >> dear Greg, >> >> thank you for your prompt response, >> yes, that notebook works just fine, >> however if i try to call py3Dmol.view() many more times, only

[Rdkit-discuss] interactive py3Dmol in jupyter notebook - not all py3Dmol.view() are visible

hello, i'm using rdkit with py3Dmol in jupyter notebook, as in this example: http://nbviewer.jupyter.org/github/greglandrum/rdkit_blog/bl ob/master/notebooks/Trying%20py3Dmol.ipynb is there a limit of how many py3Dmol.view() frames can be in one notebook? i'm asking because it seems that jupyter

Re: [Rdkit-discuss] interactive py3Dmol in jupyter notebook - not all py3Dmol.view() are visible

/master/notes_m1.ipynb best regards, gosia 2017-03-28 16:02 GMT+02:00 Greg Landrum <greg.land...@gmail.com>: > I may not have understood the question correctly: when I open that page > all frames are active. > > On Tue, Mar 28, 2017 at 3:56 PM, gosia olejniczak < > gosia.ole

[Rdkit-discuss] RMSD value between two non-covalent molecular complexes

dear RDKit experts, is it possible to calculate RMSD value between two non-covalent molecular complexes? For instance: complex1: X(conformer1) + H2O complex2: X(conformer2) + H2O i tried GetBestRMS and GetO3A.Align but the program clearly neglects H2O and calculates the RMSD only between

Re: [Rdkit-discuss] RMSD value between two non-covalent molecular complexes

rmsd values seem to include h2o; also h2o are drawn with py3Dmol); best regards, gosia 2017-06-21 16:37 GMT+02:00 gosia olejniczak <gosia.olejnic...@gmail.com>: > Hi Paolo, > > Thank you for the prompt answer! > > i'll try it out, but: > - the whole complex "X+h

[Rdkit-discuss] starting 3D structures in conformer generation

dear RDKit experts, i have a question about conformer generation, maybe best posed on an example: i'm working with macrocycles which have few amide groups. As in each amide group H(-N) and O(=C) atoms can have two positions with respect to a rigid part of a molecule (amide groups are direct