 |
 |
I asked the PyMOL mailing list, and Thomas Holder had this solution that I thought might be useful for other people to know about: To get those points in as pseudoatoms, you could also simply place a CIF atom site header above the data and load it as a .cif file. data_foo loop_ _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.ignore_size_a _atom_site.ignore_size_b _atom_site.ignore_size_c 145.32307 113.91329 116.36907 0.44800 0.47168 0.80000 #7278cc 147.35472 113.65778 116.36907 0.44800 0.47168 0.80000 #7278cc 149.39126 113.87088 116.36907 0.44800 0.47168 0.80000 #7278cc 141.61303 115.28156 115.56962 0.44800 0.47168 0.80000 #7278cc The color will be ignored because # is the comment delimiter. The only issue is that all atoms will have the same (empty) identifiers, so in order to select individual atoms, run something like this: PyMOL> alter all, resi=index > On 21 Sep 2015, at 18:11, Paul Emsley <[log in to unmask]> wrote: > > > > On 21/09/2015 21:58, Suzanne wrote: >> I'm trying to export the dots generated by running HOLE in Coot on my protein and open them in pymol. With the latest version of Coot I can export a .dat file that seems to contain the coordinates of the dots, but I can't open it in pymol. One option that occured to me is to edit the .dat file to make a 'fake' PDB file with hydrogens at the coordinates where the dots were, but I wondered first if anybody has an easier way to do it. > > Dear Suzanne, > > Well done on finding the .dat file. > > This is a question for the Pymol list. It should be trivial to make a Graphical Object (as Coot would call it) from the dat file in PyMol. A few lines of code, I'd say. Send off a few lines of the .dat file and see what the come up with (I don't know how to do it.) I'd be interested to know the answer. I'm pretty sure that faking a PDB file is not the right way. > > Regards, > > Paul. > >