Re: [PyMOL] CONECT table

http://www.pymolwiki.org/index.php/Connect_mode -David > On Oct 6, 2014, at 6:35 PM, Markus Heller wrote: > > Hello, > > How can I get PYMOL to use the CONECT table from a PDB file? My protein is > glycosylated, and I'd like to properly and automatically display the > glycosides including t

[PyMOL] CONECT table

Hello, How can I get PYMOL to use the CONECT table from a PDB file? My protein is glycosylated, and I'd like to properly and automatically display the glycosides including their linkage to the protein. Thanks and Cheers Markus -- Markus Heller, Ph.D. NMR Scientist CDRD - The Centre for Drug

Re: [PyMOL] Color according to RMSD

Hi Cedric, The first part is numeric inaccuracy. You get all atomic rmsds in the range of 0 - 1e-12 or so. Spectrum colors according to the extent of this range. For the other one, note that the RMSD (mean sum of MSDs) is pretty low. Usually, it's due to a few residues that don't align perfectly,

[PyMOL] Select residues involved in H-bonds

Hi all, Is there an easy way to first detect H-bonds, either by using the distance command or a something a bit more elaborate (e.g. along the lines of http://www.pymolwiki.org/index.php/Displaying_Biochemical_Properties#Hydrogen_bonds_and_Polar_Contacts) *and* automagically select all residues

[PyMOL] Color according to RMSD

Hey :) In response to an earlier question regarding coloring objects according to per residue RMSD, I wrote a small routine to color according to atom RMSD, after an alignment. Maybe it'll be of any use to someone... The script performs an alignment and then gets the corresponding atoms, for whic

Re: [PyMOL] Help with rms_cur command

Doh! Thanks. From: David Hall [mailto:li...@cowsandmilk.net] Sent: Monday, October 06, 2014 1:00 PM To: Soisson, Stephen M Cc: Subject: Re: [PyMOL] Help with rms_cur command almost definitely is http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg1.html -David On Mon, Oct

Re: [PyMOL] Help with rms_cur command

almost definitely is http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg1.html -David On Mon, Oct 6, 2014 at 12:17 PM, Soisson, Stephen M < stephen_sois...@merck.com> wrote: > Hi everyone- > > > > I’m having a few issues with the rms_cur command that I am hoping someone > can h

[PyMOL] Help with rms_cur command

Hi everyone- I'm having a few issues with the rms_cur command that I am hoping someone can help with. I've pre-aligned several structures using 2 of 3 chains for the alignment. I now wish to calculate the rmsd over just a portion of the third chain without doing any further alignment. It loo

Re: [PyMOL] [gmx-users] constraint and restraints

Hi Niyaz, In pymol you can try this (assuming your proteins are called proteinA and proteinB): import numpy d = numpy.array(cmd.get_model("proteinA").get_coord_list()) d -= numpy.array(cmd.get_model("proteinB").get_coord_list()) d = (d**2).sum(axis=1).tolist() tmp = list(d) alter proteinA, b=tmp.