Hi Thomas,
Thanks for clarifying this for me! Cheers, Joseph. Joseph S. Brock | PhD Researcher Drew Lab Department of Biochemistry and Biophysics Stockholm University ________________________________ From: Thomas Holder <thomas.hol...@schrodinger.com> Sent: Friday, 26 October 2018 3:41:40 PM To: Joseph Brock Cc: Jarrett Johnson; Pymol User list Subject: Re: [PyMOL] distance Hi Joseph, Thanks for the example, I can reproduce it! Not sure if this should be considered a bug, or just a misleading user interface. "involving side chains" really means "side chains within selection". There are none if you only select the ligand. If I instead click on "to other atoms in object" I'll get the expected result. You might also find one of these command line options useful: distance polar1, (resn GSH), not (resn GSH), mode=2 distance polar2, (resn GSH), (sidechain), mode=2 distance polar3, (resn GSH), not (solvent), mode=2 Cheers, Thomas > On Oct 26, 2018, at 2:34 PM, Joseph Brock <joseph.br...@dbb.su.se> wrote: > > Hi again Jarrett, > > I have built the latest version from git (PyMOL 2.3.0a0 Open-Source) on my > system. > > The behaviour is still there, but I realise that this it is now only when the > selection is a ligand. For instance trying to find polar contacts between a > ligand and sourrounding side chains. If I make a selection involving both the > ligand and side chains of interest first however, it works fine. > > It is an easy workaround, but i would be curious to know if you can replicate > it on your system. For instance if you fetch pdb id: 1EEM and make a > selection from resname GSH, then try to find polar contacts involving side > chains from the action menu, you should see what I mean. > > Cheers, > Joseph. > > > Joseph S. Brock | PhD > Researcher > Drew Lab > Department of Biochemistry and Biophysics > Stockholm University > From: Joseph Brock <joseph.br...@dbb.su.se> > Sent: Friday, 26 October 2018 8:57:44 AM > To: Jarrett Johnson > Cc: Pymol User list > Subject: Re: [PyMOL] distance > > Thanks Jarrett! I will try that! > > Cheers, > Joseph. > > > Joseph S. Brock | PhD > Researcher > Drew Lab > Department of Biochemistry and Biophysics > Stockholm University > From: Jarrett Johnson <jarrett.john...@schrodinger.com> > Sent: Friday, 26 October 2018 12:23:46 AM > To: Joseph Brock > Cc: Pymol User list > Subject: Re: [PyMOL] distance > > Built from source (github repo). > > On Thu, Oct 25, 2018 at 5:56 PM Joseph Brock <joseph.br...@dbb.su.se> wrote: > Hi Jarret, > > Thanks for the reply! > > Unfortunately so ;( > > Did you build from source or install via apt-get? > https://pymolwiki.org/index.php/Linux_Install > > Cheers, > Joseph. > > > Joseph S. Brock | PhD > Researcher > Drew Lab > Department of Biochemistry and Biophysics > Stockholm University > From: Jarrett Johnson <jarrett.john...@schrodinger.com> > Sent: Thursday, 25 October 2018 11:34:28 PM > To: Joseph Brock > Cc: Pymol User list > Subject: Re: [PyMOL] distance > > Hi Joseph, > > I'm not able to replicate that on my end using open-source PyMOL 2.2 on > Ubuntu 16.04. Does this behavior also occur for molecules fetched straight > from the PDB? > > Jarrett J. > > On Thu, Oct 25, 2018 at 4:44 PM Joseph Brock <joseph.br...@dbb.su.se> wrote: > Hi pymol users, > > I've observed a weird behaviour with the open source pymol (v 1.7.2.1-2.2 > running on ubuntu 16.04). > > When I try to create some distance objects either via the command line of the > actions menu, an object is created but no dashed lines appear. When I "zoom" > this object it is very far in space from the atoms I selected to make the > distances between, and there is still nothing I can do to make the dashed > lines appear. > > If anyone can let me know what I'm doing wrong I would appreciate it! > > Cheers, > Joseph. > > > Joseph S. Brock | PhD > Researcher > Drew Lab > Department of Biochemistry and Biophysics > Stockholm University > > -- > Jarrett Johnson > PyMOL Developer > Schrödinger, Inc. -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc.
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