Re: [Jmol-users] Displaying ligand environments

2014-01-09 Thread Robert Hanson
There are some new syntaxes that also make this particular task very easy. By the way, see the RCSB beta site, which has a new "Ligand in pocket" view. For example, the Ligand tab below the applet at http://ccnightly.rcsb.org/pdb/explore/jmol.do?structureId=1eve&bionumber=1 This utilizes the CON

[Jmol-users] Jmol 14.0.5/14.1.5

2014-01-09 Thread Robert Hanson
___JmolVersion="14.0.5" JmolVersion="14.0.5_dev_2014.01.09" bug fix: LCAOCartoon translucency broken bug fix: translucent backbone broken bug fix: pqr,p2n readers broken bug fix: isosurface map property xxx can fail if surface is a fragment that (somehow) has a point not associated with

Re: [Jmol-users] Displaying ligand environments

2014-01-09 Thread Glen van Ginkel
Thanks Maciek, That worked a treat! Glen On 09/01/14 12:01, Maciek Wójcikowski wrote: > Hi Glen, > > Have you tried double within function? I use following command to > display residues within 10A from any ligand: > > display within(groups,within(10,TRUE,*/2)) > > Note: receptor is model #1 and

Re: [Jmol-users] Displaying ligand environments

2014-01-09 Thread Maciek Wójcikowski
Hi Glen, Have you tried double within function? I use following command to display residues within 10A from any ligand: display within(groups,within(10,TRUE,*/2)) Note: receptor is model #1 and multiple ligands are in model 2 as frames. Change "*/2" to your ligand selection. Pozdrawiam, |

[Jmol-users] Displaying ligand environments

2014-01-09 Thread Glen van Ginkel
Hi all, After loading a PDB file I'm trying to restrict the view to the environment (surrounding residues) of a specific ligand. I'm able to select atoms within a given distance, but for amino acids that are truncated due to the distance cut-off I'd like to show the whole residue. Put another way,