Re: [PyMOL] rejected atoms during alignment

not a great answer, but do you know about the object parameter > for the align command? I often type something like > > align struct1, struct2, object=alignment > > and then just look at which things were included/excluded. > > -michael > > On 8/3/06, Marc Bruning wrot

[PyMOL] rejected atoms during alignment

hello, is there any way to find out which atoms are discarded during the refinement cycles of the "align" command? regards, marc

[PyMOL] gui/viewer position

hello, is it possible to define the gui and viewer positions on startup separately? thanks, marc

Re: [PyMOL] setting correct bond length

try converting the coordinates into mol-format. On Friday 03 March 2006 13:05, Gerhardt, Stefan wrote: > Dear all, > > I am trying to display a bound azetidine ring, but pymol is drawing also a > bound between the C2 and C4 ring carbons. > > <<...OLE_Obj...>>bond length N-C 1.46Å, C-C 1.54Å a

Re: [PyMOL] (kein Betreff)

hello, is there a way to only select residues that are involved in polar contacts? thanks, marc

Re: [PyMOL] automated H-bond computation & visualization in pyMOL?

hello, is this feature accessible from the command line as well? cheers, marc On Monday 17 October 2005 22:16, Warren DeLano wrote: > Michael > > d/l a recent build http://delsci.com/beta > > and use the "find"->"polar contacts" option under the objects Action "A" > menu in the viewer window. >

[PyMOL] alignment question

hello, is there any possibility to get a list of the pairs of atoms that are matched using the align command? cheers, marc

Re: [PyMOL] select all aminoacids and not ligand

d are the same? > > and > > 2005/7/12, Marc Bruning : > > in case your ligand has a different chain id than your protein, you could > > use that to distinguish. > > > > On Tuesday 12 July 2005 11:59, Andrea Spitaleri wrote: > > > Hi all > > > is

Re: [PyMOL] select all aminoacids and not ligand

in case your ligand has a different chain id than your protein, you could use that to distinguish. On Tuesday 12 July 2005 11:59, Andrea Spitaleri wrote: > Hi all > is there any shortcut to select all aminoacid in a complex and not the > ligand? something like > select my, all and not "ligand" wh

[PyMOL] display variables

dear list, is it possible to distribute the pymol gui and the viewer between different display variables, say the gui to "display:0.0" and the viewer to "display:0.1"? regards, marc bruning

[PyMOL] pdb loader service

hello, is it possible to use the pdb loader in a *.pml style script? thanks, marc