Re: [PyMOL] Discrepancy between select within and distance?

Hi, I thinks this is the expected behaviour 2013/5/19 asdf asdf > Hello, > > I'm measuring the distance between certain residues in an alignment and > I've noticed a discrepancy in the selections returned by the "select within > command" and the actual distances measured to the atoms returned

Re: [PyMOL] Discrepancy between select within and distance?

Hi, Folmer is correct on both accounts. First, "select" was selecting across various states into one multistate selection. Then, the distance command was operating on the first state, which is its default behavior. So, replace select asdf, 1MM2CA w. 5 of 2kgi///22/CA with select as

Re: [PyMOL] internal surface

Hi Yarrow, See demo #2 on the PyMOLWiki gallery page ( http://pymolwiki.org/index.php/Gallery). Cheers, -- Jason On Fri, May 10, 2013 at 5:42 PM, Yarrow Madrona wrote: > Hello pymol Gurus, > > I previously made a figure where the protien is cut in half and you can > see the ligand binding ca

[PyMOL] how to show ligand surface

I have a question I've never been able to figure out. If I have a pdb file with a ligand bound in a protein I can show the protein as a mesh or surface but I can't ever show the surface of the ligand. Any advice? What am I missing? Thank you very much. Yours &c. John --

Re: [PyMOL] how to show ligand surface

Try to extract the ligand from the protein, so you get two separate objects. Best Troels Emtekær Linnet 2013/5/20 John Quinn > I have a question I've never been able to figure out. If I have a pdb file > with a ligand bound in a protein I can show the protein as a mesh or > surface but I can'

Re: [PyMOL] how to show ligand surface

Hi Troels, I've tried that in the past (and just tried again to make sure) but it doesn't work for me. By the way, I'm running the latest open source version of PyMol installed via fink on a Mac Yours &c. John Quinn 133 Jay St. Albany, NY 12210 (518) 312-7033 jqu...@uchicago.edu On May 20,

Re: [PyMOL] how to show ligand surface

Hi, Extracting/copying the ligand is one way ( http://www.pymolwiki.org/index.php/Surface#Creating_a_Closed_Surface). You can also set surface mode (http://pymolwiki.org/index.php/Surface_mode) or flag a selection (http://www.pymolwiki.org/index.php/Flag). Cheers, -- Jason On Mon, May 20, 2013

Re: [PyMOL] how to show ligand surface

John, fetch 1rx1, async=0 set surface_mode, 3 as surface, org Cheers, -- Jason On Mon, May 20, 2013 at 3:21 PM, John Quinn wrote: > Hi Troels, > > I've tried that in the past (and just tried again to make sure) but it > doesn't work for me. > > By the way, I'm running the latest open sourc

Re: [PyMOL] how to show ligand surface

Thank you. That was perfect. I see that Mesh_mode works the same way. Yours &c. John Quinn 133 Jay St. Albany, NY 12210 (518) 312-7033 jqu...@uchicago.edu On May 20, 2013, at 4:21 PM, Jason Vertrees wrote: > Hi, > > Extracting/copying the ligand is one way > (http://www.pymolwiki.org/inde

[PyMOL] Label by selection identifier

Hello, This should be straightforward, Is it possible to label selections by their name? If I have a selection named "foo" and I say label foo, "foo", it of course labels all the atoms. Is it possible to get one label for the entire selection without using pseudoatoms? Jordan --