[PyMOL] Getting object names

Hi all, I know that you can get ALL pymol object names by running cmd.get_names() but if you have objects in a group is there a way to get just the names of the objects under that group? Thanks, Bradley -- Bradley J. Hintze Graduate Student Duke University School of Medicine ---

[PyMOL] set sphere_scale question

Hi all, I have a question regarding the changing of sphere size in a PyMOL API. When I use the command as presented on the PyMOLwiki, namely: cmd.set ("sphere_scale", size=1, selection='', state=0, updates=1, log=0, quiet=1) I get an error saying set() got an unexpected keyword argument 'size'

Re: [PyMOL] Disappearing right-hand control panel

Thanks, putting the missing END element seemed to rectify the problem. On Sat, Dec 11, 2010 at 4:26 AM, Thomas Holder < spel...@users.sourceforge.net> wrote: > do you have END as last element of obj? This is required for LINES. > > Bradley Hintze wrote, On 12/10/10 19:25: > &g

Re: [PyMOL] Disappearing right-hand control panel

ure what the deal is. Bradley On Fri, Dec 10, 2010 at 12:11 PM, Jason Vertrees < jason.vertr...@schrodinger.com> wrote: > Hi Bradley, > > This sounds like a mobile video card problem. Are you on a laptop? > Perhaps one with an Intel GM45 card? What OS? > > Cheers, > > --

[PyMOL] Disappearing right-hand control panel

Hi, I'm using pymol 1.3 and I have a pml script. when I do a show as command the right-hand column disappears. I appears again if i puch escape to access the command line. Anyone have any idea what is going on here? Bradley -- Bradley J. Hintze Graduate Student Duke University School of Medicin

[PyMOL] dss

Is there a way i can call dss from a script? e.g. cmd.dss. -- Bradley J. Hintze Graduate Student Duke University School of Medicine 801-712-8799 -- Start uncovering the many advantages of virtual appliances and start usi

[PyMOL] find pairs?

I found this in the pymol user manule find_pairs DESCRIPTION "find_pairs" is currently undocumented. ## Is there anywhere that find_pairs has documentation or a good description?? -- Bradley J. Hintze Graduate Student Duke University School of Medicine 8

[PyMOL] More DSS questions

Hi, Is there more 'under the hood' to DSS? Specifically, is there a way one can see in some sort of output that a given oxygen is pointing to a given nitrogen? -- Bradley J. Hintze Graduate Student Duke University School of Medicine 801-712-8799 -

Re: [PyMOL] DSS

d > http://pymolwiki.org/index.php/WriteSS. > > Cheers, > > -- Jason > > On Tue, Jun 22, 2010 at 4:04 PM, Bradley Hintze > wrote: >> Hi all, >> >> Is there a way to get an output from PyMol's DSS command (like a dssp >

Re: [PyMOL] draw vector

, pos=[x2, y2, z2] > distance /pt1, /pt2 > set dash_gap, 0 > > You can also create CGO lines between two points, if you want. > > Cheers, > > -- Jason > > On Thu, Jul 22, 2010 at 11:58 AM, Bradley Hintze > wrote: >> Hi all, >> >> Can I draw a vector

[PyMOL] draw vector

Hi all, Can I draw a vector if I give two XYZ coords in pymol? e.g. draw_vector(x1, y1, z1, x2, y2, z2) Thanks, Bradley -- Bradley J. Hintze Graduate Student Duke University School of Medicine 801-712-8799 -- This SF.

[PyMOL] get coordinates

Hi all, Is there an easy way to get coordinates of a given atom? e.g. 'get_coordinates /model//A/ALA`76/CA' for the CA coordinates of resi 76 All the examples on the wiki use "iterate" to get the coordinates of a selection. Is there a simple way to get one coordinate of a given atom? -- Bradle

[PyMOL] DSS

Hi all, Is there a way to get an output from PyMol's DSS command (like a dssp output)? -- Bradley J. Hintze Graduate Student Duke University School of Medicine 801-712-8799 -- ThinkGeek and WIRED's GeekDad team up for t

[PyMOL] Select Residus on Surface

Is there a way to select only surface residues? -- Bradley J. Hintze B.S. Biochemistry Utah State University 801-712-8799 -- Crystal Reports - New Free Runtime and 30 Day Trial Check out the new simplified licensing optio

[PyMOL] importing in scripts

I am trying to import a BioPython module into a pymol script but pymol can' find it. When I import it from the DOS>python command line it imports fine. Obviously pymol isn't looking in the right place for the module. Is there a way to force pymol to look in the right place? -- Bradley J. Hintze B

[PyMOL] Show Dashes

When you have a measurement object in the panel you can show dashes using 'dashes' under the 'S' menu. I have a bunch of measurements grouped together on the panel (you can hide and chow the group). How can I have the show 'dashes' option in the 'S' menu of the whole group? -- Bradley J. Hintze B

[PyMOL] Tk and scripting

I am writing a script for PyMol and noticed you that PyMol freezes when you try to bring up your own Tkinter windows. Is there a way to get around this so I can get my Tk window up? -- Bradley J. Hintze Biochemistry Undergraduate Utah State University 801-712-8799

[PyMOL] Embedded Groups?

Hi all! I use the new group objects tool and love it. I was wondering if it is possible to create embedded groups; a group within a group? If not, can that function be added in later releases? -- Bradley J. Hintze Biochemistry Undergraduate Utah State University