[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: It crates vectors as shown

Re: [PyMOL] Disappearing right-hand control panel

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, -- Jason On Thu, Dec 9, 2010 at 11:13 AM, Bradley Hintze

[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

[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

Re: [PyMOL] DSS

. Cheers, -- Jason On Tue, Jun 22, 2010 at 4:04 PM, Bradley Hintze bradle...@aggiemail.usu.edu wrote: 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

[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

Re: [PyMOL] draw vector

=[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 bradle...@aggiemail.usu.edu wrote: Hi all, Can I draw a vector if I give two XYZ coords in pymol? e.g

[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? -- Bradley

[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

[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

[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

[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