Re: [PyMOL] Labeling CGO objects

Hi Warren | CGO labels are currently insufficient and need work. Right now, the only | way to access high-quality labels (using scalable TrueType fonts) is to | create fake atoms and then label them. What's the recommended way to do this? Can you just put them anywhere you like, irrespective of

Re: [PyMOL] Pymol cone shape?

Hi William You can do it, or something that's as close to a cone as you could wish for, by using a triangle fan. The apex of the fan is the top of the cone and then you just add points around the base of the cone at whatever granularity you like. That would take some programming though, but it's

Re: [PyMOL] Installing pymol (again)

Brian Goodfellow suggested I use macpymol. I did and it Just Works. I don't know how I managed to overlook that link the first time round... Terry

[PyMOL] Installing pymol (again)

I'm trying to install pymol on a MacBook Pro (intel). I've tried three approaches and hit problems on each of them. After several hours of effort I thought I'd ask here. Details below. I'd be happy to be able to build in any way, I guess the problem in Method 1 is probably the easiest to solve. T

Re: [PyMOL] transparency and cgo

> "Greg" == Grégori Gerebtzoff writes: Greg> You can also embed the transparency (ALPHA) value into your cgo file Greg> like this: Thanks Greg. I've just spent a couple of hours playing with this. Regards, Terry

[PyMOL] Launching

I've just installed pymol 0.99rc6 on Mac OS X (10.3.9). Because I'm still running Panther and I no longer have the system python installed (instead I have 2.4) I couldn't use macpymol-0_99rc6.tar.gz as pymol no longer comes with its own copy of python. macpymol-0_99rc6.tar.gz fails trying to load s

Re: [PyMOL] transparency and cgo

> "Zheng" == Zheng Yang writes: Zheng> Try this: set cgo_transparency, VALUE, CGO-OBJECT NAME Zheng> e.g. set cgo_transparency, 0.5, Sphere Hi Zheng Thanks for your answer, that works well (note for others: pymol > 0.99 seems required, the command is not recognized under 0.98). Terry

[PyMOL] transparency and cgo

Is there any way to specify / produce transparency when using CGO in pymol? It doesn't look like it, but I thought I'd ask Terry

[PyMOL] Small problem in examples/devel/cgo_plane.py

The following is from the end of examples/devel/cgo_plane.py: cmd.set('auto_zoom', 0, quiet=1) auto_zoom = cmd.get('auto_zoom') cmd.load_cgo(obj,'cgo_plane') cmd.set('auto_zoom', auto_zoom, quiet=1) Part of the intention seems to be to save and restore the value of auto_zoom. If t

[PyMOL] Lists vs Tuples inconsistency in cmd.load_cgo()

I spent quite a bit of time last night chasing down the following. This: cmd.load_cgo([SPHERE, 0.0, 0.0, 0.0, 1.0], 'a') puts a sphere on the screen as expected. But this: cmd.load_cgo((SPHERE, 0.0, 0.0, 0.0, 1.0), 'a') seemingly has no effect at all. I.e., if you pass a tuple instead of a

[PyMOL] selecting cgo objects with the mouse

I have a plugin that creates a collection of CGO objects. I'm wondering if it's possible to allow the user to select a CGO with the mouse - and if so, how I'd go about doing it. Regards, Terry

Re: [PyMOL] Question on rotation

Hi Tsjerk > "Tsjerk" == Tsjerk Wassenaar writes: Tsjerk> There's a bit more to it. In the pymol view, the camera is located Tsjerk> at the origin, so to rotate your coordinates you first have to move Tsjerk> the center to the origin, do the rotation and move the thing Tsjerk> back. I've scrip

[PyMOL] Question on rotation

I wrote a pymol plugin that produces a bunch of cgo. The images I generate have a cube drawn around them. I've been asked if it's possible to allow the user to initially rotate the image to their heart's content and then have the plugin draw the surrounding cube. I.e., once the image is rotated, t

RE: [PyMOL] Producing publication quality images

Thanks Warren, I'll try that. I got two other replies, neither mentioning the 300dpi arg to png. If that isn't recognized, I'll upgrade. Terry

[PyMOL] Producing publication quality images

Hi. I'm wondering if there's a way to make pymol produce high-quality images suitable for publication. I've used ray/png to produce images, but the person I pass them on to tells me they're only 50 to 100 dpi, and they're wanting 300 dpi if possible. Is there a way to do this in pymol? Or can I e

RE: [PyMOL] Drawing surfaces in pymol?

| This isn't really something PyMOL was designed to do. You could construct | such a surface using Python CGO facility, but that means doing the | tesselation, surface normal calculation, and any culling yourself. Thanks. Is this what you do already in pymol to make surfaces that envelop points?

[PyMOL] Drawing surfaces in pymol?

I've been using PyQt/Coin/SoQt/pivy to draw surfaces using SoNurbsSurface. I'm wondering if something like this is possible in pymol? I.e., I specify a set of points in 3D space and use pymol to lay an interpolated surface over them. I don't want the surface to fully envelop the points in the way

[PyMOL] ray

Here's another question about ray. At what level in pymol is it implemented? Is it part of what's provided by OpenGL, or done at some higher/other level? Terry

Re: [PyMOL] Small problem or inconsistency in showing cgo objects?

| Seems that "hide" means roughly the same as setting the | representation to "none". | | "Enable/disable" are the equivalents to clicking on the "name-button". | | So, if you change the test script to have "cmd.disable('two')" at the | end instead of 'hide', then it seems to do what you want

[PyMOL] Small problem or inconsistency in showing cgo objects?

Hi. I've run into a slight pymol UI problem with cgo objects and I'm wondering if I should be doing something differently or if it's a pymol idiosyncrasy. Here's a script: from pymol.cgo import * from pymol import cmd one = [ SPHERE, 0.0, 0.0, 0.0, 1.0 ] two = [ SPHERE, 2.0, 0.0,

Re: [PyMOL] grid/cube representation

| | As a follow up to my last email asking whether there is a way to make 3D | grid representations of molecules I have found a picture of the kind | of thing I am after. Is there a way to make anything similar to this | http://www.techfak.uni-bielefeld.de/ags/ai/projects/docking/images/align

[PyMOL] Embedding pymol

While I've got your attention Is it possible to embed a pymol window into a bigger independent application? I am writing some code using PyQt and various other things (like PyOpenGL, Open Inventor, pivy), and it would be nice to be able to be able to pop a window with pymol in it (if that's t

RE: [PyMOL] Using the Pymol Run command

Hi Warren and Gilleain - thanks for your rapid answers. For now I am simply using 'run' on the command line and it works fine. | Gilleain is right on about the run command. On Windows and linux, you | can also create .pym files that will specifically open into PyMOL. I don't understand this. |

[PyMOL] Using the Pymol Run command

there is another way to do what I'm trying to achieve. Without trying to understand too much of the pymol source, I can see it does use execfile under some circumstances. Is there some recommended way to run a file of code? Maybe my code should simply call execfile itself? Thanks for any h