Re: [PyMOL] bond connection file

Hi Vishwas, atom connectivity is the same for all states unless you have a "discrete" object. Try this: PyMOL> set connect_mode, 1 PyMOL> load file.pdb, discrete=1 Cheers, Thomas Vishwas Vasisht wrote, On 10/05/12 08:59: > Hi Thomas, > > Thanks, it works for single frame. But when I u

Re: [PyMOL] bond connection file

Does every MODEL ENDMDL have a unique Connection list? Can you show me your PDB file? Jordan On Oct 5, 2012, at 1:59 AM, Vishwas Vasisht wrote: > Hi Thomas, > > Thanks, it works for single frame. But when I use multiple frame (using > MODEL and ENDMDL), the connections which i speci

Re: [PyMOL] I just built pymol, comes up but hangs on any attempt to view a "test" pdb.

Mike, Many distros have PyMOL already in their package management system. Have you tried that first? I suggest downloading the latest code, v1.5.0.4, from the open-source project page, if you want to build by hand. To build, you need Python 2.7 or later and the process is very simple: sudo pyth

Re: [PyMOL] I just built pymol, comes up but hangs on any attempt to view a "test" pdb.

> From: jason.vertr...@schrodinger.com > Date: Fri, 5 Oct 2012 09:08:44 -0500 > Subject: Re: [PyMOL] I just built pymol, comes up but hangs on any attempt to > view a "test" pdb. > To: marchy...@hotmail.com > CC: li...@cowsandmilk.net; pymol-users@list

Re: [PyMOL] I just built pymol, comes up but hangs on any attempt to view a "test" pdb.

Hi Mike, >> I suggest downloading the latest code, v1.5.0.4, from the open-source >> project page, if you want to build by hand. >> > see comments in my last post, I think that is what I did. Although > autoreconf may not have helped anything. I see the confusion now. We'll update SourceForge on

Re: [PyMOL] I just built pymol, comes up but hangs on any attempt to view a "test" pdb.

> From: jason.vertr...@schrodinger.com > Date: Fri, 5 Oct 2012 09:36:29 -0500 > Subject: Re: [PyMOL] I just built pymol, comes up but hangs on any attempt to > view a "test" pdb. > To: marchy...@hotmail.com > CC: li...@cowsandmilk.net; pymol-users@lists

Re: [PyMOL] Shader issues and automatic disabling (was Re: I just built pymol, comes up but hangs on any attempt...)

Hi Ben, >> If your machine does have shader issues and they don't automatically >> disable, please let us know. > > What would be the symptoms/output if this is happening? > > I get occasional reports from our users with errors like this: > > CShaderPrg_New-Error: vertex shader compilation faile

[PyMOL] Shader issues and automatic disabling (was Re: I just built pymol, comes up but hangs on any attempt...)

Hi Jason, > If your machine does have shader issues and they don't automatically > disable, please let us know. What would be the symptoms/output if this is happening? I get occasional reports from our users with errors like this: CShaderPrg_New-Error: vertex shader compilation failed name='d

Re: [PyMOL] 3D projector for low cost 3D Protein Cave

Hello stereophiles, many thanks to Jason Vertrees, Roger Rowlett and Sabuj Pattanayek for sending me information about their 3D stereo beamer setup. I recently purchased the following equipment and was not even sure it would work: - Optoma GT750, 1280 x 720 pixel resolution, 3000 ansi lumen

Re: [PyMOL] Shader issues and automatic disabling (was Re: I just built pymol, comes up but hangs on any attempt...)

Hi Jason, > The key seems to be, > > > PyMOLShader_NewFromFile-Warning: default shader files not found, loading > > from memory. > > We load shaders from disk, but when they're not found we just read in > some basic default shaders from code, which is what this is doing. Did > you move or cha

Re: [PyMOL] Shader issues and automatic disabling (was Re: I just built pymol, comes up but hangs on any attempt...)

Ben, > Ah, I bet this is because they are running it via X-forwarding over an > ssh tunnel. I'm pretty certain that one of the reports came from a user > running PyMOL this way, and I can duplicate the error messages running over > a tunnel. > > Is this actually going to break anything? Yes -- vo

[PyMOL] ray_trace_mode 1

Hi all, I would like to use ray_trace_mode 1 to render some structures. However, I am also using isomeshes within the same picture and do not want them to have a black outline. Is there any way to have the black outline only for specified objects or to make them transparent in isomeshes? Ch

Re: [PyMOL] Shader issues and automatic disabling (was Re: I just built pymol, comes up but hangs on any attempt...)

Hi Jason, > > Ah, I bet this is because they are running it via X-forwarding over an > > ssh tunnel. I'm pretty certain that one of the reports came from a user > > running PyMOL this way, and I can duplicate the error messages running over > > a tunnel. > > > > Is this actually going to break any

Re: [PyMOL] ray_trace_mode 1

Hi Arne, Unfortunately, ray_trace_mode is a global setting. You get the gain on all objects. I agree is looks poor on isomeshes. We should consider making ray_trace_gain object/atom level. Cheers, -- Jason On Fri, Oct 5, 2012 at 2:26 PM, Arne Dieckmann wrote: > Hi all, > > I would like to use

Re: [PyMOL] 3D projector for low cost 3D Protein Cave

On Fri, Oct 5, 2012 at 3:48 PM, Bradford R. Battey, Jr. wrote: > On Oct 5, 2012, at 4:33 PM, Sabuj Pattanayek wrote: > >> We've tried the Asus VG278H with the built-in emitter and the nvidia >> 3d vision v2 goggles (one pair included with the monitor) in Linux and >> it works without the need for