Re: [PyMOL] New to PyMol. Want to extract sequence from .pse file w/ colors.

Hi Shane, I have a script which saves a colored sequence in HTML format. See attachment. Example usage: run save_colored_fasta.py save_colored_fasta seq.html It should be possible to copypaste the colored sequence from your browser to excel. Cheers, Thomas Shane Neeley wrote,

[PyMOL] Little coordinate cross in Pymol?

Dear all, is it possible to show in Pymol a little coordinate cross with axes x,y,z, for example like in VMD, please? I have a protein made from dummy atoms and there is no unit cell. I just want to show clearly which plane is shown when presenting the model in my document. Thank you for your

Re: [PyMOL] Little coordinate cross in Pymol?

http://pymolwiki.org/index.php/Axes -David On Feb 27, 2012, at 5:38 AM, Gudrun Lotze gudrun.lo...@gmx.net wrote: Dear all, is it possible to show in Pymol a little coordinate cross with axes x,y,z, for example like in VMD, please? I have a protein made from dummy atoms and there is no

Re: [PyMOL] Little coordinate cross in Pymol?

Dear all, I used the following script David pointed out: from pymol.cgo import * from pymol import cmd w = 0.06 # cylinder width l = 0.75 # cylinder length h = 0.25 # cone hight d = w * 1.618 # cone base diameter obj = [CYLINDER, 0.0, 0.0, 0.0, l, 0.0, 0.0, w, 1.0, 0.0, 0.0, 1.0, 0.0,

Re: [PyMOL] pymol 1.4.1 (incentive), segfault upon help-about

Hi Jason, I just installed pymol 1.5.0.3 on our linux machines and the segfault in libtcl8.5.so upon help-about is still present. Do you have any hint when this will be fixed? Best regards, Joachim -- Dr. rer. nat. Joachim Greipel Med. Hochschule Hannover Biophys. Chem. OE 4350

Re: [PyMOL] Little coordinate cross in Pymol?

Hi Gudrun, On 02/27/2012 01:36 PM, Gudrun Lotze wrote: The axes appear, but the screen in pymol is now split into two sections with the cross covering one part. Is there a chance to move the cross closer to the model in one screen section? A bit like shown in picture on page

Re: [PyMOL] pymol 1.4.1 (incentive), segfault upon help-about

Try install tkinter Tkinter uses tcl 8.4 (something...) Troels Emtekær Linnet Lyongade 24. 4.mf, 2300 København S Mobil: +45 60210234 2012/2/27 greipel.joac...@mh-hannover.de Hi Jason, I just installed pymol 1.5.0.3 on our linux machines and the segfault in libtcl8.5.so upon help-about

Re: [PyMOL] Little coordinate cross in Pymol?

Dear Gudrun, I have no experience with PyMOL on Mac. Maybe this helps: http://pymolwiki.org/index.php/Mouse_Controls Deselecting objects does not help, because by default you transform in camera space, which affects all objects. What you need is transformation in model space, which is achieved

[PyMOL] Question about ray tracing, set_view, surface smoothness

Dear all, I wish to ray trace my object so it looks nice. I have chosen a mesh as surface representation. I did viewport 1024, 768 ray 1024, 768 But the mesh is black afterwards and not anymore blue. Is there a chance to keep the color and have less dominant lines for the mesh? Is there a

Re: [PyMOL] Question about ray tracing, set_view, surface smoothness

Hi Gudrun, But the mesh is black afterwards and not anymore blue. You may want to check your light position, or try a slighter blue. Is there a chance to keep the color and have less dominant lines for the mesh? I'm not artistically skilled enough to know about less dominant lines, but the