Re: [PyMOL] Increase sphere size for heavy element
Hi Martin, PyMOL alter elem W, vdw=2.0 PyMOL rebuild Cheers, Thomas Martin Hediger wrote, On 02/26/13 08:38: Hi PyMOL users If I display these coordinates HETATM 38 C LIG 2 1.535 2.288 -4.156 1.00 0.00 C HETATM 39 C LIG 2 2.284 1.535 -3.066 1.00 0.00 C HETATM 40 O LIG 2 3.406 2.362 -2.714 1.00 0.00 O HETATM 41 C LIG 2 1.426 1.234 -1.850 1.00 0.00 C HETATM 42 S LIG 2 -0.260 0.689 -2.100 1.00 0.00 S HETATM 43 C LIG 2 1.886 1.450 -0.593 1.00 0.00 C HETATM 44 S LIG 2 0.838 1.262 0.813 1.00 0.00 S HETATM 45 C LIG 2 3.318 1.872 -0.336 1.00 0.00 C HETATM 46 C LIG 2 4.139 1.803 -1.624 1.00 0.00 C HETATM 47 W LIG 2 -1.132 -0.004 0.041 1.00 0.00 W HETATM 48 O LIG 2 0.155 -1.665 0.118 1.00 0.00 O HETATM 49 C LIG 2 0.721 -3.870 -0.567 1.00 0.00 C HETATM 50 C LIG 2 0.384 -2.594 -0.826 1.00 0.00 C HETATM 51 C LIG 2 -5.606 -3.611 -1.000 1.00 0.00 C HETATM 52 O LIG 2 -6.664 -4.080 -0.564 1.00 0.00 O HETATM 53 N LIG 2 -4.607 -4.417 -1.426 1.00 0.00 N using Preset/Ball-and-stick, the tungsten atom is drawn with a very small radius. Can this radius be increased? Thanks Martin -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_feb ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Display style for partial bond
Hi Martin, only distance measures can draw dashed lines in PyMOL, so try this: unbond elem W, elem C show sticks show sphere, elem W distance transbonds, elem W, elem C hide label set dash_round_ends, off set dash_radius, 0.2 set dash_length, 0.4 set dash_gap, 0.15 ray The dashes will display as nice cylinders when ray traced and also with the new shader rendering in PyMOL 1.5 (set use_shaders). Cheers, Thomas Martin Hediger wrote, On 02/26/13 09:57: Dear PyMOL Users If you load these coordinates in PyMOL HETATM1 W LIG 1 -1.357 -0.079 0.052 1.00 0.00 W HETATM2 C LIG 1 -0.713 -1.686 1.008 1.00 0.00 C HETATM3 C LIG 1 -0.323 -1.855 -0.270 1.00 0.00 C HETATM4 H LIG 1 -0.664 -2.180 1.970 1.00 0.00 H HETATM5 H LIG 1 -0.441 -2.597 -1.043 1.00 0.00 H you'll see that a bond between W and C is drawn. However, this is supposed to be a transition state, so a dashed bond would be more appropriate. Can this somehow be drawn? Thanks, Martin -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_feb ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] How to display .mtz files and work with them
Hi Matthias, I can at least try and answer some of your questions: 1. You can simply click on the command button (rhs side grey window... Command Builder Volume) to get back to the command info you want. Alternatively type in your commands into the viewer window and use escape to see the details 2. At this stage I'm not sure you can generate the volume around your protein. The way to get around this is to generate symmetry related molecules and look at one of those in the unit cell. (Jason will know more) 3. Best to generate 2fofc and fofc maps in say ccp4 and display these (but not sure if you can use the volume or just the classical mesh) I too would like to be able to do this to use the great graphics output from pymol Hope this helps Joel From: Matthias Haffke [mailto:matze_haf...@hotmail.com] Sent: Wednesday, 27 February 2013 9:17 a.m. To: pymol-users@lists.sourceforge.net Subject: [PyMOL] How to display .mtz files and work with them Dear all, I am having some trouble working with PyMOL and the new feature of loading and displaying .mtz files. Sorry for the number of questions (and sorry if most seem trivial...), but I couldn't find the answers in the PyMOLWiki and not in the Schrodinger documentations. PyMOL Version is 1.5.0.5 and it's running on Win7 Prof 64 bit. 1.) When loading a .mtz file, you start with the new volume representation. Options for color gradients, sigma levels, etc. are displayed in a nice graph in the command line window - but the command line is gone and I don't get any feedback about commands I write in PyMOL. How do I turn this graphical representation of the sigma levels color gradients on and off? 2.) The volume is represented for one unit cell - and for one unit cell only. I would like to display the density just around one molecule in the unit cell or around a symmetry mate OUTSIDE the unit cell - which is the command to do so? Things like map_trim don't work (which is not a surprise - I am obviously not displaying a map as one used to do in the older PyMOL versions). You can't align the group, which is created by loading a .mtz file to a selection or molecule by using the drop down menus or I couldn't find any other way to limit the map to one molecule or one chain in of my .pdb file. Any help on this is greatly appreciated. 3.) What I basically want to do (in other words): Open a .pdb file. Open a .mtz file. Display the electron density at 2.0 sigma around one specific chain or around one specific symmetry mate of my molecule. Can't be that difficult, can it? ;-) Many thanks for any help! Matthias -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_feb___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
