[PyMOL] Loading multiple ligands into a single view
Hello all, I have a *.sdf (it can be a *.mol2 if that makes it easier) that contains multiple ligands. I'd like to open this one file and see them all at once. It currently loads each ligand into its own state. Is there a way to over-ride this behaviour? Tom -- Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)! Finally, a world-class log management solution at an even better price-free! Download using promo code Free_Logger_4_Dev2Dev. Offer expires February 28th, so secure your free ArcSight Logger TODAY! http://p.sf.net/sfu/arcsight-sfd2d___ 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] colors and font size while ray tracing
Hi Madhavi, with regards to your first question: I usually add text after rendering the stereo figures. That gives much better control and has the advantage that label come out cleaner. Look into Canvas, Photoshop or GIMP to do this. As an additional tip you can control the depth of the labels this way as well. Lets say you want to label Leu76 in the back of the figure, create one label, copy it to the other panel and place the same part of the text on the same atom or point of the residue you want to label. Group the labels and move them to an unobstructive position. Repeat for the other labels. Spheres: Tough to tell, may be you inadvertently changed the depth queue settings and the spheres got lighter. Did the the rest of the figure change as well? HTH Carsten -Original Message- From: Nalam, Madhavi [mailto:madhavi.na...@umassmed.edu] Sent: Thursday, January 20, 2011 2:36 PM To: 'pymol-users@lists.sourceforge.net' Subject: [PyMOL] colors and font size while ray tracing Hello: I am trying to generate stereo figures for my manuscript. When I try to ray trace at higher resolution, the font size (I use label_font_id=4) is becoming very small. If I use any fonts from the settings tab, the font size doesn't change with ray tracing. If I am correct, many journals prefer Helvitica/Arial fonts for the publication quality figures. So my question is are the fonts found in the settings preferred by the journals? If not, can anyone please tell me what can be done to keep the font size from decreasing during ray tracing? Also, I have vdW spheres shown as dots in the figure. The color of the dots for the vdW spheres is very light after I ray trace the figure. Last week when I ray traced the figure from the same PyMOL session, the colors are much darker!! As far as I know, I haven't changed anything in the session file. So can anyone please tell me how to increase the darkness of the vdW spheres? I use PyMOL version 1.3.x on Windows. Thanks in advance, Madhavi --- --- Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)! Finally, a world-class log management solution at an even better price- free! Download using promo code Free_Logger_4_Dev2Dev. Offer expires February 28th, so secure your free ArcSight Logger TODAY! http://p.sf.net/sfu/arcsight-sfd2d ___ 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 -- Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)! Finally, a world-class log management solution at an even better price-free! Download using promo code Free_Logger_4_Dev2Dev. Offer expires February 28th, so secure your free ArcSight Logger TODAY! http://p.sf.net/sfu/arcsight-sfd2d ___ 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] Loading multiple ligands into a single view
Hello Tom, On Fri, 21 Jan 2011 15:28:26 +1100 Tom Dupree t.dup...@unsw.edu.au wrote: Hello all, I have a *.sdf (it can be a *.mol2 if that makes it easier) that contains multiple ligands. I'd like to open this one file and see them all at once. It currently loads each ligand into its own state. Is there a way to over-ride this behaviour? You don't need to over-ride the loading behaviour. You can simply set the all_states variable to 1 (or on): set all_states, 1 (or use the Settings - Edit all menu item). Cheers, Rob -- Robert L. Campbell, Ph.D. Senior Research Associate/Adjunct Assistant Professor Botterell Hall Rm 644 Department of Biochemistry, Queen's University, Kingston, ON K7L 3N6 Canada Tel: 613-533-6821Fax: 613-533-2497 robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc -- Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)! Finally, a world-class log management solution at an even better price-free! Download using promo code Free_Logger_4_Dev2Dev. Offer expires February 28th, so secure your free ArcSight Logger TODAY! http://p.sf.net/sfu/arcsight-sfd2d ___ 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] Loading multiple ligands into a single view
On Fri, 21 Jan 2011 10:10:02 -0500 Robert Campbell robert.campb...@queensu.ca wrote: Hello Tom, On Fri, 21 Jan 2011 15:28:26 +1100 Tom Dupree t.dup...@unsw.edu.au wrote: Hello all, I have a *.sdf (it can be a *.mol2 if that makes it easier) that contains multiple ligands. I'd like to open this one file and see them all at once. It currently loads each ligand into its own state. Is there a way to over-ride this behaviour? You don't need to over-ride the loading behaviour. You can simply set the all_states variable to 1 (or on): set all_states, 1 (or use the Settings - Edit all menu item). I could have added that you can set this variable specifically for one (or more) objects. Say you have a set of structures that you want to see all at once (we'll call it multi), but you have another object with multiple states, but you only want to see those one at a time and step through them (we'll call it single), then you can set the above variable to 1 for just the one object: set all_states, 1, multi set all_states, 0, single Cheers, Rob -- Robert L. Campbell, Ph.D. Senior Research Associate/Adjunct Assistant Professor Botterell Hall Rm 644 Department of Biochemistry, Queen's University, Kingston, ON K7L 3N6 Canada Tel: 613-533-6821Fax: 613-533-2497 robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc -- Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)! Finally, a world-class log management solution at an even better price-free! Download using promo code Free_Logger_4_Dev2Dev. Offer expires February 28th, so secure your free ArcSight Logger TODAY! http://p.sf.net/sfu/arcsight-sfd2d ___ 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
