Re: [PyMOL] antialiasing and povray
If you just type povray you'll get all command line options. Tsjerk On 7/25/05, andrea spitaleri wrote: > try povray +A0.3 file.pov >zero -^ > > regards > > > > Cameron Mura wrote: > > > hi, > > Is there anything special I need to do/set to achieve antialiased > > images via pymol + POV-ray? > > To be more explicit, i'm using robert campbell's make_pov.py to have > > pymol dump the scene into a povray input file, and then ray-tracing w/ > > a minimalistic command-line (e.g., "povray +Iwhatever_pov.inp +W640 > > +H480")... all of this is w/ "antialias" set 'on' in pymol.. i'm > > unfamiliar w/ povray, so any tips or advice would be greatly appreciated. > > thanks, > > cameron > > > > > > --- > > SF.Net email is sponsored by: Discover Easy Linux Migration Strategies > > from IBM. Find simple to follow Roadmaps, straightforward articles, > > informative Webcasts and more! Get everything you need to get up to > > speed, fast. http://ads.osdn.com/?ad_id=7477&alloc_id=16492&op=click > > ___ > > PyMOL-users mailing list > > PyMOL-users@lists.sourceforge.net > > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > > > > --- > SF.Net email is sponsored by: Discover Easy Linux Migration Strategies > from IBM. Find simple to follow Roadmaps, straightforward articles, > informative Webcasts and more! Get everything you need to get up to > speed, fast. http://ads.osdn.com/?ad_id=7477&alloc_id=16492&op=click > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users >
[PyMOL] Manually move one molecule relative to another
Hi all, I was wondering if there's a way to manually move a molecule relative to other molecules (such as in the case of manual docking) using the mouse. I searched the previous posts and found that MovF/RotF are the way to do that. But, when using these mouse functions to move the molecule, one atom of the molecule moves erratically and the molecule is then distorted. It appears to be a bug. Thanks a lot, Frank
[PyMOL] Re: putty/sausage NMR figure (Douglas Kojetin)
hi Doug & others who deal with bundles, Many thanks for the suggestion. I worked something up using CNS/ python scripts -- but if anyone comes up with an all PyMOL alternative, please share with the list! Doug i've written a quick-n-dirty python module to have pymol deal w/ multiple conformers of the same protein (NMR bundles, MD ensembles, etc) by calculating the average structure and two types of residue-specific RMSDs -- (i) RMSDs w/ respect to the average structure and (ii) a pairwise RMSD that's averaged over all unique pairs (it's my understanding that the first measure (which is <= the second measure for a given residue) is more frequently used in the NMR world?). You can find the "average3d.py" module (and samples of its usage) on my pymol page by scrolling down to the "Averaging Structures!" row of the table in the "PyMOL Examples" section (http://mccammon.ucsd.edu/~cmura/PyMOL ; i should put it on pymolwiki soon). details), load that into pymol, and voila. If the effect isn't enough, you could always multiply your RMS values by some value (eg. 10). Good luck! JP Cartailler This type of pre-processing of B-factors shouldn't be necessary -- you should be able to get the desired effect by tweaking putty cartoon settings (particularly 'cartoon_putty_scale_power'). you can see the relevant settings (and their default vals) via Zaq Panepucci's nifty grepset: PyMOL>import grepset PyMOL>grepset putty cartoon_putty_quality 11.0 cartoon_putty_radius 0.4 cartoon_putty_range2.0 cartoon_putty_scale_max4.0 cartoon_putty_scale_min0.6 cartoon_putty_scale_power 1.5 good luck, cameron === pymol-users-requ...@lists.sourceforge.net wrote (on 07/21/2005 08:13 PM): === Subject: Re: [PyMOL] putty/sausage NMR figure From: Douglas Kojetin Date: Thu, 21 Jul 2005 10:49:21 -0400 To: pymol To: pymol CC: "Cartailler, Jean-Philippe" Many thanks for the suggestion. I worked something up using CNS/ python scripts -- but if anyone comes up with an all PyMOL alternative, please share with the list! Doug On Jul 20, 2005, at 1:18 PM, Cartailler, Jean-Philippe wrote: One way to do this would be to calculate RMSD between your models (using whatever package) and replace the B-factor column with those values (make sure you respect the PDB format (B-factors are in columns 61 - 66, with first column as "1" - see http://www.rcsb.org/pdb/docs/format/pdbguide2.2/part_62.html for details), load that into pymol, and voila. If the effect isn't enough, you could always multiply your RMS values by some value (eg. 10). Good luck! JP Cartailler -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Douglas Kojetin Sent: Tuesday, July 19, 2005 3:48 PM To: pymol Subject: [PyMOL] putty/sausage NMR figure Hello All- From what I've read, the 'cartoon putty' command uses the PDB B- factor value to determine the appearance of the sausage diagram. How can I use the 'cartoon putty' command with NMR structures in a way that represents the structure ensemble, similar to that as the MOLMOL sausage diagram? Thanks, Doug -- Cameron Mura UCSD
Re: [PyMOL] Manually move one molecule relative to another
S. Frank Yan wrote: Hi all, I was wondering if there's a way to manually move a molecule relative to other molecules (such as in the case of manual docking) using the mouse. I searched the previous posts and found that MovF/RotF are the way to do that. But, when using these mouse functions to move the molecule, one atom of the molecule moves erratically and the molecule is then distorted. It appears to be a bug. No. Set the mouse in editing mode. Hold the shift key and put the mouse on any atom of the ligand. (While holding the shift key) Press the right key and move for rotation and Press the middle key and move for translation. Works like a charm. I do all manual dockings on pymol because bond rotation etc is so easy! And the best part is if you move the ligand into a bad conformation, just hit Ctrl-Z to regain the last conformation. Make sure that the ligand is a separate object from the protein. Hope this helps. -- :-) Ramesh K. Sistla May the wicked become good, may the good attain peace May the peaceful be freed from bonds, may the freed set others free -- Rig Veda
