Re: [PyMOL] putty/sausage NMR figure
Hi Doug, Well, you could write a function average(Object1, Object2, ...) which would return an object containing the average structure and the fluctuations from this average in the b-factor field.., I think :) Might be a useful feature, so if I'll find some time... (but feel free to try to beat my to it ;)) Cheers, Tsjerk On 7/21/05, Douglas Kojetin wrote: > 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 > > > > > > --- > > 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_idt77&alloc_id492&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_idt77&alloc_id492&opclick > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users >
Re: [PyMOL] putty/sausage NMR figure
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 --- 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_idt77&alloc_id492&op=click ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] putty/sausage NMR figure
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 --- 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
