From: Ramachandran M. <mu...@xr...> - 2007-02-08 22:01:39
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Hi Has anyone successfully used Caver plugin using gromac trajectory files? Any suggestion is appreciated. Thanks Murali -- Dr. Ramachandran Murali Associate Professor 243 John Morgan Building Department of Pathology & Lab. Medicine University of Pennsylvania Philadelphia, PA-19104-6082 Ph: 215-573-9256; Fax: 215-898-2401 |
From: Ramachandran M. <mu...@xr...> - 2007-02-08 21:41:57
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Hi Has anyone successfully used Caver plugin using gromacs trajectory files? Any suggestion is appreciated. Thanks Murali -- Dr. Ramachandran Murali Associate Professor 243 John Morgan Building Department of Pathology & Lab. Medicine University of Pennsylvania Philadelphia, PA-19104-6082 Ph: 215-573-9256; Fax: 215-898-2401 |
From: <sun...@al...> - 2013-07-23 00:31:19
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Dear pymol users, Does anyone use the caver plugin of pymol to analyze a ion channel? I don't know how to specify selection for the starting of plugin. Should the starting point be at the center of the channel where there is empty and no atoms in the molecule? or should it be certain atom of the molecule? If it should be the latter, what is the correct syntax of the selection? For example, if I want to select CA atom of Try21 in chain A, should I input the following command? chain A and resid 21 and CA But this is wrong and does not work. Could someone give me some tutorial? Thanks. Yeping Sun |
From: Thomas H. <tho...@sc...> - 2013-07-23 07:04:42
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Hi Yeping, unfortunately, the caver plugin doesn't take a selection expression, but only selection names. Regarding your selection expression, you miss the "name" operator. So this should work: PyMOL> select startsele, chain A and resid 21 and name CA In Caver: "Specify selection: startsele" Hope that helps. Cheers, Thomas sun...@al... wrote, On 07/23/13 02:31: > Dear pymol users, > > Does anyone use the caver plugin of pymol to analyze a ion channel? I > don't know how to specify selection for the starting of plugin. Should > the starting point be at the center of the channel where there is empty > and no atoms in the molecule? or should it be certain atom of the > molecule? If it should be the latter, what is the correct syntax of the > selection? For example, if I want to select CA atom of Try21 in chain A, > should I input the following command? > > chain A and resid 21 and CA > > But this is wrong and does not work. > > Could someone give me some tutorial? Thanks. > > Yeping Sun -- Thomas Holder PyMOL Developer Schrödinger Contractor |
From: Thomas H. <tho...@sc...> - 2013-07-23 08:27:21
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Hi Gianluigi, I can only reproduce your problem with retain_order=1, not with retain_order=0 (which is the default). Could it be that in your pymolrc, you do "set retain_order, 1"? I don't think there is a difference between 1.6 and previous versions. Cheers, Thomas Gianluigi Caltabiano wrote, On 07/23/13 09:48: > Hi all, > > Since 1.6.0.0 on my Mac (OSX 10.8.4) I am experiencing an annoying > behaviour both when creating a new object from two existing and when > mutating a residue via mutagenesis wizard (both with Macpymol and X11) > > Creating a new object from two existing, mess up the two (different) chains. > set retain_order, 1 does not change this behaviour. > > As for the new object creating try to reproduce this: > > fetch 4DAJ > create MA, 4DAJ and chain A > create MB, MA > alter MB, chain='B' > create dim, MA MB > > > The new object is not ordered on a chain basis, but on residue number. > > Something very similar happens using mutagenesis wizard, in that case it > mess the new residue with the first residue. In this cases closing PyMol > and reopening (or chainging to Hybrid) often, but not always, works. > Still is a pain in the back. > > Any clues? > > cheers, > > Gianluigi -- Thomas Holder PyMOL Developer Schrödinger Contractor |
From: Thomas H. <tho...@sc...> - 2013-07-23 08:50:01
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Hi Gianluigi, PyMOL might find more pymolrc files than you are aware of. Just to be sure, try this to get a hint: PyMOL> print invocation.options.deferred Also, check which plugins are installed and eventually disable them. Cheers, Thomas Gianluigi Caltabiano wrote, On 07/23/13 10:44: > Hi Thomas, > > thank you for answering so fast. > > I do not have set retain_order, 1 in my pymolrc, but you are right, if I > set retain_order, 0 the problem disappears. It is strange because I do > not generally use retain_order, but still I might have used it and for > some reason it have been kept by pymol. > > cheers, > > Gianluigi > > ------------------------------------------------------------------------ > Da: Thomas Holder <tho...@sc...> > A: Gianluigi Caltabiano <chi...@ya...> > Cc: pymol-users <pym...@li...> > Inviato: Martedì 23 Luglio 2013 9:27 > Oggetto: Re: Residue numeration problem > > Hi Gianluigi, > > I can only reproduce your problem with retain_order=1, not with > retain_order=0 (which is the default). Could it be that in your pymolrc, > you do "set retain_order, 1"? > > I don't think there is a difference between 1.6 and previous versions. > > Cheers, > Thomas > > Gianluigi Caltabiano wrote, On 07/23/13 09:48: >> Hi all, >> >> Since 1.6.0.0 on my Mac (OSX 10.8.4) I am experiencing an annoying >> behaviour both when creating a new object from two existing and when >> mutating a residue via mutagenesis wizard (both with Macpymol and X11) >> >> Creating a new object from two existing, mess up the two (different) > chains. >> set retain_order, 1 does not change this behaviour. >> >> As for the new object creating try to reproduce this: >> >> fetch 4DAJ >> create MA, 4DAJ and chain A >> create MB, MA >> alter MB, chain='B' >> create dim, MA MB >> >> >> The new object is not ordered on a chain basis, but on residue number. >> >> Something very similar happens using mutagenesis wizard, in that case it >> mess the new residue with the first residue. In this cases closing PyMol >> and reopening (or chainging to Hybrid) often, but not always, works. >> Still is a pain in the back. >> >> Any clues? >> >> cheers, >> >> Gianluigi -- Thomas Holder PyMOL Developer Schrödinger Contractor |