On Thu, Jul 06, 2006 at 10:14:33AM -0500, Scott P Brown wrote: > That's not a very helpful response, as it may not be clear how > one maps an atom selection in Pymol to the corresponding line > in a PDB file.
Helfpulness is in the eye of the beholder. I certainly intended, and still expect, that what I posted might have been of some help to the original poster, and to the quality of the list in general. I thought of digging up and posting a link to the PDB specification--specifically to that of the ATOM record and to the coordinate fields of that record--and getting into the whole question as to how one works with text files on particular platforms, but it just didn't seem the right thing to do at the time. Someone who shows an explicit unfamiliarity with what a PDB file provides or does not provide is, in my opinion, best nudged in the direction of learning about this crucial file format itself--certainly about the ATOM record if nothing else. Such familiarity is more general and more useful over the long-term than knowledge about the peculiarities of the current syntax of a single command in just one of the many programs which work with PDB files. Of course, your mileage may vary. The primary question was how to get the coordinates of an atom, with the original poster using a selection as an example. My response addressed the primary question. Your response addresses the example. Even so, I found your response helpful, since I wasn't familiar with iterate_state before (though I see it has been mentioned in passing over the years in example code). My archive of this list has some holes, but for the most part it now stretches back over 4 years and over four thousand posts. Any post which in turn elicits a detailed answer on a feature of PyMOL, from someone who has not in that time (as best I can tell) ever before offered their expertise, counts as a helpful post indeed. I look forward to reading further helpful posts from you in the future, and hope that those posts needn't be in reaction to something I've sent that has been found wanting. Regards, -- Joe > To print out the coordinates within Pymol, you need to use the command > iterate_state, e.g.: > > iterate_state 1, <selection_name>, print x,y,z > > Where <selection_name> is the name of the object for the atom(s) you've > selected, and x, y, &z are the coordinates of the atom(s). > "D. Joe Anderson" <dee...@iastate.edu> > Sent by: pymol-users-boun...@lists.sourceforge.net > 07/06/2006 09:10 AM > > To > pymol-users@lists.sourceforge.net > cc > > Subject > Re: [PyMOL] How do you show the coordinates of an atom? > > > > > > > On Wed, Jul 05, 2006 at 04:33:16PM -0400, John Anderson wrote: > > > or are the coordinates in the pdb file? > > They are, yes. > > -- > D. Joe > > > > > > Using Tomcat but need to do more? Need to support web services, security? > Get stuff done quickly with pre-integrated technology to make your job easier > Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users -- D. Joe Anderson, Asst. Sci. 2252 Molecular Biology Bldg Biochem, Biophys, & Mol Bio Iowa State Univ, Ames, IA 50010 How to help someone use a computer http://polaris.gseis.ucla.edu/pagre/how-to-help.html
