a bit off topic, but I am happy to oblige:
On Tue, Jun 2, 2015 at 11:12 AM, Mungo Carstairs (Staff) < [email protected]> wrote: > > I have a problem aligning structures in Jmol (based on sequence alignment, > and alpha carbons), whenever the CA atoms appear in alternate locations. > > Essentially I need a variant of the selection pattern e.g. > > {1-40.*CA} > > which would exclude any alternate locations (so I don't match too many > atoms). > > > As I am sure you know, alternate locations have special, not necessarily predictable, character codes. Generally there would be two or more alternate locations -- something like A and B, or 1 and 2. So one would not usually remove all alt locs. The simple thing to do is use the CONFIGURATION command or select option: select 1-40.ca and configuration=1 This selects for the first listed altloc, whatever it may be, along with altloc="" Note that CONFIGURATION was broken some time before 2015.01.27 but fixed that day. So check your version if that does not work. Bob -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Department of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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