Mauricio Carrillo Tripp wrote: > The different sets of atoms > created by individual BIOMT transformations are selectable using the > "symop" selection option: > > select symop=3 > select symop<6 > > etc. (There is a bug there -- symop=1 specifically is not > selectable in > 11.5.32) > > > OK, so for example, if I want to display 1/2 capsid, I will have to load > the PDB file 30 times, each time using a different select in the > loading filter.
heavens, no. You just load it once, then display only the parts of the capsid you want (if you can settle for just *.CA atoms). If you want all the atoms, I think you probably can't load 1/2 the capsid anyway. > By using the append option in the load command, all 30 biomolecules > will 'live' on different frames, which can be independently selected by > frame, OR the symop operator. correct? you just select and display them in the sets you want. Maybe display symop=2 or symop=3 or .... and that would display whatever part of the capsid you want to display. > > > > > > 2) have the option to apply symmetry to any number of chains in the > > ASU (many capsids have more than one chain in the ASU), I > believe one > > can do that with the filter as is, right? I'm thinking of the option > > to show chain A of biomol 1 and chain C of biomol 7 (or any > > combination), again, to present an specific interface. > > > So tell me more about what it means when there are multiple > biomolecules. What would that indicate? > > > The spherical virus capsid (biounit) is made up of 60 identical copies > of the ASU (biomol 1). > The ASU in itself can be made up of one or more independent chains, > which in general > terms corresponds to the triangulation number value (T). So for > example, a T=3 capsid has > 3 independent chains (A,B,C) forming the ASU, which in turn will give > 180 (3x60) chains forming the > full capsid. I understand. > The PDB file contains coordinates for the first copy of the ASU, and > also the 60 > transformations (biomat 1...60) that need to be applied to those > coordinates in order to generate the full > capsid (usually the first transformation is the identity). So each PDB > file, in essence, contains a full > capsid (functional biounit), in a very reduced space (file size). Yes. > In addition to the intra-unit interfaces (protein-protein interactions > between the chains that form the > ASU), one is also interested in seeing/studying the inter-unit > interfaces (protein-protein interactions > between the chains of different copies of the ASU). Some of these > inter-unit interfaces are formed by > up to six copies of the ASU, all sharing a common symmetry axis (in > this case, a 6-fold symmetry axis). > Right, so probably what we want to add to the filter is the capability of selecting specific BIOMT records. > > In most cases there is no need to generate a full capsid (it looks > pretty awesome > though ;). Because of symmetry, ~1/4 capsid contains all interfaces of > interest. Still a lot of atoms if you want all of them. -- Robert M. Hanson Professor 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 ------------------------------------------------------------------------- This SF.net email is sponsored by the 2008 JavaOne(SM) Conference Don't miss this year's exciting event. There's still time to save $100. Use priority code J8TL2D2. http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
