> I believe the key might be to pass parameters to the file loader to > specify WHICH alt locations you want to load --- you could load as > many as you like;
Yes, perhaps something like this would work. > they would come in (in a sense) like vibrations, and Yes, I see that they have some similiarity with vibrations. In some ways also seems similar to 'growing a crystal'. > you would not have to pull in the whole file. In the prototype I have > implemented > > load "filename" 4 > > The four means "just load the fourth model". It is not clear to me what you mean by the 'fourth model'. > It works great. The idea > is that one might have, say, a collection of crystal structures. One > is only going to look at one at a time, so this allows selective (and > much speedier, because of all the necessary symmetry handling) file > loading. > > I could imagine this becoming something like: > > load "filename" 4,7,8,12 > > (commas ignored; just for readability here) > > which would say, "load three models from "filename" -- the 4th, the > 7th, .... I am somewhat confused. I don't think that a 'model number' or 'pseudo-model number' is sufficient to describe what needs to be done. Here is the problem ... as I understand it ... A protein is a long chain A segment of the chain may have a string of atoms that can appear at multiple locations. I have called this a 'run'. Within the PDB file these 'alternate locations' (altLocs) are identified by an alpha character. The default is a ' ', the first altLoc is generally 'A', the second is 'B', etc. There can be more than one 'run'. The set of all possible models is the combination of all altLoc runs paired with all other altLoc runs. Say that I have a chain that looks like this ' ' ' ' ' ' OR 'A' OR 'B' OR 'C' # 4 possibilities for this run ' ' ' ' OR 'A' OR 'B' # 3 possibilities for this run ' ' ' ' ' ' OR 'A' OR 'B' # 3 possibilities for this run ' ' There are 4 * 3 * 3 = 36 possible conformations for this protein. (perhaps some combinations would not work because of interference between atoms, but that is not my issue). So, it seems to me that we need a syntax that says something like ... choose 'A' out of the first run, ' ' out of the second run, and 'B' out of the 3rd run. We need a syntax that describes what all of the possible combinations are, and a syntax for the user to describe which combination they want to see. Another twist ... for this problem in particular it seems to me that people would want to load them up and look at them in order to evaluate whether or not they make sense. So it seems like forcing them to choose which one they want to see before they can see it seems like a problem. Miguel ------------------------------------------------------- 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&kid0709&bid&3057&dat1642 _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
