Quoting: El 10/01/2008, a las 16:21, Angel Herraez escribió:
> It's great you solved it, Carles > >> Anyway, I think that the developers should keep an eye on the >> 'select' >> command, it is quite slow for the overall speed of jmol > > I suspect that Jmol may be doing this: > > select C1, N2, C3, O4, N5, C6, N7, C8, C9, C10, N11, C12, O13, N14, > C15, O16, C17, C18, C19, C20, N21, C22, O23, N24, C25, O26, C27, C28, > C29, C30, N31, C32, O33, N34, C35, O36, C37, C38, C39, C40, N41, C42, > N43, C44, C45, N46, N47, C48, N49, C50, C51, N52, C53, N54, C55, C56, > N57, N58, C59, N60, C61, C62, N63, C64, N65, C66, C67, N68, N69, C70, > N71, C72; > > 1) Look at every atom and see if it is called C1. Put it or not in > the selected set. > 2) Look again at every atom and see if it is called N2. > 3) etc. Yes, that's what I thought too. But I had (erroneously) inferred that the other selectors (comparison, etc) would also have that kind of delay. > > > that gave me the idea; using the comparison, there is a single > expression to be checked once for each atom. > > Don't thnik so, but maybe setting a user-defined atom set first and > then selecting it by name would speed up things: > > define stretch1 atomno<=72 > define stretch2 atomno>=73 and atomno<=82 > define stretch3 atomno>=83 and atomno<=92 > select stretch1; color [0, 0, 0]; > select stretch2; color [0, 72, 0]; > select stretch3; color [0, 115, 0]; > No luck here :( > Note that your massive one-by-one selection is very uncommon. One > usually selects by chain, by element, by molecule, by residue... and > it's also unusual to have a 1000 bp DNA molecule, more so without > residue numbers. How do you manage it within the screen space? > > Regards > We're planning to publish it soon, so the details are confidential for now, but I've written browser for managing long DNA molecules. I'll send more feedback and the URL ASAP Thanks for your help :) Cheers, Carles > > ------------------------------------------------------------------------- > Check out the new SourceForge.net Marketplace. > It's the best place to buy or sell services for > just about anything Open Source. > http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/marketplace > _______________________________________________ > Jmol-users mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/jmol-users -- Carles Fenollosa Bielsa Barcelona Supercomputing Center / Life Sciences Nexus II / Jordi Girona, 29 / 08034 Barcelona +34 93 413 76 02 ------------------------------------------------------------------------- Check out the new SourceForge.net Marketplace. It's the best place to buy or sell services for just about anything Open Source. http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/marketplace _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
