Hello I have a tricky issue in saving and retrieving the state after the model has been modified by calculate hydrogens; minimize; or minimize addHydrogens;
Summary: Running the state as a script brings a model with all hydrogens and some other atoms also as hydrogens (but not all); other atoms are lost. This is in JSmol 14.0.10 (meant to be put in an "open this model in a big window), but the generated state is wrong even when applied to Jmol app. The model does not come from file but from a structure drawn in JSME. Procedure is: 1. draw a structure in JSME 2. transfer it as molFile 3. add hydrogens and minimize 4. get the state 5. apply the state to another instance of JSmol --or to the Jmol app It is step #3 that creates the problem and, specifically, the addition of Hs If I transfer as JME string rather than molFile data, the problem seems to be also there (since Hs are being added internally by Jmol). No problem when I transfer as Smiles Test case: go to http://biomodel.uah.es/en/DIY/JSME/ (that uses 14.1.8, but the problem is the same) Draw something, transfer as MOL, open JSmol console and show state copy it and paste back into the consle or Jmol app's console JME transfer is working fine in that page; I must find out what's the difference with my current page -- But I really want to use MOL transfer Thanks ------------------------------------------------------------------------------ Flow-based real-time traffic analytics software. Cisco certified tool. Monitor traffic, SLAs, QoS, Medianet, WAAS etc. with NetFlow Analyzer Customize your own dashboards, set traffic alerts and generate reports. Network behavioral analysis & security monitoring. All-in-one tool. http://pubads.g.doubleclick.net/gampad/clk?id=126839071&iu=/4140/ostg.clktrk _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
