Abstract from: 5-monos.txt [dirdif manual chapter 5] 22 March 2008 ------------------------------------------------------------------------ Test runs on structure MONOS You may wish to get acquainted with DIRDIF by running an example. We have provided the data for the test structure MONOS. Preliminaries - change directory to dirdif/MONOS - Look at the MONOS data files . The crystal data for MONOS are given in the CRYSIN file. The molecule contains a sulfur-bridged six-membered ring which is given in ORBASE under the model name MONOS. - Run DIRDIF with the data of test structure MONOS, solving the structure of MONOS along two different routes: route 1: call program PATTY, using DIRDIF in automatic mode ------------------------------------------------------------- Enter at the terminal: =====> DIRDIF MONOS PATTY The program PATTY finds the sulphur atom at a pseudo-special position, with x=0.0 ! This site generates a mirror plane in the model. To handle this problem the program PHASEX runs through an enantiomorph fixing procedure. The course of the recycling procedure can be followed on the screen. When the program has finished the structure has been solved. The LIS1 file gives the most interesting features of the procedure and a line-plot of the structure. The ATOMS file contains the parameters of the atoms of the structure. Look at the newly created files using your local editor. route 2: option ATMOD (in interactive mode) + program ORIENT ------------------------------------------------------------- Assume that we know a rigid fragment of the structure, which is available in the ORBASE file. We start with calling ATMOD for an interactive retrieval of the rigid fragment, denoted 'monos'. The model, retrieved from ORBASE is a set of atomic parameters (7 atoms) which is to be stored in file ATMOD. Enter at the terminal: =====> DIRDIF MONOS ATMOD In the following dialog you may also answer in lower case. | You answer at On the screen appears: | the terminal: | - No ATMOD file. Can you supply the atomic parameters | now at the termonal (T) or did you Select or do you | Suggest an item from ORBASE (S) | S - Enter model code or number | MONOS - Schematic picture of the model. To quit: enter: | Q - Is this result acceptable? (Y/....) | Y To start ORIENT, enter at the terminal: =====> DIRDIF MONOS ORIENT The program ORIENT reads the model and rotates it, etcetera. ------------------------------------------------------------------------ For more details, see dirdif/docs/5-monos.txt ------------------------------------------------------------------------