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How to Read in a Structure from a File and Save Results

Read in the Protein 4dfr.pdb

Adjust Silent Hydrogen Counts for Methotrexate

The topology of methotrexate as a small molecule is insufficiently specified in a .pdb file. Moloc tries to find out its true topology from its geometry (bond distances, bond angles, planarity). For inaccurate geometry this may not be successful. Thus, for heterogens the user has to check whether the topology was properly assigned. To this end an entry has to be in the active status, which can be set in the display menu '.' in which you should still find yourself. From its origin from a .pdb file, methotrexate is considered a polymer. To have it considered as a simple small molecule take the following steps see also: Now, adjust the silent hydrogen counts of the heavy atoms:

Store Methotrexate onto Disk File

Although it's structure is still the same as in the .pdb file the topology of methotrexate has changed through the modified H-counts. In order to save these changes the molecule has to be stored in a file format that is able to preserve the H-counts:

Project Startup by Means of Input List Files (.ils): my_project.ils

You may want to have the 3 entries (chain, water, methotrexate) always available in Moloc, when you start the program without having to repeat the above file reading procedure. This can be arranged by the following steps: