Help:Uploading molecules: Difference between revisions

For very large files, such as large [[Complexes|complexes]] or [[Morphs|morphs]], you may wish to take steps to reduce file size further prior to using file compression. In the end, the scene using your upload PDB file should load for a user in a reasonable amount of time. The best way to do this is to exclude portions of the PDB file not critical to scenes you will generate. Generally, one can save just the alpha carbons of the protein residues as Jmol can still represent the proteins in many forms, including cartoon, backbone, trace, and ribbons. Ways to do this, include using the 'Pick Cα, backbone and side chain atoms' option at [http://dicsoft2.physics.iisc.ernet.in/pdbgoodies/index.html PDB Goodies], using a filter in the load command in the Jmol application, such as 'load =2hyn filter "*.ca" ' to just load alpha carbons and write the coords (see [[Jmol/Visualizing large molecules|Visualizing large molecules#Displaying Only Alpha Carbon Atoms|Displaying Only Alpha Carbon Atoms]], or download and use an executable DOS program called 'alphac' created by Eric Martz. For important residues, the full information can be added back to the edited PDB file. Appropriate names for such a file may include the letters 'CA' and the alterations should be clearly note in the description and you should also note on the actual page using the file as it may substantially affect on possible views that users may generate on your page using the Jmol menu or console, or on scenes users may generate building on your scenes. See '[[Jmol/Visualizing large molecules|Visualizing large molecules]]' for additional considerations.