Help:Uploading molecules: Difference between revisions
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=Additional considerations for large files= | =Additional considerations for large files= | ||
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. | 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 | * Ways to extract only the alpha carbons include: | ||
* An option for Windows-users is downloading [http://www.umass.edu/microbio/rasmol/pdbtools.htm Eric Martz's PDB Tools] and using an included MS-DOS program, alphac.exe. | **Use the 'Pick Cα, backbone and side chain atoms' option at [http://dicsoft2.physics.iisc.ernet.in/pdbgoodies/index.html PDB Goodies]. | ||
**Use a filter in the load command in the [[Jmol/Application|Jmol application]] to load only the alpha carbons, and then write a new file with the coordinates. [[Jmol/Visualizing large molecules#Displaying Only Alpha Carbon Atoms|Here are '''instructions'''.]] | |||
** An option for Windows-users is downloading [http://www.umass.edu/microbio/rasmol/pdbtools.htm Eric Martz's PDB Tools] and using an included MS-DOS program, alphac.exe. This program keeps alpha carbons and phosphorus atoms from nucleic acids. | |||
** Michael Palmer's [http://watcut.uwaterloo.ca/cgi-bin/makemultimer/ MakeMultimer] has an option to return only backbone atoms (4 atoms per amino acid instead of a single alpha carbon atom). It also returns nucleic acid backbones (6 atoms per nucleotide). | |||
* For important residues, the full information can be added back to the reduced PDB file, by re-inserting portions of the original source PDB file. | * For important residues, the full information can be added back to the reduced PDB file, by re-inserting portions of the original source PDB file. | ||
* Appropriate names for such a file may include the letters ''ca'' and the alterations should be clearly noted in the description. You should also note the modifications on the actual Proteopedia page where the file is displayed, as the modifications may substantially affect possible views that other users may generate using your file. | * Appropriate names for such a file may include the letters ''ca'' and the alterations should be clearly noted in the description. You should also note the modifications on the actual Proteopedia page where the file is displayed, as the modifications may substantially affect possible views that other users may generate using your file. | ||
See '[[Jmol/Visualizing large molecules|Visualizing large molecules]]' for additional tips and solutions for dealing with issues related to PDB file size. | See '[[Jmol/Visualizing large molecules|Visualizing large molecules]]' for additional tips and solutions for dealing with issues related to PDB file size. | ||
