Jmol can get files directly from the Protein Data Bank website. (Official Protein Data Bank document) Atomic Coordinate Entry Format. If you need support for partial charges, see the similar PQR format below.įiles may contain an inline script starting with REMARK jmolscript. This format supports formal charges, and only hydrogen isotopes (as D and T) they are all read by Jmol. Can also contain temperature factor, formal charge, element symbol, alternate locations. Jmol reads PDB files (and can write PDB files under some circumstances).Ĭontains atom coordinates and information on biomolecular residues, sequence, chains, hydrogen and disulfide bonds, secondary structure, biologically relevant sites, cofactors.
This format supports partial charges and isotopes, but only partial charges are currrently supported by Jmol.Ī single MOL2 file may contain several structures, which will be read by Jmol as multiple models or frames. Some extra information on SD files at US EPA DSSTox.Įxample files for MOL and SDF v2000 and v3000.Ĭontains atom coordinates, bonds, substructure information. The third line is for comments, and may contain an inline script starting with jmolscript.The second line is in principle reserved for information on the originating program, date, user, etc.The first line is reserved for the molecule name and will be so used by Jmol in the popup menu.Load myfile.mol filter "2D" That will load the flat model and, before it is displayed, will add hydrogens if needed and then run a minimization the result is a 3D model of the input 2D structure with a feasible conformation. or you can load the file using the filter "2D" switch of the load command, in this way:.you can run the minimize command after loading this will apply a simple UFF force field to reach a reasonable 3D structure.Jmol has two ways to deal with such flat models: The defining tag (2D or 3D) must be located in line 2, columns 21-22, but is ignored by Jmol, which just uses the Z coordinates provided, be they zero or not. There are often MOL and SD files with two-dimensional data (i.e, all atoms have Z=0) Jmol will read them too, but the resulting flat model will not be realistic. A variant used in PubChem adds partial charges using a custom field, and this is also read by Jmol. These formats support formal charges and isotopes both are read by Jmol. V2000 (the most common) is limited to 1000 atoms. Original from Molecular Design Limited, then Elsevier MDL, then Symyx Technologies, then BIOVIA Dassault Systèmes, widely adopted by many other programs.Ĭontains atom coordinates and bonds. Jmol reads MOL v2000 and v3000, and SD files (and can write them too). This newer format applies to both MOL and SDF, hasn't got the 1000-atom limit and is also supported by Jmol. MOLv3000 = extended molfile or extended connection table SD files share the MOL format but may contain several structures (separated by lines with $$$$), which will be read by Jmol as multiple models or frames. 1 File Formats for the Atomic Coordinates of the Molecule.What follows is a collection of specifications and comments on several formats, but is not a complete listing of all formats supported.įeel free to add a subsection with a description of a format you know well.
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Where fileName includes the path, the file name itself and the file extension paths may be absolute or relative a full URL may also be used.įileFormat will be a keyword recognized by Jmol that designates that format. You can instruct Jmol as to which format to assume using this special command syntax: The file extension is not taken into account for identifying the format. Jmol will read any file and try to determine its format from its content.
File > Get MOL will ask for some kind of supported chemical name or id and retrieve the file from Cactus Resolver at NCI (see Database Connection).File > Get PDB will ask for a 4-character PDB ID and retrieve the file from PDB at RCSB (see Database Connection).File > Open URL will ask for a location on the web.File > Open will open a standard dialog for browsing local disk.These files are loaded into Jmol by either of the following methods: File Formats for the Atomic Coordinates of the Molecule
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