Changes between Version 4 and Version 5 of FAQ_MoleculeViewer


Ignore:
Timestamp:
Jan 4, 2011, 5:12:48 PM (6 years ago)
Author:
braffert
Comment:

Adding documentation for viewing lammps files, and trajectory to sequence conversion

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  • FAQ_MoleculeViewer

    v4 v5  
    66  3. Molecule Viewers as Output
    77  4. Sending PDB files to the Molecule Viewer
     8  5. Sending LAMMPS files to the Molecule Viewer
     9  6. Displaying trajectories as sequences
    810
    911----
     
    181183}}}
    182184
     185== Sending LAMMPS files to the Molecule Viewer ==
     186
     187The Molecule Viewer can also display LAMMPS dump files in a manner similar to PDB files, as described above.
     188The contents of a standard atom style LAMMPS dump file can be placed in the '''<lammps>''' sub-element as follows:
     189
     190{{{
     191<?xml version="1.0"?>
     192<run>
     193    <tool>
     194        <title>Sending LAMMPS file to Molecule Viewer</title>
     195    </tool>
     196    <input>
     197    </input>
     198    <output>
     199        <structure>
     200            <components>
     201                <molecule>
     202                    <lammps>
     203ITEM: TIMESTEP
     2040
     205ITEM: NUMBER OF ATOMS
     2063
     207ITEM: BOX BOUNDS
     208-4.0 4.0
     209-4.0 4.0
     210-4.0 4.0
     211ITEM: ATOMS id type x y z
     2121 1 -1.24935 -3.41562 0.0
     2132 2 0.08092 -3.19426 0.0
     2143 3 0.00055 -1.40789 0.0
     215                    </lammps>
     216                </molecule>
     217            </components>
     218        </structure>
     219    </output>
     220</run>
     221}}}
     222
     223The '''<lammpstypemap>''' sub-element can be used to map the atom type numbers in the dump file to specific elements.
     224The contents of this element should be a whitespace delimited sequence of element names corresponding to the desired element for each atom type.
     225For example, a type map of "H S C" will map atom type 1 to hydrogen, 2 to sulfur, and 3 to carbon.
     226
     227== Displaying trajectories as sequences ==
     228By default, if a PDB or LAMMPS trajectory is given to the molecule viewer, only the first frame of the trajectory will be visible.
     229To view the entire trajectory as an animation, put a "yes" in the '''<trajectory>''' sub-element.
     230When this option is enabled, the PDB or LAMMPS data will be automatically split into unique molecule elements for each time step, and placed into a [wiki:rp_xml_ele_sequence sequence] element.
     231Example:
     232
     233{{{
     234<?xml version="1.0"?>
     235<run>
     236    <tool>
     237        <title>Viewing trajectory as sequence</title>
     238    </tool>
     239    <input>
     240    </input>
     241    <output>
     242        <structure>
     243            <components>
     244                <molecule>
     245                    <trajectory>yes</trajectory>
     246                    <pdb>
     247
     248                        ...
     249
     250                    </pdb>
     251                </molecule>
     252            </components>
     253        </structure>
     254    </output>
     255</run>
     256}}}
    183257
    184258[wiki:FAQ Back to Frequently Asked Questions]