How to Upload .crd File on Vmd
Next: Labels Form Upwardly: Description of each VMD Previous: Breathing Form Contents Index Subsections
- Reading Frames
- Writing Frames
- Deleting Frames
- Corporeality Chooser
Edit Animation Class
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This grade is used to add, relieve, or delete coordinates sets (likewise referred to hither as frames) from a molecule. Usually these coordinates come from successive frames of a trajectory but, as shown in the tutorial A Quick Animation, can also be distinct conformations of the same construction.
When this class is used, information technology will affect simply the molecule selected in the Selected Molecule chooser. There are three types of actions which can have place; read frames from or write frames to a file (in the CRD, DCD or PDB format) or delete frames from the current animation.
Reading Frames
VMD tin can read in new coordinate sets from PDB files (to add a single new frame to the blitheness), from ascii CRD files (which may contain several frames), from binary DCD files (which may besides contain several frames), or from Gromacs trajectory files. The new coordinate sets are appended to the end of the stored animation listing for the selected molecule. At present, there is no way to use Babel to append non-natively-supported files. The format is determined by selecting the appropriate name in the File Type chooser. If you want to read in all the information from the file, make certain that the Corporeality chooser says `All', then press the Read button in the lesser right corner. This will bring up the file browser and then you can select the file. (Different the Files form, the file is loaded immediately subsequently the filename is entered in the file browser.)
Sometimes y'all may not want to read in a whole CRD/DCD file. For instance, you may only want the last frame, or every tenth frame. Y'all can do this by choosing the `Selected' selection in the Amount chooser. This brings up the frame skip selection controls. Once you've chosen the appropriate values, press the Read button to bring upwards the file browser and finish as mentioned in the previous paragraph. The Amount options are ignored when reading in PDB files.
Writing Frames
Using the `Write File' action, you tin write the loaded frames to file in either the PDB or the CRD ASCII formats, or you may write to a binary file post-obit the DCD format. This may be used to write out a new trajectory in a single file after assembling many frames from different sources (such as PDB CRD, DCD or Gromacs files, or even from a remote simulation). You lot tin can besides employ this, in combination with Read File, as a way to brand PDB files from a DCD/CRD trajectory.
Y'all can either save the entire stored trajectory, or a slice of the information by using the Amount chooser. Then select the appropriate output file type in the File Type chooser, and press the Write push button in the lesser right corner. This brings up the file browser, which you can use to enter the new filename. Once you press the Write button in the browser, the file will be written without further confirmation. See section on atomselect control for information on how to write atom coordinates for an atom pick in a PDB file.
Deleting Frames
This provides a way to delete frames from memory. Get-go, choose the frames you lot wish to delete with the Amount chooser and (possibly) the frame skip controls, and then press the Delete push. There is no confirmation of deletions.
1 problem with this machinery is there is no style to delete every frame except for those given by the frame skip. You tin become around this by writing the skip selection to a CRD/DCD file, deleting all the frames from memory, and then reading the skip back in from deejay.
Amount Chooser
The significant of this option varies depending on the action. If `All' is selected, so all the frames volition be read from the file, or all the frames volition be written to the file, or all the frames will be deleted from memory.
The other selection is `Selected.' This will bring up three controls, labeled Begin, Terminate, and Skip. These make information technology possible to utilize a subset of the frames, starting at frame Begin and selecting every Skip frames until the End is reached. For case, to select every fifth frame between frames 14 and 98, set:
- Begin to xiv
- Cease to 98
- Skip to 5
(Retrieve that frame numbers in VMD start at 0, so frame 0 is the kickoff frame.) The value `-1' is a special number; setting Begin to -1 is the same as starting at the first frame, Finish = -1 is the same as ending at the last frame, and Skip = -one is the same every bit taking one step.
When the Action is `Read File', the selection is applied to the frames from the file to be read. When it is `Write File', the pick determines the frames to exist written, and when `Delete Frames', the pick determines the frames to be deleted from memory.
Next: Labels Form Upwards: Description of each VMD Previous: Animate Form Contents Index vmd@ks.uiuc.edu
Source: https://www.ks.uiuc.edu/Research/vmd/vmd-1.7.1/ug/node42.html
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