SOMO PDB Editor Module

| # Manual

## SOMO - PDB Editor Module: Cut/Splice

In this module, functional, but with additional development planned, provides the ability to cut and splice on individual chains of two PDB files. No fitting on differently labeled chains is currently possible, although planned. This program is tied to the PDB Editor's main window, with From associated with the center editor panel and the To associated with the right editor panel. This can be very useful, but can be a source of trouble if you are not aware of the connection. The PDB Editor is useful for selecting ranges for the merging, fitting and cut-back regions. Trial results can also be saved and visualized in the PDB Editor. But if you load or clear in the PDB Editor, it will clear the associated information from the PDB Cut/Splice tool.

Prerequesites The residue numbers and chains must match. Of course, some can be missing, but the idea is that this program finds an overlapping sequence of residue numbers in matching chains. There can be multiple chains, but the fitting is done for each chain independently. From the user defined sequential range of the overlapping sequence, of at least 3 residues, a fit is performed, and the merge sequence is transformed by the fit and added to the target structure.

Only one end of an individual chain can be handled at a time. i.e. if you want to add from a file to both the beginning and end of a chain, you will have to run Cut/Splice two times.

First You must load a file using Chains from. This is the file from which you will be taking a sequence of residues to merge. Note: this PDB will automatically be loaded in the center panel of the main PDB Editor window.

Second You must load a file using Chains to. This is the file to which you will be adding a sequence of residues. Note: this PDB will automatically be loaded in the right panel of the main PDB Editor window.

Third You must Compute guess. If your PDBs are compatible, the identified chains and ranges will be added to the top area. If not, recheck the prerequisites.

If all is well, at this point you should see one line for each chain where the there are overlaps and values set for Merge start and Merge end, Fit start and Fit end. They may or not be the values you want. They may not even be valid values. If the chains nicely overlap, say Chains from has residues 1-52 and Chains to has residues 49-100 (notice the required minimal overlap), then the program should figure this out and be all setup to merge.

In the image below, we have made separate PDBs out of residues 1-51 and 49-100 of an existing PDB. Then followed the procedures above to produce:

Chain: This identifies a chain where a merge is possible.

Merge start, Merge end : This is the sequence of residues from the Chains from PDB's identified chain that will be merged into the Chains to PDB's matching chain.

Fit start, Fit end : This is the sequence of residues from the Chains from PDB's identified chain and the Chains to PDB's matching chain that will be used for coordinate transformations. The program will compute the transformation based on a best fit over this range. Currently only "CA" atoms are used in the transformation.

Cut start, Cut end : This is the sequence of residues from the Chains to PDB's identified chain that will be cut off before any fitting and merging. This can be useful if there is more than the minimal overlap available.

Validate : If you have followed the steps above, then you are ready to Validate. This will recheck any adjustments you have made to the values Merge start, Merge end, Fit start, Fit end, Cut start and Cut end. If everything is ok, the text area will show "Validation OK". If not, there is some issue with the settings, and you will receive messages briefly describing the issue.

Trial : This will run the fitting procedure and produce the output in the main PDB Editor window's right panel. If you have a multiple model NMR style Chains to PDB file, all models will be processed.

Start : This will only be enabled if a Target has been entered and the ranges are ready of Trial. If so, the Target file will be created. If you have a multiple model NMR style Chains to PDB file, all models will be processed.

Stop : For long running fitting procedures, you can terminate by pressing this button. This may be useful when processing to a large multiple model PDB file.

Clear : This will clear the table.

Load : This will load the table from a file.

Save : This save the table values to a file.

Cut back : This button will be enabled after Validate if it is determined that a cut back is possible. Pressing the button will automatically compute the Cut start and Cut end values. For example, suppose you had an overlap of more than three residues on a chain. Then you could adjust the Merge end value. Then Validate, and the Cut back to automatically set the values.

These are useful tools for interacting with the main PDB Editor window. The From is associated with the center panel, and the To is associated with the right panel. Be careful, changes made in the PDB editor effect the PDB cut/splice tool, so if you see something strange going on, it is likely that you have done something in the PDB editor.

From->Merge : When you select a range of residues in the PDB Editor window's center panel, this button is enabled to copy over the range values to the Merge values.

From->Fit : When you select a range of residues in the PDB Editor window's center panel, this button is enabled to copy over the range values to the Fit values.

To->Fit : When you select a range of residues in the PDB Editor window's right panel, this button is enabled to copy over the range values to the Fit values.

To->Cut : When you select a range of residues in the PDB Editor window's right panel, this button is enabled to copy over the range values to the Cut values.

www contact: Emre Brookes

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Last modified on 8 May, 2012