On Feb 27, 2006, at 3:37 PM, Goel, Manisha wrote:
Hi,
I have often come across detailed answers from chimera group for a variety of modelling problems on pdb-l or bioinformatics mailing lists.
My problem should relatively easy to solve except that I havn't been able to figure it out myslef on chimera.
I just need to make a covalent bond between a sugar molecule and an aminoacid (aa-COOH + sugar-OH --> H2O + aa-sugar). Is there an easy way of doing this manipulation in Chimera ?
The answer is "it depends". If the sugar and amino acid are in the same model, then it's easy. Just select the two atoms you want to bond and in the command line (Favorites->Command Line) type "bond sel". If the sugar and amino acid are in different models then it's trickier, since the definition of "model" is that there are no covalent bonds between models, so you need to get the structures into the same model. One way is to edit the original input files together (if they were PDB files, make sure to get rid of the END record in the middle of the combined files). Another way, if you have the 1.2199 release, is to save the two models in Mol2 format (File...Save Mol2). In the Save Mol2 dialog, select both models and make sure the "Save multiple models in" menu is set to "a single file [combined @MOLECULE section]". If you read the resulting saved Mol2 file back into Chimera, then the two structures will be in one model. You can then use "bond sel" to make the bond. --Eric Eric Pettersen UCSF Computer Graphics Lab pett@cgl.ucsf.edu http://www.cgl.ucsf.edu