[Chimera-users] Creating output with IDATM naming

Eric Pettersen pett at cgl.ucsf.edu
Mon Feb 3 14:17:26 PST 2014


Hi Nikolay,
	It's pretty easy.  Open the Attribute Calculator tool (in Structure Analysis).  Set the "Calculate attribute" field for atoms to "saveName" and the Formula field to "atom.name" and click Apply.  This will stash all the atom names in a "saveName" attribute so we can restore them later.  Then set the attribute to "name" and the formula to "atom.idatmType" and click Apply.  Now all the atom names have been changed to the IDATM type.  The display may change in response.  Now save your PDB file.  Then restore the original names by calculating attribute "name" with formula "atom.saveName".

--Eric

                        Eric Pettersen
                        UCSF Computer Graphics Lab
                        http://www.cgl.ucsf.edu

On Jan 31, 2014, at 12:49 PM, Nikolay Igorovich Rodionov wrote:

> Hi,
> 
> Does anyone know a way to rename all of the atom names in a PDB file to their IDATM types, so that a new PDB file can be generated with the IDATM naming scheme? 
> 
> Best,
> Nikolay Rodionov 
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