[Chimera-users] swapna: preserve option

Elaine Meng meng at cgl.ucsf.edu
Wed Sep 7 08:30:57 PDT 2011

Hi Bala,
You are looking at the development (latest) documentation.   The "preserve" option in swapna was added recently, so to use it you need a recent daily build of Chimera... it is not available in version 1.5.3.  If you use the documentation in your Help menu, it should match your downloaded software.

Here is the swapna documentation for version 1.5.3

When you have problems, you should always say what version you are using and give an example of the exact command that you tried.  Otherwise it may not be enough information for us to figure out what is happening.


P.S. I looked at the "changes since last production release" page to figure this out,

On Sep 7, 2011, at 1:21 AM, Bala subramanian wrote:

> Friends,
> 1) I used swapna command with preserve true option but chimera complains it as mangled specifier. The preserve option is denoted in online documentation
> http://plato.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/swapna.html
> 2) Just for a try i downloaded the 1VT7.pdb and changed the Guanine (first residue in chain A) to Adenine: swapna A :1.A but i found that added A is rotated. I mean the plane of A is not matching with that G (originally present in the structure). I am not sure if the preserve option is working. To be precise, i want added base to have the same plane as the original one.
> Thanks,
> Bala

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