[phenixbb] mutate to polyAla

Thu May 14 04:48:22 PDT 2009

Pavel,

Sometimes truncation/mutation  to poly-gly or poly-Ser is desirable. If
not already present could this be another option? Another interesting
option would be to be able to change OR keep the residue names of the
template to be mutated. Sometimes it is useful to chop the sidechains,
but still be able to tell what residue this is supposed to be via the
residue name. Again some of this may already be present, haven't had a
chance to play around with this.

From: phenixbb-bounces at phenix-online.org
[mailto:phenixbb-bounces at phenix-online.org] On Behalf Of Pavel Afonine
Sent: Wednesday, May 13, 2009 3:56 PM
To: PHENIX user mailing list
Subject: Re: [phenixbb] mutate to polyAla

I just realized that you could do it even without using
truncate_to_polyala:

phenix.pdbtools model.pdb keep="backbone"

or, equivalently:

phenix.pdbtools model.pdb remove="sidechain"

and it works for both: proteins and RNA/DNA. 

Pavel.

On 5/13/09 12:43 PM, Francis E Reyes wrote: 

Though the original question was for protein, is there a mutate to  
poly C for RNA as well? :)

It just came to mind right now.

FR

On May 13, 2009, at 1:42 PM, Pavel Afonine wrote:

	Hi,

	the next nightly build of PHENIX will have this option available
from
	phenix.pdbtools.

	Example:

	phenix.pdbtools model.pdb truncate_to_polyala=true

	As always, any feedback will be very appreciated.

	Pavel.

	On 5/7/09 7:01 AM, Francis E Reyes wrote:

		Is there an option or a phenix.* utility to mutate a MR
model to poly
		ALA before the MR is done?

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---------------------------------------------
Francis Reyes M.Sc.
215 UCB
University of Colorado at Boulder

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