Re: [AMBER] about rms atomic fluctuation for protein crystal .thank you very much!

From: Pawel <>
Date: Tue, 15 Oct 2013 19:26:42 -0400

Hi Aimee,
On 10/15/2013 09:09 AM, Yongxiu Li wrote:
> 1. if the "bfac_lat_calpha" in figure8 are calculated using a different
> approach than the one used in BasicAnalysis, how can I do it?
If I understand correctly (I did not work on that paper myself), the
alignment of asymmetric units was done by solving a least squares
minimization problem to find (for each frame) the best location of the
crystallographic origin in space so that after performing the
appropriate symmetry operations and translations in reverse on each of
the asymmetric units, the resulting RMSD between the asymmetric units
would be minimized. Unfortunately I don't have the code for that
approach. If it would be very useful to you, let me know and I'll

> So as you said, I need to rescal coordinates.
> However, after reading this paper I am confused that wether only
> computing the lattice property (for example:rmsd_latt and
> bfactor_latt)need rescal coordinates but computing the other
> property(like rmsd_ASU ,bfactor_ASU and Distance deviation matrices)
> needn't rescale the coordinates?
If you are simulating an NPT ensemble, you should rescale the
coordinates for all of these analyses. This should be done in though I think the version of that script that you have
does not do so. Like I said these scripts Analysis directory are all
beta versions. However you should be able to do the rescaling easily by
adding one or two line around line 95 of the script. If you have
problems, let me know and I'll dig up a version that does this.


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Received on Tue Oct 15 2013 - 16:30:02 PDT
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