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

From: Yongxiu Li <>
Date: Tue, 29 Oct 2013 16:03:39 +0800

        Thank you very much! I am so sorry for that I read the again and I think I have done the rescaling. I think
these lines do the all rescaling "
    for frame in range(frames):
     #get frame box
     #convert to unit cell box
     #add angle information as provided by user
      #calc orthogonalization matrix
      #matrix product
       # reverse symmetry operate to original asym unit by
       # applying the symmetry translation and rotation
        coords[:,:,:]=dot( (coords[:,:,:]-t),linalg.inv(s) ) "
I'm not proficient in Python, so whether I understand is right? If not,
can you tell me how to do in python script? If I am right, I still can't
understand that compared with figure8 in Case's paper,why the
bfac_lat_calpha-arf.dat which I gained is so big.
btw,in the attachment is the lattice atomic root mean squared
fluctuations of a-carbons by amber ff99SB-tip3p.
Thank you very much!
Aimee Li


On 10/16/2013 07:26 AM, Pawel wrote:
> 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
> investigate.
>> 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.
> Pawel
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Received on Tue Oct 29 2013 - 01:30:02 PDT
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