VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sun Mar 21 2021 - 00:18:28 CDT

This is not surprising at all. PDB files store coordinate and box data at
rather low precision. So some rounding is to be expected.

Axel. 

--
Dr. Axel Kohlmeyer akohlmey_at_gmail.com https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!v4lhU3vYwmRSGoq607sASkgrKmVK9xNVyyVCxIwt-jv2Tbo7b1v2rMV22TpEzk9Ycw$ 
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste, Italy
On Sun, Mar 21, 2021, 00:31 Ramon Mendoza Uriarte <ramendoza_at_uchicago.edu>
wrote:
> Hello VMD Community,
>
> I loaded a molecule with its respective .psf and .coor files, where the
> .coor file was read as a NAMD Binary Coordinates file. I then wanted to
> write out the pdb file; for example, by doing the following in the
> TkConsole:
>
> set all [atomselect top "all"]
> $all writepdb new.pdb
>
> However, I found it surprising that this yields slightly different
> coordinates and box dimensions. For instance:
>
> From .coor: (-12.171550750732422, 5.363558769226074, -15.094483375549316),
> (-11.626058578491211, 4.931212425231934, -15.867215156555176),
>                       (-12.769146919250488, 6.002536773681641,
> -15.656786918640137) <--- A small subset of all the coordinates
>                       cellBasisVector1 87.59627914428711 0 0
>                       cellBasisVector2 0 88.96563339233398 0
>                       cellBasisVector3 0 0 97.37928009033203
>                       cellOrigin 0.1676909178495407 0.361166387796402
> 0.04699717089533806
>
> From new.pdb: (-12.17199993133545, 5.363999843597412,
> -15.093999862670898), (-11.62600040435791, 4.931000232696533,
> -15.866999626159668),
>                             (-12.769000053405762, 6.002999782562256,
> -15.656999588012695) <--- A small subset of all the coordinates
>                             cellBasisVector1 87.59599685668945 0 0
>                             cellBasisVector2 0 88.96599960327148 0
>                             cellBasisVector3 0 0 97.37999725341797
>                             cellOrigin 0.16769009828567505
> 0.36116769909858704 0.04699849709868431
>
> So far, I have tried a Google and VMD archive search; however, I have not
> determined why this occurred. Additionally, I am using VMD for
> LINUXAMD64, version 1.9.4a51. Any comments on why this occurred would be
> appreciated.
>
> Thank you,
> Ramon
>