[chimerax-users] Alternative locations

[Elaine Meng]

Hi Mike,
Alternate locations are for different positions of the same atoms in the same residue type (chemically identical, just different positions).  Looks like your file is trying to multiplex the ribose 2' -OH and 2' -H (deoxy) within the same residue, which is not in the PDB format specs.  It just so happens that Chimera tolerates it but ChimeraX does not.

<https://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM>

I hope this helps,
Elaine 
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Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Aug 14, 2022, at 3:05 PM, Michael Bruist via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> In a demonstration page for students, I wish to show how the presence of the 2’OH on a ribonucleotide creates a clash at the active site of DNA polymerase. We are also trying to see if 2’OH’s create clashes within the primer. I have created a PDB file with deoxyribose as alternative location A and ribose as alternative location B. This works in original Chimera, but I am not getting it to work in ChimeraX. I am not able to specify the alternative atoms by their A and B designations. I do not see alternative locations in the hierarchy under target specification in the documentation. 
> My PDB file is attached. Residues 106-113 have alternate locations included. The command “altlocs change A :113" does not seem to change anything, nor does changing the selection buttons in the Altexplorer.<1qsy_d_rPrimer_d_rATP.pdb>
> 
> Mike Bruist
> mbruist at sju.edu