[Chimera-users] issues with visualization of saxs models in chimera

Eric Pettersen pett at cgl.ucsf.edu
Tue Oct 20 09:05:42 PDT 2020

Hi Anabel,
	SAXS "PDB" files frequently have atoms that lie exactly on a grid, which causes some calculations in Chimera to fail. If you can prevent Chimera from trying to create bonds and/or "missing segment" pseudobonds between your "atoms", then those problematic calculations don't happen. The easiest way to do this is to change all your ATOM records into HETATM records. Make sure to keep the columns the same, so actually change "ATOM " (i.e. and the two trailing spaces) into "HETATM".


	Eric Pettersen
	UCSF Computer Graphics Lab

> On Oct 20, 2020, at 7:35 AM, Anabel Pacios Michelena <anabel.pacios_michelena at uni-wuerzburg.de> wrote:
> Dear Chimera team,
> I am a user from your software and I would like to have a superimposition of some crystallographic structures in a recent saxs pdb model I obtained. However, I cannot visualize the saxs pdb file with Chimera. Would you have any tips or inputs how can I do this?
> Thank you very much in advance for all your help,
> Kind regards,
> Anabel
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