[Chimera-users] looking for help in UCSF Chimera

[Eric Pettersen]

Hi,
	What created these PDB files?  I only looked briefly at the first one (top-2-2242.pdb), but for instance residue 66 in chain A has two copies of every atom (at different coordinates) except for the C and the O.  I’m guessing the the original PDB file had alternate-location indicators to differentiate between the atoms, but that those indicators were dropped by whatever program wrote this version of the file.  At any rate, Chimera will not be able to perform minimization on such a file.  So the first thing you need to do is fix the program that wrote this file so that it outputs a legal PDB file.
	Once you’ve done that, then I can help you with any further problems you have.  You should report errors to chimera-bugs at cgl.ucsf.edu rather than chimera-users.  Besides regular email, you can also use Help->Report A Bug in the Chimera menus to do so.

--Eric

	Eric Pettersen
	UCSF Computer Graphics Lab

> On Aug 6, 2017, at 5:01 AM, Ch Bilal <ch.bilal321 at outlook.com> wrote:
> 
> Respected Sir/Madam.
> 
> Its Bilal here and i m doing research on a protein "rstA". I am  UCSF Chimera user and i am facing an error while energy minimization i got a pop up windows with  this error "No MMKT name of atom "HN1" in standard residue "LYS",  please help me out i am attaching my complexes with this mail as well please find the attachment.
> Thank you!
> <top-2-2242.pdb><top-3-1610.pdb><top-4-530.pdb>_______________________________________________
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