[Chimera-users] MD movie error

Eric Pettersen pett at cgl.ucsf.edu
Mon Jul 16 08:52:23 PDT 2018

Hi ChuHui,
	Each model in the file has many different residues with the same residue and chain ID and Chimera can’t handle that when trying to match the atoms in later models to those in earlier models.  For example, each model in the file has a residue 3864 as a water with no chain ID, and then again as a sodium ion with no chain ID.
	If you don’t care specifically about the waters or ions (or both), one thing you could try is to open the file in Chimera as a regular multi-model PDB (rather than as a trajectory), and then delete the waters and/ or ions (i.e. ‘del solvent’ and/or ‘del ions’), and then save the PDB as a single file again.  Then that file should be able to be opened as a trajectory.


	Eric Pettersen
	UCSF Computer Graphics Lab

> On Jul 15, 2018, at 7:24 PM, ChuHui Fu <cfu at haverford.edu> wrote:
> Hi all, 
> When I was trying to use MD Movie option on the attached  pdb trajectory file, chimera kept telling me that there were missing residues. 
> "Chimera Error
> Residue 3864.het not in first model on line 126754 of 
> /homes/cfu/model1_sep_475.B_md_traj_system.pdb"
> But I checked that the number of atoms in each one of the pdb files and there didn't seem to be any missing. Then I separated the trajectory files and use vimdiff to compare the models pairwise, but doesn't seem like there are different residues, (unless I missed them). 
> Can anyone suggest what I might have done wrong? 
>>  model1_sep_475.B_md_traj_system.pdb <https://drive.google.com/a/haverford.edu/file/d/1w82K6a2FfLDzphcn6Jj2VwCjokFbXzqu/view?usp=drive_web>​
> Thanks!!
> -- 
> ChuHui Fu 
> B.S.Candidate in Chemistry 
> Haverford College, Class of 2019
> cfu at haverford.edu <mailto:cfu at haverford.edu>
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