[Chimera-users] CjimeraX PDB save

Eric Pettersen pett at cgl.ucsf.edu
Mon Apr 2 15:18:50 PDT 2018

Just a short erratum:  the PDB limit is actually 62 chains (all upper and lower case letters plus digits).


> On Apr 2, 2018, at 2:51 PM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:
> Hi John,
> 	The PDB format only supports single-character chain IDs (one of the reasons for mmCIF format), so it is impossible to save structures with more than 36 chains in PDB format without losing chain information.
> 	A semi-workaround is to:
> 1) In ChimeraX: split the structure into multiple structures, one per chain (“split #1”)
> 2) Save those models into a multi-MODEL PDB file (“save ~/rib.pdb models #1”)
> 3) Read them into Chimera.
> 4) If there are <= 36 models, combine them into a single model (“combine” button of the Model Panel), otherwise you just have to work with them as separate models.
> —Eric
> 	Eric Pettersen
> 	UCSF Computer Graphics Lab
>> On Apr 2, 2018, at 2:29 PM, John Mercer, Ph.D. <jmercer at duke.edu <mailto:jmercer at duke.edu>> wrote:
>> Hi Elaine,
>> I load a ribosome mmcif file in ChimeraX and save it at as a PDB file. It loads and works fine in Chimera but all the chain identifiers have disappeared. Is there away to save a PDB file from ChimeraX that retains the identifiers? I am wanting to use the larger set of tools in Chimera when only mmcif files are available. 
>> Best,
>> -John
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