[Chimera-users] mmCIF lacks peptide bonds

[david gae]

Hi Mike, 

I believe PYMOL draws bonds where atoms are within a certain distance (I think it is in pymol source /pymol/layer2/ Atominfo.cpp) or where there is explicit record found in the cif file, hence you see connectivity.

According to the CHIMERA website (https://www.cgl.ucsf.edu/chimera/data/mmcif-oct2013/mmcif.html <https://www.cgl.ucsf.edu/chimera/data/mmcif-oct2013/mmcif.html>), CHIMERA has a dictionary of standard bond template for 265 residues and uses that to create your bonds. Perhaps your converted mmCIF has non-standard residues? 

In any case, I think RCSB requires coordinates and structure factor file only (but this could have changed in recent years). My personal opinion is that I wouldn’t worry too much about bond connectivity, but that your R statistics for your structure is reasonable for your resolution. 

Hope this helps, 
Dave
> On Apr 8, 2016, at 10:49 AM, Michael Blaisse <mblaisse at berkeley.edu> wrote:
> 
> Hello,
> 
> I'm solving a crystal structure and as I'm preparing to submit the final structure to PDB, I used the PDB_Extract tool to convert my final refined .pdb to an mmCIF file as per the request of PDB. After I do this, however, I noticed that if I open the CIF file in Chimera, it does not have any connectivity between the residues. This does not appear to be a problem in PyMOL. 
> 
> Less importantly, I also had a question about the Sequence view in Chimera. I have a break in my chain due to unmodelled residues, and I noticed that if I float my cursor over a residue in the sequence, it shows the correct residue number at the bottom of the window, however the numbering at the side of the sequence view window is wrong after the break because it does not take the chain break into account.
> 
> I appreciate any advice/help people can offer.
> 
> Thanks,
> Mike
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