[Chimera-users] mmCIF lacks peptide bonds

[Conrad Huang]

Hi, Mike.

The problem is that Chimera depends on the presence of the 
"entity_poly_seq" table for inter-residue connectivity, and your mmCIF 
file does not have that table.  I've modified Chimera so that, instead 
of just giving up when entity_poly_seq is missing, it uses a 
simple-minded heuristic to connect adjacent amino acids with the same 
chain identifier.  That should be in the daily builds 
(http://www.cgl.ucsf.edu/chimera/download.html#daily) dated April 14 or 
later.  Can you please give that a spin tomorrow, or when you have a 
chance?  Thanks.

Conrad

On 4/9/2016 12:44 PM, Elaine Meng wrote:
> Silly me, if I select only the N,C atoms before adding all reasonable bonds, I get the desired 2396 bonds total for 2gbp.  Thus you can minimize the “danger” by selecting only the relevant atoms for bond addition.
>
> Elaine
>
> On Apr 9, 2016, at 12:29 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>
>> Hi Mike,
>> I was waiting for someone who knows more about our mmCIF-reading code to give a more explanatory answer, but in the meanwhile, a solution may be to add the bonds using the Build Structure tool.
>>
>> I assumed you meant the C-N peptide bonds between successive amino acids within a chain.  Since I didn’t have an example I tried to generate one by deleting those bonds, commands:
>>
>> open 2gbp
>> sel
>> [… that reports 2396 bonds ]
>> ~sel
>> ~ribbon; display
>> ~bond @n,c
>>
>> If I select again it now reports 2088 bonds.  OK, now to test the solution..
>>
>> In Build Structure (in menu under Tools… Structure Editing) I went to the Adjust Bonds section (and with all atoms selected) clicked “Add” reasonable bonds between selected atoms, then refreshed the selection again to check how many bonds were added.  However, I got 2397 instead of 2396, so there was apparently one more than in the original structure.  So that is the main danger/difficulty… if you get more or fewer bonds than expected, figuring out which they are. You can delete any extra with ~bond, specifying only the offending pair(s) of atoms.
>>
>> Simply adding the bonds doesn’t change the bond length.  I see there is a separate option to change bond length right below, which might be a little confusing.
>>
>> There is also a “bond” command to add a bond, but it takes only two atoms.  Only the GUI can be used to add bonds en masse.
>>
>> Docs for Adjust Bonds, including criteria for what is a reasonable bond:
>> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#bond>
>>
>> … for commands bond and ~bond
>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/bond.html>
>>
>> I hope this helps,
>> Elaine
>> -----
>> Elaine C. Meng, Ph.D.
>> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>>
>> On Apr 9, 2016, at 11:58 AM, david gae <ddgae at ucdavis.edu> wrote:
>>
>>> 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), 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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