[Chimera-users] Delete pseudobonds

[Elaine Meng]

I actually tested the procedure of removing all the CONECT records from Javier’s file, opening the edited file, and then adding the bond between the two atoms, so I can confirm that it works.  The structure is a cyclic peptide, and the bond in question was from the last residue up to the first.

However, I didn’t try the alternative procedure Eric mentions, which might be easier.
Elaine

> On Jul 12, 2018, at 11:13 AM, Eric Pettersen <eric.pettersen at gmail.com> wrote:
> 
> Hi Javier,
> 	It could be tricker than that, because there may be no explicit CONECT record creating the bond — Chimera considers consecutive residues in ATOM records to be connected unless there is a TER card between them.  So you might have to insert a TER between them.  Another alternative is to hide or close the “missing structure” pseudobonds as Elaine outlined, and then force the hidden covalent bond to show with the command:
> 
> 	setattr b display 2
> 
> This forces all bonds into being displayed if and only if the two endpoint atoms are displayed.  The hidden covalent bonds normally have a ‘display’ value of 0. i.e. never display them.
> 
> —Eric
> 
> 	Eric Pettersen
> 	UCSF Computer Graphics Lab
> 
>> On Jul 12, 2018, at 9:37 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>> 
>> Hi Javier,
>> You can delete it using the Pseudobond Panel (in menu under Tools… General Controls): click “missing segments” on the left to choose it, then click the “close” button on the right (different than the Close button at the bottom, which closes the panel).
>> 
>> However, this does not solve your problem:  Chimera already considers those atoms to be covalently bonded because of the CONECT records in your file, and will not let you add another bond.  The only reason it  was shown as a pseudobond instead of regular bond is that the distance was abnormally long (>3 A).
>> 
>> If you want to add a bond between the atoms you should remove the CONECT records from your PDB file before opening.  Then there will not be any covalent bond between the atoms yet, so you can select and bond them.
>> I hope this helps,
>> Elaine
>> -----
>> Elaine C. Meng, Ph.D.
>> UCSF Chimera(X) team
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>> 
>>> On Jul 12, 2018, at 1:34 AM, Javier Marchena <javier.mar97 at gmail.com> wrote:
>>> 
>>> Hi,
>>> 
>>> A pseudobond has been automatically created in one of my structures, because of "missing segments". I want to delete the pseudobond in order to create a real covalent bond between those two atoms. But I have problems with deleting the pseudobond, I have not found a way to do it. Could you help me out?
>>> 
>>> Thanks in advance.
>>> 
>>> PS: I send you the molecule in pdb format just for you to see the pseudobond.
>> 
>> 
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