Re: [COOT] Linking two sidechains with a double bond and refining

[David Dranow]

Hi David Briggs,

Thank you for the suggestion of AceDrg.  I gave it a try, using the Coot way 
and the Jligand way for AceDrg. For some reason the Coot method didn't make a 
cif, only jligand did.  But the cif didn't have any effect on refinement.  What 
did work for Phenix was to define the planarity in a phil file:

planarity {

  action = *add

  atom_selection = \

chain A and resname LIG and resid 3 and name C1 or \

chain A and resname LIG and resid 3 and name C2 or \

chain A and resname IGL and resid 6 and name C3 or \

chain A and resname IGL and resid 6 and name C4 

  sigma = 0.02

}



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Re: [COOT] Linking two sidechains with a double bond and refining

[David Dranow]

Hi Joel,

That's a great idea! I've considerd it, and technically it would work as you 
suggest to refine correctly.  However, that would look like more carbons come 
from one of the two precursor molecules than the other, which chemically would 
be wrong. I really want to avoid giving the impression that different chemistry 
happened to form this covalent bond. It's just unfortunate that the created 
bond isn't more easily defined for these programs. 

Thanks,
David



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Re: [COOT] Linking two sidechains with a double bond and refining

[David Briggs]

Hi David,

Rob Nicholls gave a talk about AceDrg and link generation at a CCP4 SW a few 
years ago..

https://www.youtube.com/watch?v=p4oTJ0bjD3M

I think this will contain the answers you are looking for.

Cheers,

David



--

Dr David C. Briggs CSci MRSB (he/him)

Principal Laboratory Research Scientist

Signalling and Structural Biology Lab

The Francis Crick Institute

London, UK

Working hours: Mon-Fri 0900-1700

==

about.me/david_briggs | 
OrcID | Google Scholar 



From: Mailing list for users of COOT Crystallographic Software 
 on behalf of David Dranow 

Sent: 01 August 2023 03:43
To: COOT@JISCMAIL.AC.UK 
Subject: Re: Linking two sidechains with a double bond and refining


External Sender: Use caution.


Message was attached instead of in the body for some reason. Here it is"

Hi Learned Friends,

I'm trying to refine a structure that has a very similar staple to the one in 
8GJS.  In that structure, there's a double bond between residue 5 and 12 in 
chain B.  I've tried to define a link using jligand and I get a cif that looks 
like it would define the double bond.  But when I load that into Coot and try 
to refine the link, the bond blows up, bonded atoms seperate.  Has anyone had 
any luck with this?  What should I use to define a double bond link such that 
Coot (and Phenix) doesn't blow it up, but also keeps the appropriate atoms in 
plane (either trans or cis, NOT something in between).

Thanks,
David



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Re: [COOT] Linking two sidechains with a double bond and refining

[Joel Tyndall]

Hi,

Not looking deep at your sequence/link, have you tried to move the link to a 
single bond and avoid the double as the linked bond? This way you can 
paraetrise the double bond correctly. Not sure is global phasing could help..
Joel

-Original Message-
From: Mailing list for users of COOT Crystallographic Software 
 On Behalf Of David Dranow
Sent: Tuesday, August 1, 2023 2:43 PM
To: COOT@JISCMAIL.AC.UK
Subject: Re: Linking two sidechains with a double bond and refining

Message was attached instead of in the body for some reason. Here it is"

Hi Learned Friends,

I'm trying to refine a structure that has a very similar staple to the one in 
8GJS.  In that structure, there's a double bond between residue 5 and 12 in 
chain B.  I've tried to define a link using jligand and I get a cif that looks 
like it would define the double bond.  But when I load that into Coot and try 
to refine the link, the bond blows up, bonded atoms seperate.  Has anyone had 
any luck with this?  What should I use to define a double bond link such that 
Coot (and Phenix) doesn't blow it up, but also keeps the appropriate atoms in 
plane (either trans or cis, NOT something in between).

Thanks,
David



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Re: [COOT] Linking two sidechains with a double bond and refining

[David Dranow]

Message was attached instead of in the body for some reason. Here it is" 

Hi Learned Friends,

I'm trying to refine a structure that has a very similar staple to the one in 
8GJS.  In that structure, there's a double bond between residue 5 and 12 in 
chain B.  I've tried to define a link using jligand and I get a cif that looks 
like it would define the double bond.  But when I load that into Coot and try 
to refine the link, the bond blows up, bonded atoms seperate.  Has anyone had 
any luck with this?  What should I use to define a double bond link such that 
Coot (and Phenix) doesn't blow it up, but also keeps the appropriate atoms in 
plane (either trans or cis, NOT something in between).  

Thanks,
David



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