[Chimera-users] pseudobond problem while writing mol2 format

[Eric Pettersen]

Happy to help!

—Eric

> On Dec 6, 2019, at 12:03 PM, Palani, Kirubakaran <Kirubakaran.Palani at fccc.edu> wrote:
> 
> Hi Eric,
>  
> That looks pretty much what I needed. Thanks for the prompt response also for the point making about the atom type changes.
>  
> Best regards,
> Kiruba
>  
> From: Eric Pettersen <pett at cgl.ucsf.edu <mailto:pett at cgl.ucsf.edu>>
> Reply-To: "chimera-users at cgl.ucsf.edu <mailto:chimera-users at cgl.ucsf.edu> BB" <chimera-users at cgl.ucsf.edu <mailto:chimera-users at cgl.ucsf.edu>>
> Date: Friday, December 6, 2019 at 2:28 PM
> To: "Palani, Kirubakaran" <Kirubakaran.Palani at fccc.edu <mailto:Kirubakaran.Palani at fccc.edu>>
> Cc: "chimera-users at cgl.ucsf.edu <mailto:chimera-users at cgl.ucsf.edu>" <chimera-users at cgl.ucsf.edu <mailto:chimera-users at cgl.ucsf.edu>>
> Subject: Re: [Chimera-users] pseudobond problem while writing mol2 format
>  
> EXTERNAL MESSAGE. DO NOT open attachments or click links from unknown senders or unknown emails.
>  
> Hi Kiruba, 
> For each of those pseudobonds, there is a hidden “real” bond.  To have the Mol2 file treat the segments as disconnected, the hidden bonds have to be deleted.  I have attached a simple Python script that does that.  So you would open your PDB file, run the script (simply opening the .py file will run it) and then save your Mol2.
> Keep in mind that deleting those hidden bonds will change the corresponding atom types.  So for instance the backbone nitrogens will be given the Mol2 type N.4 (appropriate for N-terminal) rather than N.am (appropriate for amide).
>  
> —Eric
>  
> 
> 
> Eric Pettersen
> UCSF Computer Graphics Lab
>  
> 
> 
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