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From: CCP4 bulletin board on behalf of Pavel Mader
Sent: Monday, November 4, 2019 6:06:11 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] why does Coot ignore CONECT?
Hi Paul,
thank you for your
On 04/11/2019 17:06, Pavel Mader wrote:
Hi Paul,
thank you for your answer. My problem is that I am building a cyclic peptide with non-standard amino acids,
the side chains of which are linked by click chemistry... I know how to make modified amino acids that will
make peptide bonds with
176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>
Komu: CCP4BB@JISCMAIL.AC.UK
Datum: 4. 11. 2019 12:16:38
Předmět: Re: [ccp4bb] why does Coot ignore CONECT?
"
What does refmac do if you feed it the coordinates with side chains close
enough to bond? In some cases it makes a full link dictionary with bonds
angle
ected), but I don't consider this as a good
> general practice for building long polypeptide chains...
>
> Thanks in advance for any hints guiding me in the right direction.
>
> Pavel
> -- Původní e-mail --
> Od: Paul Emsley
> Komu: CCP4BB@JISCMAIL.AC.UK
> Datu
is as a good general practice for building
long polypeptide chains...
Thanks in advance for any hints guiding me in the right direction.
Pavel
-- Původní e-mail --
Od: Paul Emsley
Komu: CCP4BB@JISCMAIL.AC.UK
Datum: 1. 11. 2019 21:16:11
Předmět: Re: [ccp4bb] why does Coot ignore CONEC
Hi Paul,
I think this is a very good call as CONECT records are notoriously unreliable.
Many PDB files don't have them and many programs don't update them when you
change atom numbers. Even in annotated PDB entries there are many problems with
those. It's better to forget about them altogether
On 01/11/2019 20:17, Pavel Mader wrote:
Hello,
Hello.
I have a question, can anyone explain, why does Coot not display a covalent bond manually specified by
CONECT line in a pdb file?
Because I have never thought them necessary. Using SSBOND, LINK and residue dictionaries seemed to me to
Hello,
I have a question, can anyone explain, why does Coot not display a covalent
bond manually specified by CONECT line in a pdb file? The same file shows
the covalent bond if displayed in Pymol.
Thank you in advance,
Pavel
