Re: [COOT] Connecting non-adjacently numbered residues

[Paul Emsley]

Yes please.

Paul.

On 31/03/2022 20:20, Eleanor Dodson wrote:
> Could Andrew T please send an example of a data set that fails for
> testing?
>
> Eleanor
>
> On Wed, 30 Mar 2022 at 22:24, Paul Emsley  > wrote:
>
>
> On 29/03/2022 22:26, DeLaitsch, Andrew T. wrote:
>>
>>
>> I am working on refining antibody-HIV-Env structures in COOT. The
>> problem I have is that both antibodies and HIV-Env have
>> standardized numbering systems (e.g. Kabat for antibodies and
>> HXB2 for HIV-Env) which result in sequential residues in the
>> protein's primary structure not having sequential numbering
>> (e.g., residues numbered 143 and 152 should be connected by a
>> peptide bond). When doing refinements in COOT, this
>> non-sequential numbering causes problems, as the peptide bond is
>> not formed and the residues get 'forced' apart from one another
>> as the program thinks there should be more residues in-between
>> the two. Is there a simple way to go about fixing this?
>> Currently, my workaround is to renumber residues so that they are
>> sequentially numbered, and then after the final refinement go
>> into the PDB and change the numbering. However, this workaround
>> is less-than-ideal as there are a many segments to renumber, and
>> also I rely on the HXB2 numbering while doing the refinement to
>> know which residues are which in my structure.
>>
>
> Why is it that so many correspondents on this list don't mention
> the version of Coot that they are using, where the got it from or
> how I (or anyone) might reproduce the problem?
>
> Hmm.
>
>
> Paul.
>
>
>
> 
>
> To unsubscribe from the COOT list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1
>



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Re: [COOT] Connecting non-adjacently numbered residues

[Eleanor Dodson]

Could Andrew T please send an example of a data set that fails for testing?

Eleanor

On Wed, 30 Mar 2022 at 22:24, Paul Emsley  wrote:

>
> On 29/03/2022 22:26, DeLaitsch, Andrew T. wrote:
>
>
>
> I am working on refining antibody-HIV-Env structures in COOT. The problem
> I have is that both antibodies and HIV-Env have standardized numbering
> systems (e.g. Kabat for antibodies and HXB2 for HIV-Env) which result in
> sequential residues in the protein's primary structure not having
> sequential numbering (e.g., residues numbered 143 and 152 should be
> connected by a peptide bond). When doing refinements in COOT, this
> non-sequential numbering causes problems, as the peptide bond is not formed
> and the residues get 'forced' apart from one another as the program thinks
> there should be more residues in-between the two. Is there a simple way to
> go about fixing this? Currently, my workaround is to renumber residues so
> that they are sequentially numbered, and then after the final refinement go
> into the PDB and change the numbering. However, this workaround is
> less-than-ideal as there are a many segments to renumber, and also I rely
> on the HXB2 numbering while doing the refinement to know which residues are
> which in my structure.
>
>
> Why is it that so many correspondents on this list don't mention the
> version of Coot that they are using, where the got it from or how I (or
> anyone) might reproduce the problem?
>
> Hmm.
>
>
> Paul.
>
>
>
> --
>
> To unsubscribe from the COOT list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1
>



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Re: [COOT] Connecting non-adjacently numbered residues

[Rozeboom, H.J.]

Hi,

Add something like this in the header:
LINKRALA A  74 VAL A  84gap

With regards,

Henriette Rozeboom

Biotechnology

Faculty of Science and Engineering, University of Groningen

9747 AG Groningen, The Netherlands

+31(0)50 363 3904


On Tue, Mar 29, 2022 at 11:37 PM DeLaitsch, Andrew T. 
wrote:

> Hi,
>
> I am working on refining antibody-HIV-Env structures in COOT. The problem
> I have is that both antibodies and HIV-Env have standardized numbering
> systems (e.g. Kabat for antibodies and HXB2 for HIV-Env) which result in
> sequential residues in the protein's primary structure not having
> sequential numbering (e.g., residues numbered 143 and 152 should be
> connected by a peptide bond). When doing refinements in COOT, this
> non-sequential numbering causes problems, as the peptide bond is not formed
> and the residues get 'forced' apart from one another as the program thinks
> there should be more residues in-between the two. Is there a simple way to
> go about fixing this? Currently, my workaround is to renumber residues so
> that they are sequentially numbered, and then after the final refinement go
> into the PDB and change the numbering. However, this workaround is
> less-than-ideal as there are a many segments to renumber, and also I rely
> on the HXB2 numbering while doing the refinement to know which residues are
> which in my structure.
>
> Thanks,
> Andy
>
> --
>
> To unsubscribe from the COOT list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1
>



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Re: [COOT] Connecting non-adjacently numbered residues

[Paul Emsley]

On 29/03/2022 22:26, DeLaitsch, Andrew T. wrote:



I am working on refining antibody-HIV-Env structures in COOT. The 
problem I have is that both antibodies and HIV-Env have standardized 
numbering systems (e.g. Kabat for antibodies and HXB2 for HIV-Env) 
which result in sequential residues in the protein's primary structure 
not having sequential numbering (e.g., residues numbered 143 and 152 
should be connected by a peptide bond). When doing refinements in 
COOT, this non-sequential numbering causes problems, as the peptide 
bond is not formed and the residues get 'forced' apart from one 
another as the program thinks there should be more residues in-between 
the two. Is there a simple way to go about fixing this? Currently, my 
workaround is to renumber residues so that they are sequentially 
numbered, and then after the final refinement go into the PDB and 
change the numbering. However, this workaround is less-than-ideal as 
there are a many segments to renumber, and also I rely on the HXB2 
numbering while doing the refinement to know which residues are which 
in my structure.




Why is it that so many correspondents on this list don't mention the 
version of Coot that they are using, where the got it from or how I (or 
anyone) might reproduce the problem?


Hmm.


Paul.




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[COOT] Connecting non-adjacently numbered residues

[DeLaitsch, Andrew T.]

Hi,

I am working on refining antibody-HIV-Env structures in COOT. The problem I 
have is that both antibodies and HIV-Env have standardized numbering systems 
(e.g. Kabat for antibodies and HXB2 for HIV-Env) which result in sequential 
residues in the protein's primary structure not having sequential numbering 
(e.g., residues numbered 143 and 152 should be connected by a peptide bond). 
When doing refinements in COOT, this non-sequential numbering causes problems, 
as the peptide bond is not formed and the residues get 'forced' apart from one 
another as the program thinks there should be more residues in-between the two. 
Is there a simple way to go about fixing this? Currently, my workaround is to 
renumber residues so that they are sequentially numbered, and then after the 
final refinement go into the PDB and change the numbering. However, this 
workaround is less-than-ideal as there are a many segments to renumber, and 
also I rely on the HXB2 numbering while doing the refinement to know which 
residues are which in my structure.

Thanks,
Andy



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