Re: [ccp4bb] different residues as alternate occupancy?

[Jon Agirre]

Another relatively frequent case concerns carbohydrates at the reducing end
of a polysaccharide, where both alpha and beta anomeric forms can occur.
Because the PDB gives two different CCD IDs to alpha and beta anomeric
forms of the same monosaccharide – e.g. BGC and GLC for glucopyranose – you
have the same problem described here. See Fig9 in
https://journals.iucr.org/d/issues/2017/02/00/ba5257/ for an example (sorry
for the plug!).

On Tue, 25 Jun 2019 at 16:00, Guenter Fritz <
guenter.fritz.phenix.c...@gmail.com> wrote:

> Dear all,
> thank you all for feedback help.
> Best wishes!
> Guenter
>
> Dear Guenter, yes look at crambin (pdbcode 1EJG).
>
>
> This crashes Coot until you add*
>
>   allow_duplicate_sequence_numbers()
>
> to $HOME/.coot.py in OSX or the appropriate place on Windows. For
> Windows, as there is no $HOME, Coot uses .coot.py or .coot-preferences/
> directory for configuration - these can be found (added to) the
> directory in which Coot was installed (e.g. C:\WinCoot).
>
> To resolve your problem look at
>
> https://www.phenix-online.org/newsletter/CCN_2015_07.pdf#page=12
>
> example 5
>
> Br, Georg.
>
>
> Am 2019-06-24 um 4:22 PM schrieb Savvas Savvides:
>
> The structure of milk proteins obtained from in vivo-grown crystals from a
> viviparous cockroach could also serve as an interesting case:
>
> http://dx.doi.org/10.1107/S2052252516008903
>
> best wishes
> Savvas
>
>
> On 24 Jun 2019, at 16:03, Holton, James M <
> 270165b9f4cf-dmarc-requ...@jiscmail.ac.uk> wrote:
>
> A classic case of this is crambin.  Residue 25 of 3nir.
>
> -James Holton
> MAD Scientist
>
> On 6/24/2019 1:00 AM, Guenter Fritz wrote:
>
> Dear all,
>
> I am refining a multimer and mass spec data of the sample indicate
> that there is a mixture of two variants which differ in one amino acid
> residue. The density that we see is therefore most likely an average
> of both variants. I have created a pdb file with "alternate residues"
> each with 0.5 occupancy at this position to use it in refinement.
> However, the programs detect this as an error in the pdb file.
>
> Has anyone  faced such a problem previously? Any suggestions are very
> much appreciated.
>
> Thanks a lot and best regards, Guenter
>
> 
>
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>
>
>
> 
>
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>
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-- 
Dr Jon Agirre
Royal Society University Research Fellow
York Structural Biology Laboratory / Department of Chemistry
University of York, Heslington, YO10 5DD, York, UK
http://www.york.ac.uk/chemistry/research/ysbl/people/staff/jagirre/
Office: /B/K/065 Phone: +44 (0) 1904 32 8252
Twitter: @glycojones



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Re: [ccp4bb] different residues as alternate occupancy?

[Guenter Fritz]

Dear all,
thank you all for feedback help.
Best wishes!
Guenter


Dear Guenter, yes look at crambin (pdbcode 1EJG).


This crashes Coot until you add*

  allow_duplicate_sequence_numbers()

to $HOME/.coot.py in OSX or the appropriate place on Windows. For
Windows, as there is no $HOME, Coot uses .coot.py or .coot-preferences/
directory for configuration - these can be found (added to) the
directory in which Coot was installed (e.g. C:\WinCoot).

To resolve your problem look at

https://www.phenix-online.org/newsletter/CCN_2015_07.pdf#page=12

example 5

Br, Georg.


Am 2019-06-24 um 4:22 PM schrieb Savvas Savvides:
The structure of milk proteins obtained from in vivo-grown crystals 
from a viviparous cockroach could also serve as an interesting case:


http://dx.doi.org/10.1107/S2052252516008903

best wishes
Savvas


On 24 Jun 2019, at 16:03, Holton, James M 
<270165b9f4cf-dmarc-requ...@jiscmail.ac.uk 
> wrote:


A classic case of this is crambin. Residue 25 of 3nir.

-James Holton
MAD Scientist

On 6/24/2019 1:00 AM, Guenter Fritz wrote:

Dear all,

I am refining a multimer and mass spec data of the sample indicate
that there is a mixture of two variants which differ in one amino acid
residue. The density that we see is therefore most likely an average
of both variants. I have created a pdb file with "alternate residues"
each with 0.5 occupancy at this position to use it in refinement.
However, the programs detect this as an error in the pdb file.

Has anyone  faced such a problem previously? Any suggestions are very
much appreciated.

Thanks a lot and best regards, Guenter



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Re: [ccp4bb] different residues as alternate occupancy?

[Georg Mlynek]

Dear Guenter, yes look at crambin (pdbcode 1EJG).


This crashes Coot until you add*

  allow_duplicate_sequence_numbers()

to $HOME/.coot.py in OSX or the appropriate place on Windows. For
Windows, as there is no $HOME, Coot uses .coot.py or .coot-preferences/
directory for configuration - these can be found (added to) the
directory in which Coot was installed (e.g. C:\WinCoot).

To resolve your problem look at

https://www.phenix-online.org/newsletter/CCN_2015_07.pdf#page=12

example 5

Br, Georg.


Am 2019-06-24 um 4:22 PM schrieb Savvas Savvides:
The structure of milk proteins obtained from in vivo-grown crystals 
from a viviparous cockroach could also serve as an interesting case:


http://dx.doi.org/10.1107/S2052252516008903

best wishes
Savvas


On 24 Jun 2019, at 16:03, Holton, James M 
<270165b9f4cf-dmarc-requ...@jiscmail.ac.uk 
> wrote:


A classic case of this is crambin.  Residue 25 of 3nir.

-James Holton
MAD Scientist

On 6/24/2019 1:00 AM, Guenter Fritz wrote:

Dear all,

I am refining a multimer and mass spec data of the sample indicate
that there is a mixture of two variants which differ in one amino acid
residue. The density that we see is therefore most likely an average
of both variants. I have created a pdb file with "alternate residues"
each with 0.5 occupancy at this position to use it in refinement.
However, the programs detect this as an error in the pdb file.

Has anyone  faced such a problem previously? Any suggestions are very
much appreciated.

Thanks a lot and best regards, Guenter



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Re: [ccp4bb] different residues as alternate occupancy?

[Savvas Savvides]

The structure of milk proteins obtained from in vivo-grown crystals from a 
viviparous cockroach could also serve as an interesting case:

http://dx.doi.org/10.1107/S2052252516008903 


best wishes
Savvas


> On 24 Jun 2019, at 16:03, Holton, James M 
> <270165b9f4cf-dmarc-requ...@jiscmail.ac.uk> wrote:
> 
> A classic case of this is crambin.  Residue 25 of 3nir.
> 
> -James Holton
> MAD Scientist
> 
> On 6/24/2019 1:00 AM, Guenter Fritz wrote:
>> Dear all,
>> 
>> I am refining a multimer and mass spec data of the sample indicate 
>> that there is a mixture of two variants which differ in one amino acid 
>> residue. The density that we see is therefore most likely an average 
>> of both variants. I have created a pdb file with "alternate residues" 
>> each with 0.5 occupancy at this position to use it in refinement.  
>> However, the programs detect this as an error in the pdb file.
>> 
>> Has anyone  faced such a problem previously? Any suggestions are very 
>> much appreciated.
>> 
>> Thanks a lot and best regards, Guenter
>> 
>> 
>> 
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
> 
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1




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Re: [ccp4bb] different residues as alternate occupancy?

[Holton, James M]

A classic case of this is crambin.  Residue 25 of 3nir.

-James Holton
MAD Scientist

On 6/24/2019 1:00 AM, Guenter Fritz wrote:
> Dear all,
>
> I am refining a multimer and mass spec data of the sample indicate 
> that there is a mixture of two variants which differ in one amino acid 
> residue. The density that we see is therefore most likely an average 
> of both variants. I have created a pdb file with "alternate residues" 
> each with 0.5 occupancy at this position to use it in refinement.  
> However, the programs detect this as an error in the pdb file.
>
> Has anyone  faced such a problem previously? Any suggestions are very 
> much appreciated.
>
> Thanks a lot and best regards, Guenter
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1




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[ccp4bb] different residues as alternate occupancy?

[Guenter Fritz]

Dear all,

I am refining a multimer and mass spec data of the sample indicate that 
there is a mixture of two variants which differ in one amino acid 
residue. The density that we see is therefore most likely an average of 
both variants. I have created a pdb file with "alternate residues" each 
with 0.5 occupancy at this position to use it in refinement.  However, 
the programs detect this as an error in the pdb file.


Has anyone  faced such a problem previously? Any suggestions are very 
much appreciated.


Thanks a lot and best regards, Guenter



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