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Dear Remie,
there is a difference between the bonds you see in Coot and the bonds
that are recognised by e.g. refmac5. Can you measure the bond length
after refinement and compare it with the expected value? Does the bond
length deviate from the target value? If not, your bond is probably
recognised, i.e. restrained during refinement, although it is not
displayed as such.
Regards,
Tim
On 04/09/2014 06:02 AM, Remie Fawaz-Touma wrote:
> Thanks to Maisam and Paul (answers below) but I still could not see
> the links in coot after refining.
>
> In coot before refinement, the glucoses are connected, but when I
> refine, they become disconnected, then if I add a link in coot by
> doing Extension>Modeling>Add a link, I get disconnected bonds.
>
> The LINK I see in pdb as text is for Arg and other residues but not
> for the sugars
>
> Please advise on what I should do to see the sugars connected after
> refinement,
>
> Thank you so much,
>
> Remie
>
>
> On Apr 4, 2014, at 10:45 PM, Remie Fawaz-Touma
> <[log in to unmask]> wrote:
>
>> Hi all,
>>
>> I need help creating links between units of sugar (ligands) in
>> the PDB file before refining so that CCP4 recognizes the sugars
>> are attached.
>>
>> I tried the one suggestion I got before Extension > Make a Link,
>> but I get discontinued bonds instead of full bonds.
>>
>> Thanks so much for all your help in advance.
>>
>> Remie
>
> A dotted line is how Coot represents a LINK. It will not use solid
> lines for LINKs. You don't need a solid line for Coot and Refmac to
> consider the residues as bonded.
>
> If you examine the output PDB file, you will see a LINK record.
>
> Paul.
>
> If you open the pdb that Refmac generates ( As text file ) you will
> see that there is an "R" added to your link and it is "linkR", you
> need to delete that "R" and press the space button one time to
> correct for the spacing in your link description, and then coot
> will show that dotted line.
>
> If you want to see a solid line in coot for the links, your sugar
> molecules should be defined as the residues of the same chain, but
> to be honest I have never tried that myself.
>
> And if you run the refmac, and the pdb that is generated does not
> show the description of your link that means that the description
> of your link is not right.
>
> Hope this helped.
>
> Meisam
>
- --
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
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