Dear Remie,
There is an alternative route, which requires the usage of the JLigand program
of Andrey Lebedev, which is part of the CCP4 suite.
You can search for the two sugars in the JLigand library by inserting their
letter code in the "Load Ligand" window or you can use the drawing tools, if
they are new. When both sugars are displayed in JLigand, you can link them
together with the tool "Link" (left menu) and minimise the obtained molecule
(Ligand > Regularise). At this point you can save the molecule as a monomer and
this will generate the corresponding dictionary cif file.
After obtaining the cif file, you will have to restart JLigand, open the cif
file and save the molecule as PDB this time (" Save Coordinates").
You will have the option to include or not hydrogens.
Now you have cif file and PDB file for the joint sugars, both ready to be used
in COOT and in REFMAC and everything should run smoothly.
Good luck!
Dr Ivan Campeotto
Imperial College London
UK
On 9 Apr 2014, at 08:47, <[email protected]>
wrote:
> Sorry, I made a typo. One should of course delete the O1!
> Herman
>
> -----Ursprüngliche Nachricht-----
> Von: CCP4 bulletin board [mailto:[email protected]] Im Auftrag von
> Schreuder, Herman R&D/DE
> Gesendet: Mittwoch, 9. April 2014 09:17
> An: [email protected]
> Betreff: [ccp4bb] AW: [ccp4bb] Create Links in PDB
>
> Dear Remie,
>
> The first thing I would do is to download a random file form the pdb with
> sugars attached and examine how the link looks like in coot and in an editor.
> You could use e.g. (shameless plug) 4ci9.
> The next thing to do is to check the link record you created. Here the
> punch-card heritage of the pdb format is still very prominent: one space too
> much or too little and things will not work. I even have had mysterious cases
> where the link would not work, although it looked ok in the editor. I would
> copy and paste a link record from an official pdb file and edit that one,
> making sure that the positions of the atom names etc. stay exactly the same
> (do not move to the left or right).
>
> An alternative, which may even be better is to start from scratch. For
> N-linked sugars this would go as follows:
>
> go to to the linked sugar in coot
> delete the NAG attached to the Asn
> get monomer NAG
> merge molecules (to get the NAG in the same pdb file as your protein)
> delete the O4 (delete item Atom)
> fit and real space refine the NAG
> make link (between ASN ND2 and NAG C1)
>
> The same you should do for the other linked sugars. Make sure to delete the
> right oxygen which gets lost in the link. In this way you are sure your NAG
> has the right atom names and the correct cif file with restraints.
>
> Good luck!
> Herman
>
>
> -----Ursprüngliche Nachricht-----
> Von: CCP4 bulletin board [mailto:[email protected]] Im Auftrag von Remie
> Fawaz-Touma
> Gesendet: Mittwoch, 9. April 2014 06:03
> An: [email protected]
> Betreff: Re: [ccp4bb] Create Links in PDB
>
> 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 <[email protected]> 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
