[buster-discuss] Big trouble with MLY

Mon Feb 5 15:21:25 CET 2024

Dear ClAuS,

That is very easy and works ! For myosins we always use a Gelly file for the Mg2+ coordination, so I just needed to add the line there.

Sure it’ll be better to have it corrected in the next release, but for the moment it’ll do it, no problem.

Thank you very much, and have a great week,

---------------------------------------------------
Carlos KIKUTI, PhD
UMR144 - CNRS - Institut Curie
Pavillon Trouillet Rossignol
26 Rue d’Ulm - 75005 Paris, France
carlos.kikuti at curie.fr<mailto:carlos.kikuti at curie.fr>

De : buster-discuss <buster-discuss-bounces at globalphasing.com> de la part de buster-discuss-request at globalphasing.com <buster-discuss-request at globalphasing.com>
Date : vendredi, 2 février 2024 à 16:26
À : buster-discuss at globalphasing.com <buster-discuss at globalphasing.com>
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Today's Topics:

   1. Re: Big trouble with MLY (Kikuti Carlos)
   2. Re: Big trouble with MLY (ClAuS Flensburg)

----------------------------------------------------------------------

Message: 1
Date: Fri, 2 Feb 2024 11:52:55 +0000
From: Kikuti Carlos <Carlos.Kikuti at curie.fr>
To: "buster-discuss at globalphasing.com"
        <buster-discuss at globalphasing.com>
Subject: Re: [buster-discuss] Big trouble with MLY
Message-ID:
        <PR1P264MB34786F5F0069B94196DAD09387422 at PR1P264MB3478.FRAP264.PROD.OUTLOOK.COM>

Content-Type: text/plain; charset="windows-1252"

Hey Phil and Rohan,

Thank you for your replies. I have only 2 copies of MLY.cif in the computer, one is in $CCP4/lib/data/monomers/m, the other one is in Coot’s directory under $CCP4, and they are identical. So I guess Buster is taking the one from $CCP4, right?

If that’s correct, then yes, it is already as peptide:
MLY MLY N-DIMETHYL-LYSINE peptide 30 12 .

  *   Which is curious because, also for M3L for which the TER line is not added, Buster will always convert them to HETATM, even if you manually edit the pdb file.

In Coot, the peptide bonds around the newly added MLY look OK, but I created the LINKs as suggested by Rohan anyways:
LINK         N   MLY A 189                 C   THR A 188     1555   1555
LINK         C   MLY A 189                 N   LYS A 190     1555   1555

But when Buster takes it up, it is still creating the TER line at aa 188… Even if I tell it Pdb2Tnt_RunAdjustLNNN=yes

I believe this is something within the Buster/TNT/Gelly code, but my skills are not that developed to find where exactly… I wish there was a keyword like CreateTERLineBeforeSpecialResidue=no …

Anyways, for the moment I using a workaround that I’m describing for records, for when other people face the same issue:

  1.  Modify the refine.pdb: remove the TER line before the special amino acid;
  2.  Convert it to mmcif (for instance with https://mmcif.pdbj.org/converter/ );
  3.  Download the resulting mmcif file and submit that to Validate.

This is much easier (at least to me) than modifying directly the BUSTER_model.cif, which requires many more changes (all those exclamation marks).

Well, I’m still on the lookout for a real solution.

All the best,

---------------------------------------------------
Carlos KIKUTI, PhD
UMR144 - CNRS - Institut Curie
Pavillon Trouillet Rossignol
26 Rue d’Ulm - 75005 Paris, France
carlos.kikuti at curie.fr<mailto:carlos.kikuti at curie.fr>

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Message: 2
Date: Fri, 2 Feb 2024 15:25:38 +0000
From: ClAuS Flensburg <claus at globalphasing.com>
To: Kikuti Carlos <Carlos.Kikuti at curie.fr>
Cc: "buster-discuss at globalphasing.com"
        <buster-discuss at globalphasing.com>
Subject: Re: [buster-discuss] Big trouble with MLY
Message-ID: <20240202152538.GN25590 at laue.globalphasing.com>
Content-Type: text/plain; charset=us-ascii

Dear Carlos,

On Fri, Feb 02, 2024 at 11:52:55AM +0000, Kikuti Carlos wrote:
> Hey Phil and Rohan,
>
> Thank you for your replies. I have only 2 copies of MLY.cif in the computer, one is in $CCP4/lib/data/monomers/m, the other one is in Coot?s directory under $CCP4, and they are identical. So I guess Buster is taking the one from $CCP4, right?
>
> If that?s correct, then yes, it is already as peptide:
> MLY MLY N-DIMETHYL-LYSINE peptide 30 12 .
>
>
>   *   Which is curious because, also for M3L for which the TER line is not added, Buster will always convert them to HETATM, even if you manually edit the pdb file.
>
> In Coot, the peptide bonds around the newly added MLY look OK, but I created the LINKs as suggested by Rohan anyways:
> LINK         N   MLY A 189                 C   THR A 188     1555   1555
> LINK         C   MLY A 189                 N   LYS A 190     1555   1555
>
> But when Buster takes it up, it is still creating the TER line at aa 188? Even if I tell it Pdb2Tnt_RunAdjustLNNN=yes
>
> I believe this is something within the Buster/TNT/Gelly code, but my skills are not that developed to find where exactly? I wish there was a keyword like CreateTERLineBeforeSpecialResidue=no ?
>
> Anyways, for the moment I using a workaround that I?m describing for records, for when other people face the same issue:
>
>   1.  Modify the refine.pdb: remove the TER line before the special amino acid;
>   2.  Convert it to mmcif (for instance with https://mmcif.pdbj.org/converter/ );
>   3.  Download the resulting mmcif file and submit that to Validate.
>
> This is much easier (at least to me) than modifying directly the BUSTER_model.cif, which requires many more changes (all those exclamation marks).
>
> Well, I?m still on the lookout for a real solution.

BUSTER will issue TER record prior to components that are not
considered to be part of a polymer. The membership of the polymer set
is generally defined in the files sets.dat and exoticaa.dat. Specifically

...
NOTE BUSTER_DICT_ECHO Polymer: for PDB TER record and mmCIF pdbx_refine_tls_group treatment.
NOTE BUSTER_DICT_SET Polymer = Protein + Nucleic
...

The easiest method to fix your issue with TER records would be to
append MLY to the Polymer set like this:

cat > add-mly-to-polymer-set.dat <<EOF
NOTE BUSTER_DICT_SET Polymer = Polymer + {RESTYPE MLY}
EOF

and then run BUSTER with

   refine -Gelly add-mly-to-polymer-set.dat ...

Does this do what you expect it to do?

Also, note how M3L is already in the ExoticAA set which is why there
is no TER record for those. We should make the content of exoticaa.dat
consistent, and will make sure that this is done in the next release.

Best regards,

ClAuS (for BUSTER Developers)

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