Thank you all for your help :)
The only way I could solve it was to manually edit the PDB after placing
both conformations as desired.
Briefly:
i) Make "2CO" read in the PDB as a real alternate conformation: change resi
number (same as CYS), name ("B2CO" - conf B).
ii) Change "OXT" atom name to "O", otherwise you get the following mistake:
"Creating restraints.. Warning: definition not found for B/2CO 81/OXT"
iii) in my case, have fun editing all 4 chains!
ATOM 7184 N ACYS B 81 2.107 13.963 2.521 0.40 25.49
N
ATOM 7185 CA ACYS B 81 1.565 13.862 3.870 0.40 24.39
C
ATOM 7186 C ACYS B 81 1.130 12.437 4.157 0.40 21.49
C
ATOM 7187 O ACYS B 81 1.662 11.858 5.100 0.40 21.32
O
ATOM 7188 CB ACYS B 81 0.472 14.874 4.152 0.40 28.26
C
ATOM 7189 SG ACYS B 81 1.073 16.593 4.173 0.40 32.17
S
HETATM 7190 N B2CO B 81 1.880 13.980 2.186 0.60 18.58
N
HETATM 7191 CA B2CO B 81 1.588 13.944 3.653 0.60 18.40
C
HETATM 7192 C B2CO B 81 0.942 12.598 4.008 0.60 19.08
C
HETATM 7194 CB B2CO B 81 0.814 15.182 4.084 0.60 18.02
C
HETATM 7195 SG B2CO B 81 0.196 15.184 5.785 0.60 19.79
S
HETATM 7196 OD B2CO B 81 1.325 14.402 6.741 0.60 18.59
O
HETATM 7197 OE B2CO B 81 2.450 15.334 6.919 0.60 18.11
O
HETATM 7616 O B2CO B 81 1.563 11.942 5.002 0.60 20.00
O
Best,
Filipa.
Martin Maly <martin.maly...@email.cz> escreveu (segunda, 29/04/2024 à(s)
18:58):
> Dear Filipa and Nicholas,
> I confirm that in the current CCP4 version 8.0.019, refmacat is integrated
> in the ccp4i2 refinement task - now the task is called "Refmacat/Refmac5".
> Cheers,
> Martin
>
> On 29/04/2024 17:30, Nicholas Clark <
> 0000b2b1c7e93c2d-dmarc-requ...@jiscmail.ac.uk> wrote:
> > Hi Filipa,
> >
> > I had a similar issue with "CSO". To visualize the peptide bond in Coot,
> > you need to change the restraints applied to "2CO". To do this in Coot,
> > go to "Edit->Restraints" select 2CO and under "group" change this to
> > "peptide" (make sure to hit enter) then click ok. This should allow you
> > to visualize the peptide bond.
> >
> > To get refinement to work properly, I had to use refmacat (which at the
> > time was command line only, not sure if this is still the case). I'm not
> > sure if the same requirement will apply for you too. The Refmacat CCP4
> > website
> > (https://cloud.ccp4.ac.uk/manuals/html-taskref/doc.task.Refmac.html
> > <https://cloud.ccp4.ac.uk/manuals/html-taskref/doc.task.Refmac.html>)
> > seems like it's been fully integrated but someone else would know better
> > than I.
> >
> > Best,
> >
> > Nick Clark
> >
> > On Mon, Apr 29, 2024 at 10:14 AM Filipa Engrola
> > <0000ce14ef297227-dmarc-requ...@jiscmail.ac.uk
> > <mailto:0000ce14ef297227-dmarc-requ...@jiscmail.ac.uk>> wrote:
> >
> > Dear community,
> >
> > I am trying to model 2 alternate Cys conformations, one of them
> > "CYS" (occ 0.6), but the other "2CO" (Chemical identity:
> > _https://www.rcsb.org/ligand/2CO
> > <
> https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rcsb.org%2Fligand%2F2CO&data=05%7C02%7Cndclark2%40g-mail.buffalo.edu%7Cd4317bc7064c4d240ec008dc6856b39e%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638499968861707741%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=UubmJKkvQam6ukRIC%2F5onlDdiYW64nr5%2F%2BWwrtSj70I%3D&reserved=0>;_
> occ 0.4).
> >
> > I can place the residue with alt conformation but not connect it
> > with the rest of the polypeptide chain (Photo attached).
> >
> > Using Coot 0.9.8.92, and Refmac5, I have tried:
> >
> > i) calculate>Modelling>Make Link
> > After refinement, I get no link.
> > or
> > ii) calculate>Modelling>Rebuild Fragment using DB Loop"
> > It works to connect only "CYS".
> >
> > I cannot add an alternate conformation and mutate ONLY one to the
> > desired "2CO", it mutates both of them.
> >
> > Does anyone have any suggestions? :)
> >
> > Thank you in advance!
> > Best,
> > Filipa.
> >
> > image.png
> >
> > --
> > Filipa Engrola
> > PhD Candidate
> > NOVA School of Science and Technology (FCT NOVA) @UCIBIO
> >
> >
> >
> ------------------------------------------------------------------------
> >
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> https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&data=05%7C02%7Cndclark2%40g-mail.buffalo.edu%7Cd4317bc7064c4d240ec008dc6856b39e%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638499968861707741%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=SFq%2F0sZp%2BbH1rhAVw6bwsBZbY49%2FGLJDDdKNIlWAIMc%3D&reserved=0
> >
> >
> >
> >
> > --
> > Nicholas D. Clark (He/Him)
> > PhD Candidate
> > Malkowski Lab
> > University at Buffalo
> > Department of Structural Biology
> > Jacob's School of Medicine & Biomedical Sciences
> > 955 Main Street, RM 5130
> > Buffalo, NY 14203
> >
> > Cell: 716-830-1908
> >
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--
Filipa Engrola
PhD Candidate
NOVA School of Science and Technology (FCT NOVA) @UCIBIO
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