Hi Oliver! Yes that is what I see in my foot when I fetch from different sources
I started looking at the lines of the PDB too to see if there are any striking
differences.
--
Kelvin Lau
Protein production and structure core facility - PTPSP
EPFL SV PTECH PTPSP
AI 2146 (Bâtiment AI)
Station 19
Whoops sorry - corrected link:
https://www.dropbox.com/scl/fi/t113o9lgprboqycz21ryc/mdo_7tqr.mov?rlkey=y8154e0t5gc6y6odnfhplo9qf=0
> On Sep 29, 2023, at 8:31 AM, Oliver Clarke wrote:
>
> For me, MDO in 7tqr blows up if I use the model/map from “Fetch PDB & Map
> using EDS”, using Coot
For me, MDO in 7tqr blows up if I use the model/map from “Fetch PDB & Map using
EDS”, using Coot 0.9.8.91 EL (CCP4):
https://www.dropbox.com/scl/fi/yw4nkiz9zmpms7gx3ie1h/7tqr_mdo.mov?rlkey=rtpo3vcl0jy7tha1qd8t82goz=0
But interestingly, if I use the PDB and map from PDB-REDO, it refines just
Hi Kelvin,
I tried the following on 7tqr, and it seems to work.
I am using coot 0.9.8.92 (CCP4):
Get monomer MDO
merge MDO in the model and fit into the density
MDO now has number 617, this needs to be changed to 141.
Edit renumber residue: select the model, and then ‘Start Residue’ 617,
Dear all
Thank you for looking into this.
@Keitaro: I forgot to say I am on 0.9.8.91 EL (ccp4) build. If I just refine
the MDO (A/141) or residues 140-141 together, both ways, the ligand moves out
of the density and the stats become all red. However, I do see that the links
are there.
Today
As Lucrezia explained, group names in the monomer library are fixed
after Acedrg. To be a peptide, a monomer should have
N/CA/C/O/OXT/H/H2/H3 atoms with the proper bonding pattern. If the
atom names are different, they will be demoted to NON-POLYMER and an
alias will be added. This was partly
Lorrie - life is getting more complicated every day!
On Thu, 21 Sep 2023 at 23:39, Lucrezia Catapano <
ade43f7741e4-dmarc-requ...@jiscmail.ac.uk> wrote:
> Hi Kelvin,
>
> the 'group' in the monomer library do not necessarily correspond to the
> 'type' in CCD. The reason was that stricter
Hi Kelvin,
the 'group' in the monomer library do not necessarily correspond to the 'type'
in CCD. The reason was that stricter rules for peptides and other groups were
applied to the library.
For MDO, there are 2 links: MDO-pept and pept-MDO to deal with this in a
polypeptide.
Of course, you
On 21/09/2023 18:58, Paul Emsley wrote:
On 21/09/2023 18:05, Kelvin Lau wrote:
Dear all
I am having trouble with an unnatural ligand/amino acid.
I have a structure very similar to PDB 6Q6H, 7TQR. They all have an
MDO residue that replaces three residues in a series G-A-S-G-D to
become
On 21/09/2023 22:25, Kelvin Lau wrote:
Hi Eleanor
Thanks for catching that..
I was under the impression that when I am fetching the monomer, MDO,
it was defined as a peptide, not a non polymer … at least that’s what
is listed here: https://www.rcsb.org/ligand/MDO
I guess I have to go about
On 21/09/2023 21:56, Eleanor Dodson wrote:
And in fact it doesnt..
Wasn't that implied by my reply?
:-)
Paul.
To unsubscribe from the COOT list, click the following link:
Hi Eleanor
Thanks for catching that..
I was under the impression that when I am fetching the monomer, MDO, it was
defined as a peptide, not a non polymer … at least that’s what is listed here:
https://www.rcsb.org/ligand/MDO
I guess I have to go about as Paul suggested as changing it to
And in fact it doesnt..
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
MDO MDO
"{2-[(1S)-1-aminoethyl]-4-methylidene-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic
acid"
Check the dictionary has labelled it as peptide
like ALA
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
ALA ALA ALANINE *peptide* 13 6 .
On Thu, 21 Sept 2023 at 18:58,
On 21/09/2023 18:05, Kelvin Lau wrote:
Dear all
I am having trouble with an unnatural ligand/amino acid.
I have a structure very similar to PDB 6Q6H, 7TQR. They all have an MDO residue
that replaces three residues in a series G-A-S-G-D to become G-MDO-D. MDO is in
the Coot library.
I have
Dear all
I am having trouble with an unnatural ligand/amino acid.
I have a structure very similar to PDB 6Q6H, 7TQR. They all have an MDO residue
that replaces three residues in a series G-A-S-G-D to become G-MDO-D. MDO is in
the Coot library.
I have been very used to replacing cysteines with
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