Dear all,
Thank you for the suggestions. I couldn't get the TYR-NH2 cif file to
work. Refmac threw up some errors related to the cif file. Also, the
TYC is defined as L-peptide but I am not sure why this is not working.
In any case, what worked is the following,
1. I positioned the coot pointer into the appropriate density and
imported the cif file provided by Herman Schreuder (thank you!) into
it which put an NH3 "residue" into the map. I then removed the three
hydrogen atoms and merged the imported residue and the pdb using
Calculate -> Merge molecules in coot.
2. Next, I changed the residue number of NH2 using Calculate ->
renumber residues to TYR residue no + 1 and also changed the chain no
via Calculate -> change chain IDs to match that of TYR. This
immediately creates a bond between TYR and NH2. Saved the file.
3. Manually edited the pdb to move the TER card between and TYR and
NH2 and insert a TER card after NH2 and another chain (see below)
HETATM 323 N NH2 A 49 32.029 -12.304-117.822 1.00 15.07 N
TER 324 NH2 A 49
HETATM 325 O ACE B 0 -3.456 -2.323 4.274 1.00 10.32
O
4. Saved the pdb and refined in refmac without any problems.
Thank you again for excellent suggestions.
Best regards,
Abhishek
On 10/13/17, Eleanor Dodson <eleanor.dod...@york.ac.uk> wrote:
> You have labelled the TYC as an L-peptide in the dictionary have you? (
> Look at any peptide for the position and format for the label ) I thought
> REFMAC would then automatically creat a peptide link between residue n and
> n+1
>
> Eleanor
>
> PS and remove the TER record!
>
> On 13 October 2017 at 08:08, <herman.schreu...@sanofi.com> wrote:
>
>> Hi Abhisek (and BB),
>>
>> I use the attached cif file. It has an NH2 residue defined as a peptide
>> and gets automatically linked to the peptide chain in the buster
>> procedure
>> I use. So if your last residue is Tyr 100, you add NH2 101 as a HETATM in
>> the peptide chain.
>>
>> I have not tested it with Refmac though.
>>
>> Best,
>> Herman
>>
>> -----Ursprüngliche Nachricht-----
>> Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von
>> Bernhard Lechtenberg
>> Gesendet: Freitag, 13. Oktober 2017 00:13
>> An: CCP4BB@JISCMAIL.AC.UK
>> Betreff: [EXTERNAL] Re: [ccp4bb] C-terminal amide
>>
>> HI Abhisek,
>>
>> I had the same problem a few years back. Here is the solution I came up
>> with thanks to help from the CCP4bb:
>>
>> 1) Add pointer atom in Coot NH2 and create link to C-terminal residue
>> (Coot: Extensions -> Modeling -> Make link)
>> 2) create cif file with correct link description (see below)
>> 3) modify LINK record in PDB file to correct residues/ link name (TYR-NH2
>> if you use the file below with modifications for your case)
>> 4) refine in Refmac with cif as LIB in
>>
>> Augie Pioszak sent me the cif file copied below. you will have to change
>> PHE to TYR for your particular case.
>>
>> Hope that helps.
>>
>> Best,
>> Bernhard
>>
>> -------------------------------
>>
>> Bernhard,
>> You need a link record in the pdb file to link the NH2 amino group to
>> your
>> last peptide residue. When I did this a few years back I had to include
>> a
>> .cif library file describing the link for use with Refmac. See pdb entry
>> 3c4m and below for the lib description I used. I still use O, so not
>> sure
>> how coot handles it, but I would guess it will recognize the NH2 group
>> just
>> fine. Hope this helps.
>> Regards,
>> Augie Pioszak
>>
>> # --- LIST OF LINKS ---
>> #
>> data_link_list
>> loop_
>> _chem_link.id
>> _chem_link.comp_id_1
>> _chem_link.mod_id_1
>> _chem_link.group_comp_1
>> _chem_link.comp_id_2
>> _chem_link.mod_id_2
>> _chem_link.group_comp_2
>> _chem_link.name
>> PHE-NH2 PHE . . NH2 . .
>> bond_PHE-C_=_NH2-N
>> # ------------------------------------------------------
>> #
>> # --- DESCRIPTION OF LINKS ---
>> #
>> data_link_PHE-NH2
>> #
>> loop_
>> _chem_link_bond.link_id
>> _chem_link_bond.atom_1_comp_id
>> _chem_link_bond.atom_id_1
>> _chem_link_bond.atom_2_comp_id
>> _chem_link_bond.atom_id_2
>> _chem_link_bond.type
>> _chem_link_bond.value_dist
>> _chem_link_bond.value_dist_esd
>> PHE-NH2 1 C 2 N single 1.329 0.020
>> loop_
>> _chem_link_angle.link_id
>> _chem_link_angle.atom_1_comp_id
>> _chem_link_angle.atom_id_1
>> _chem_link_angle.atom_2_comp_id
>> _chem_link_angle.atom_id_2
>> _chem_link_angle.atom_3_comp_id
>> _chem_link_angle.atom_id_3
>> _chem_link_angle.value_angle
>> _chem_link_angle.value_angle_esd
>> PHE-NH2 1 O 1 C 2 N 122.000 1.600
>> PHE-NH2 1 CA 1 C 2 N 118.200 2.000
>> loop_
>> _chem_link_plane.link_id
>> _chem_link_plane.plane_id
>> _chem_link_plane.atom_comp_id
>> _chem_link_plane.atom_id
>> _chem_link_plane.dist_esd
>> PHE-NH2 plane1 1 CA 0.020
>> PHE-NH2 plane1 1 C 0.020
>> PHE-NH2 plane1 1 O 0.020
>> PHE-NH2 plane1 2 N 0.020
>> # ------------------------------------------------------
>>
>> ---------------------------------------------------------------------
>> > On Oct 12, 2017, at 2:53 PM, Abhishek Anan <rendezvous.a...@gmail.com>
>> wrote:
>> >
>> > Dear all,
>> >
>> > I am trying to solve the structure of a peptide with C-terminal amide.
>> In order to add the amide group to the c-terminal TYR, I substituted TYR
>> with TYC (tyrosinamide) and created a link between the preceding GLY and
>> TYC. When refined in refmac, the pdb inserts a TER card between GLY and
>> TYC
>> and no covalent bond is created between them. How do I fix this? I have
>> also tried to add NH2 pointer atom to TYR in coot and create a link
>> between
>> them but in vain. I also imported the NH2.cif file into coot and tried to
>> make a link but of no use. I also tried to import NH2.cif into Jligand so
>> I
>> could get a link record but it refuses to open the NH2.cif file.
>> >
>> > I would greatly appreciate any help!
>> >
>> > Best regards,
>> > Abhishek
>>
>
