Hi
Just refined a glycine and a leucine, and realized there was a problem
with the script. Here is version 0.2
Mark
On Wed, 22 Oct 2008, Jonathan Winger wrote:
> Fantastic. Thank you!
>
> jon
>
> On Oct 22, 2008, at 11:27 AM, Mark Collins wrote:
>
> > sorry that should have been
> > sed -f pdb4coot.sed file.pdb > newcoot.pdb
> > mark
> >
> > On Oct 21, 2008, at 10:53 PM, Jonathan Winger wrote:
> >
> >> Hi Mark,
> >> I compared the names of the H atoms for each of the residue types
> >> in my pdb file with their cif files in the coot monomer library
> >> (for example, see below). Then, to make the H names in the pdb
> >> file match those in the cif file, I used a text editor to search my
> >> pdb file for the string "HB2 SER" and replaced all with "HB1 SER".
> >> Next, I replaced all "HB3 SER" with "HB2 SER". (It's important to
> >> start by changing the H2s to H1s, then the H3s to H2s. Otherwise,
> >> everything ends up as a H1). I did the same sort of thing for
> >> residues with other H types, like Arg (with HG2 and 3, HD2 and 3,
> >> etc.) After doing that for all residue types, Coot could real-
> >> space refine the H atoms without any problem. It is a major PITA,
> >> though, especially if you have alternate conformations. Plus, I
> >> don't know what it will do as far as compatibility with other
> >> software down the line. So far the edited pdb files seem to work
> >> ok in phenix, but I'm still checking...
> >>
> >> Hope this helps,
> >> Jon
> >>
> >> From my pdb after adding H with Molprobity/reduce:
> >> ATOM 179 N SER A 491 -58.459 56.155 -4.915
> >> 1.00101.27 A N
> >> ATOM 180 CA SER A 491 -59.811 56.265 -5.435
> >> 1.00106.61 A C
> >> ATOM 181 C SER A 491 -60.148 57.722 -5.726
> >> 1.00108.97 A C
> >> ATOM 182 CB SER A 491 -60.812 55.672 -4.442
> >> 1.00110.28 A C
> >> ATOM 183 OG SER A 491 -62.063 55.428 -5.058
> >> 1.00114.41 A O
> >> ATOM 184 O SER A 491 -60.682 58.044 -6.786
> >> 1.00113.36 A O
> >> ATOM 0 H SER A 491 -58.405 55.839 -3.968
> >> 1.00101.27 A H new
> >> ATOM 0 HA SER A 491 -59.874 55.697 -6.375
> >> 1.00106.61 A H new
> >> ATOM 0 HB2 SER A 491 -60.413 54.733 -4.032
> >> 1.00110.28 A H new
> >> ATOM 0 HB3 SER A 491 -60.945 56.362 -3.596
> >> 1.00110.28 A H new
> >> ATOM 0 HG SER A 491 -62.695 55.040 -4.387
> >> 1.00114.41 A H new
> >>
> >> From Coot monomer lib ( /sw/share/coot/lib/data/monomers/s/SER.cif):
> >> data_comp_SER
> >> #
> >> loop_
> >> _chem_comp_atom.comp_id
> >> _chem_comp_atom.atom_id
> >> _chem_comp_atom.type_symbol
> >> _chem_comp_atom.type_energy
> >> _chem_comp_atom.partial_charge
> >> SER N N NH1 -0.204
> >> SER H H HNH1 0.204
> >> SER CA C CH1 0.058
> >> SER HA H HCH1 0.046
> >> SER CB C CH2 -0.040
> >> SER HB1 H HCH2 0.053
> >> SER HB2 H HCH2 0.053
> >> SER OG O OH1 -0.448
> >> SER HG H HOH1 0.302
> >> SER C C C 0.318
> >> SER O O O -0.422
> >>
> >>
> >>
> >>
> >> On Oct 21, 2008, at 7:13 PM, Mark Collins wrote:
> >>
> >>> hi Jon
> >>> What do you mean search and replace? Were the names of some
> >>> hydrogens incorrect. Feel free to include a few examples.
> >>> Mark
> >>>
> >>> On Oct 21, 2008, at 3:05 PM, Jonathan Winger wrote:
> >>>
> >>>> Hi Mark and Paul,
> >>>>
> >>>> I had to manually go through my pdb file and search and replace
> >>>> all the offending hydrogens. Kind of painful. I hope there's
> >>>> some way to either standardize or automate something here, or
> >>>> it's going to be rough interconverting everything all the time...
> >>>>
> >>>> Best of luck,
> >>>> Jon
> >>>>
> >>>>
> >>>> On Oct 21, 2008, at 6:59 AM, Paul Emsley wrote:
> >>>>
> >>>>>
> >>>>> Hi Mark,
> >>>>>
> >>>>> I thought we did - but maybe not :-/
> >>>>>
> >>>>> If you could send me an offending residue (just a PDB snippet,
> >>>>> no map required) I'll try to see what the issue is.
> >>>>>
> >>>>> Regards,
> >>>>>
> >>>>> Paul.
> >>>>>
> >>>>> p.s. I'll be in Manhattan tomorrow (I am teaching at Cold
> >>>>> Spring Harbor today) maybe going to Broadway. You're not a
> >>>>> million miles away, right?
> >>>>>
> >>>>>
> >>>>> Mark Collins wrote:
> >>>>>> Hi Jonathan Did you find/get a fix for this? I just switched
> >>>>>> to pdb v3 file, from the happy and well behaved v2 file. It
> >>>>>> seems that all H_3 position Hydrogens are the problem (ie HB3,
> >>>>>> HG3 etc.) and as descirbed fly off when using RSR.
> >>>>>> Thanks Mark
> >>>>>> (os 10.4 G4, coot 0.5)
> >>>>>> On Sun, 5 Oct 2008, Jonathan Winger wrote:
> >>>>>>> I'm building a structure in Coot 0.5. Upon real-space refine
> >>>>>>> or regularize, some of the hydrogens on some residues fly
> >>>>>>> off. It doesn't seem to be the old pdb v3 atom-name issue,
> >>>>>>> since other residues in the structure with exactly the same
> >>>>>>> atom names real-space refine without any trouble. Anyone
> >>>>>>> have a fix for this?
> >>>>>>>
> >>>>>>> Any help would be greatly appreciated,
> >>>>>>> Jon
> >>>>>>>
> >>>>>
> >>>
> >>> ----------------------------------------------------------------------------------------------
> >>> The most exciting phrase to hear in science, the one that heralds
> >>> new
> >>> discoveries, is not 'Eureka!' (I found it!) but 'That's funny ...'
> >>> Isaac Asimov (1920 - 1992)
> >>> ----------------------------------------------------------------------------------------------
> >>>
> >>> Mark Collins
> >>> Columbia University
> >>> Dept. of Biochemistry & Molecular Biophysics
> >>> Hendrickson Lab, Black Building 259/201 Office/Lab
> >>> 212 305 1951 (work)
> >>> [log in to unmask]
> >>>
> >>>
> >>>
> >>>
> >>
> >
> > ----------------------------------------------------------------------------------------------
> > The most exciting phrase to hear in science, the one that heralds new
> > discoveries, is not 'Eureka!' (I found it!) but 'That's funny ...'
> > Isaac Asimov (1920 - 1992)
> > ----------------------------------------------------------------------------------------------
> >
> > Mark Collins
> > Columbia University
> > Dept. of Biochemistry & Molecular Biophysics
> > Hendrickson Lab, Black Building 259/201 Office/Lab
> > 212 305 1951 (work)
> > [log in to unmask]
> >
> >
> >
> >
>
>
s/HA3\(.\)GLY/HA1\1GLY/g
s/HB3\(.\)ARG/HB1\1ARG/g
s/HB3\(.\)ASN/HB1\1ASN/g
s/HB3\(.\)ASP/HB1\1ASP/g
s/HB3\(.\)CYS/HB1\1CYS/g
s/HB3\(.\)GLN/HB1\1GLN/g
s/HB3\(.\)GLU/HB1\1GLU/g
s/HB3\(.\)HIS/HB1\1HIS/g
s/HB3\(.\)LEU/HB1\1LEU/g
s/HB3\(.\)LYS/HB1\1LYS/g
s/HB3\(.\)MET/HB1\1MET/g
s/HB3\(.\)MSE/HB1\1MSE/g
s/HB3\(.\)PHE/HB1\1PHE/g
s/HB3\(.\)PRO/HB1\1PRO/g
s/HB3\(.\)SER/HB1\1SER/g
s/HB3\(.\)TRP/HB1\1TRP/g
s/HB3\(.\)TYR/HB1\1TYR/g
s/HG3\(.\)ARG/HG1\1ARG/g
s/HG3\(.\)GLN/HG1\1GLN/g
s/HG3\(.\)GLU/HG1\1GLU/g
s/HG3\(.\)LYS/HG1\1LYS/g
s/HG3\(.\)MET/HG1\1MET/g
s/HG3\(.\)MSE/HG1\1MSE/g
s/HG3\(.\)PRO/HG1\1PRO/g
s/HD3\(.\)ARG/HD1\1ARG/g
s/HD3\(.\)LYS/HD1\1LYS/g
s/HD3\(.\)PRO/HD1\1PRO/g
s/HE3\(.\)LYS/HE1\1LYS/g
s/HG13\(.\)ILE/HG11\1ILE/g
######sed -f pdb4coot.sed old.pdb > new.pdb
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