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) > >>> [EMAIL PROTECTED] > >>> > >>> > >>> > >>> > >> > > > > ---------------------------------------------------------------------------------------------- > > 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) > > [EMAIL PROTECTED] > > > > > > > > > >
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
