Re: [COOT] Flying hydrogen issue in coot 0.5
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: ATOM179 N SER A 491 -58.459 56.155 -4.915 1.00101.27 AN ATOM180 CA SER A 491 -59.811 56.265 -5.435 1.00106.61 AC ATOM181 C SER A 491 -60.148 57.722 -5.726 1.00108.97 AC ATOM182 CB SER A 491 -60.812 55.672 -4.442 1.00110.28 AC ATOM183 OG SER A 491 -62.063 55.428 -5.058 1.00114.41 AO ATOM184 O SER A 491 -60.682 58.044 -6.786 1.00113.36 AO ATOM 0 H SER A 491 -58.405 55.839 -3.968 1.00101.27 AH new ATOM 0 HA SER A 491 -59.874 55.697 -6.375 1.00106.61 AH new ATOM 0 HB2 SER A 491 -60.413 54.733 -4.032 1.00110.28 AH new ATOM 0 HB3 SER A 491 -60.945 56.362 -3.596 1.00110.28 AH new ATOM 0 HG SER A 491 -62.695 55.040 -4.387 1.00114.41 AH 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 NNH1 -0.204 SER H HHNH1 0.204 SER CA CCH1 0.058 SER HA HHCH1 0.046 SER CB CCH2 -0.040 SER HB1HHCH2 0.053 SER HB2HHCH2 0.053 SER OG OOH1 -0.448 SER HG HHOH1 0.302 SER C CC 0.318 SER O OO-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
Re: [COOT] Flying hydrogen issue in coot 0.5
Hi JonHere is a sed script to make life easier.run on command prompt withsed pdb4coot.sed file.pdb > newcoot.pdb pdb4coot.sed Description: Binary data MarkOn 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,JonFrom my pdb after adding H with Molprobity/reduce:ATOM 179 N SER A 491 -58.459 56.155 -4.915 1.00101.27 A NATOM 180 CA SER A 491 -59.811 56.265 -5.435 1.00106.61 A CATOM 181 C SER A 491 -60.148 57.722 -5.726 1.00108.97 A CATOM 182 CB SER A 491 -60.812 55.672 -4.442 1.00110.28 A CATOM 183 OG SER A 491 -62.063 55.428 -5.058 1.00114.41 A OATOM 184 O SER A 491 -60.682 58.044 -6.786 1.00113.36 A OATOM 0 H SER A 491 -58.405 55.839 -3.968 1.00101.27 A H newATOM 0 HA SER A 491 -59.874 55.697 -6.375 1.00106.61 A H newATOM 0 HB2 SER A 491 -60.413 54.733 -4.032 1.00110.28 A H newATOM 0 HB3 SER A 491 -60.945 56.362 -3.596 1.00110.28 A H newATOM 0 HG SER A 491 -62.695 55.040 -4.387 1.00114.41 A H newFrom 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 -0.422On Oct 21, 2008, at 7:13 PM, Mark Collins wrote: hi JonWhat 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,JonOn 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 newdiscoveries, is not 'Eureka!' (I found it!) but 'That's funny ...'Isaac Asimov (1920 - 1992)--Mark CollinsColumbia UniversityDept. of Biochemistry & Molecular BiophysicsHendrickson Lab, Black Building 259/201 Office/Lab212 305 1951 (work)[EMAIL PROTECTED] --The mo
Re: [COOT] edit backbone torsions?
I totally agree that having two tool bars which are close to being identical creates confusion. My preference would be that the two widgets be merged into one, even if shorter, tool bar (please)? The idea of having a pop-out menu was inspired, but if one or two buttons have to go, so be it. The ones thrown out could (maybe) go into the "Other modelling tools" menu. Just my two Eurocents. Thanks again for the coo(l/t) software. Mark 2008/10/22 Donnie Berkholz <[EMAIL PROTECTED]> > On 11:46 Wed 22 Oct , Kevin Cowtan wrote: > > Are you looking in the model/fit/refine window, or in the toolbar? The > > toolbar does not contain everything that is in the window, due to space. > > As you no doubt know, it creates a lot of confusion and is generally > poor usability to have two things that appear almost identical but > aren't. Is there some way to make it more obvious (visually, etc) that > the toolbar is different from the M/F/R window? > > -- > Thanks, > Donnie > > Donnie Berkholz > Developer, Gentoo Linux > Blog: http://dberkholz.wordpress.com > -- Mark BROOKS Telephone: 0169157968 Fax: 0169853715 Institut de Biochmie et de Biophysique Moleculaire et Cellulaire UMR8619 - Bât 430 - Université de Paris-Sud 91405 Orsay CEDEX Skype: markabrooks
Re: [COOT] edit backbone torsions?
On 11:46 Wed 22 Oct , Kevin Cowtan wrote: > Are you looking in the model/fit/refine window, or in the toolbar? The > toolbar does not contain everything that is in the window, due to space. As you no doubt know, it creates a lot of confusion and is generally poor usability to have two things that appear almost identical but aren't. Is there some way to make it more obvious (visually, etc) that the toolbar is different from the M/F/R window? -- Thanks, Donnie Donnie Berkholz Developer, Gentoo Linux Blog: http://dberkholz.wordpress.com pgp7UuD7PKgTE.pgp Description: PGP signature
Re: [COOT] edit backbone torsions?
Oops. I should have mentioned in my previous posting that you need PYTHON as well as GTK2 to manage the toolbuttons. Sorry for any confusion caused, Bernhard > This issue was actually discussed previously here. Anyway as Kevin > already mentioned, not all buttons are available in the toolbar. > However > (in the GTK2 version) you can add your own buttons to the top > toolbar > (besides the 'Display Manager' button) using the right mouse click. > I > have provided buttons e.g. for the missing buttons 'Add Alt Conf' > and > 'Edit Backbone Torsion' (not to self: I shall include the other > missing > buttons). > > Bernhard > > > Are you looking in the model/fit/refine window, or in the toolbar? > > The > > toolbar does not contain everything that is in the window, due to > > space. > > Michele Lunelli wrote: > > > I recently switched from version 0.4 to version 0.5.1-pre-1 gtk2 > > > revision 1494. It works great, but I cannot find the "edit > > backbone > > > torsions" on the Model/Fir/refine menu or somewhere else. > > Moreover, I > > > cannot find how to modify general torsions. > > > Am I missing something? > > > > > > Thanks for helping > > > Michele > > > > > > > > >
Re: [COOT] edit backbone torsions?
This issue was actually discussed previously here. Anyway as Kevin already mentioned, not all buttons are available in the toolbar. However (in the GTK2 version) you can add your own buttons to the top toolbar (besides the 'Display Manager' button) using the right mouse click. I have provided buttons e.g. for the missing buttons 'Add Alt Conf' and 'Edit Backbone Torsion' (not to self: I shall include the other missing buttons). Bernhard > Are you looking in the model/fit/refine window, or in the toolbar? > The > toolbar does not contain everything that is in the window, due to > space. > Michele Lunelli wrote: > > I recently switched from version 0.4 to version 0.5.1-pre-1 gtk2 > > revision 1494. It works great, but I cannot find the "edit > backbone > > torsions" on the Model/Fir/refine menu or somewhere else. > Moreover, I > > cannot find how to modify general torsions. > > Am I missing something? > > > > Thanks for helping > > Michele > > > > >
Re: [COOT] edit backbone torsions?
Kevin Cowtan wrote: Are you looking in the model/fit/refine window, or in the toolbar? The toolbar does not contain everything that is in the window, due to space. Ah, I was missing this point.. Thank you, Michele
Re: [COOT] edit backbone torsions?
Are you looking in the model/fit/refine window, or in the toolbar? The toolbar does not contain everything that is in the window, due to space. Michele Lunelli wrote: I recently switched from version 0.4 to version 0.5.1-pre-1 gtk2 revision 1494. It works great, but I cannot find the "edit backbone torsions" on the Model/Fir/refine menu or somewhere else. Moreover, I cannot find how to modify general torsions. Am I missing something? Thanks for helping Michele
[COOT] edit backbone torsions?
I recently switched from version 0.4 to version 0.5.1-pre-1 gtk2 revision 1494. It works great, but I cannot find the "edit backbone torsions" on the Model/Fir/refine menu or somewhere else. Moreover, I cannot find how to modify general torsions. Am I missing something? Thanks for helping Michele
Re: [COOT] SSM problem
Yes it should. :-( Paul. In message <[EMAIL PROTECTED]> junfeng liu <[EMAIL PROTECTED]> writes: > It worked well on old versions. For coot 0.5,it works when you restart > coot or overlap small fragment on big one sometimes . > That should be a bug. Is it right Paul? > Best wishes! > liu > Engin Ozkan wrote: > > Hi everyone, > > > > I have a peculiar problem. Whenever I "copy fragment" a domain, the copied > > fragment fails in SSM. I am not talking about a small fragment, but more > > like a 250-residue domain. If I save the fragment as a molecule, go back > > and "Open Coordinates" that saved fragment, SSM works just fine for that > > reloaded fragment. > > > > It seems like a petty problem (and the workaround I found isn't that hard), > > but I was wondering if this was a bug or not (for coot 0.5 revision 1444). > > > > Thanks, > > > > Engin > > > >
Re: [COOT] SSM problem
It worked well on old versions. For coot 0.5,it works when you restart coot or overlap small fragment on big one sometimes . That should be a bug. Is it right Paul? Best wishes! liu Engin Ozkan wrote: Hi everyone, I have a peculiar problem. Whenever I "copy fragment" a domain, the copied fragment fails in SSM. I am not talking about a small fragment, but more like a 250-residue domain. If I save the fragment as a molecule, go back and "Open Coordinates" that saved fragment, SSM works just fine for that reloaded fragment. It seems like a petty problem (and the workaround I found isn't that hard), but I was wondering if this was a bug or not (for coot 0.5 revision 1444). Thanks, Engin
