[Chimera-users] Non-standard atom names

[Francesco Pietra]

Hi Eric:
Daily Build 17 Oct chimera-alpha-linux.exe (to fix protonation of aspartic and
glutamic acid issues) could be installed on Debian i386 and run perfectly. I
was also much impressed how beautifully could you fix the non-standard pdb I
was trying to work out with dockprep. Now OK, either accepting unknown charge
for 'H' in the chain-initial serine in the mol2 file, or getting no warning to
save the mol2 file when del at 1@H that hydrogen.

No words enough to thank you.

francesco

--- Eric Pettersen <pett at cgl.ucsf.edu> wrote:

> Hi Francesco,
> 	To identity the zero-charge atoms you should look in the Reply Log  
> (under Favorites) -- it will list them explicitly.
> 	I guess I don't understand how you're getting these uncharged  
> hydrogens given the procedure you outlined.  The hydrogens listed  
> definitely aren't ones you would expect in those residues.  Typically  
> the only way that happens is if there are residues with incomplete  
> side chains that then get protonated -- the protons go into positions  
> that "should" have heavy atoms and get names that don't correspond to  
> normal proton names for that residues (since they aren't normal  
> protons for that residue).  But with your procedure that should not  
> have happened.  Are you sure that you didn't uncheck the "Mutate  
> residues with incomplete side chains" step?  That step removes  
> incomplete side chains and should prevent this kind of charge problem.
> 
> --Eric
> 
>                          Eric Pettersen
>                          UCSF Computer Graphics Lab
>                          pett at cgl.ucsf.edu
>                          http://www.cgl.ucsf.edu
> 
> 
> On Oct 16, 2007, at 8:06 AM, Francesco Pietra wrote:
> 
> > Problems with atom names in preparing a protein for docking. The  
> > protein (K ion
> > channel) was obtained as monomer from Protein Data Bank and then as  
> > tetramer
> > from Protein Quaternary Structure database through Chimera Fetch  
> > ID. The
> > tetramer was stripped to leave
> >
> > --Two helices
> > --Selectivity filter
> > --Pore helix
> >
> > Prepare with Chimera 1.2422 (I had previously carried out  
> > successfully the
> > tutorial) along defaults
> >
> > Tools .. Strct edit .. Dockprep
> > All selected except "Delete non-complexed ions"
> > Add hydrogens (also consider H-bonds)
> >
> > To write mol2 use untrasnformed coordinates; use Sybyl type H  
> > naming; write
> > current selection to @SETS, Save
> >
> > reported:
> > Correct charges are unknown for 15 non-standard atom names in  
> > otherwise
> > standard residues (charges 0.0 assigned to these atoms.
> > 1 model had non integral total charge.
> >
> > Looking at the mol2 file, I could only identify nine type of atoms  
> > assiggen
> > 0.0000 charge:
> >
> > H, HD1, HD2, HE1, HE2, HG1, HG2, HH1, HH2
> >
> > such as (for a small initial portion):
> >
> > 2 H .... 1 SER1
> > 50 HD1 ... 4 LEU4
> > 95 HD1 .... 7 LEU7
> > 97 HD2 ... 7 LEU7
> > 135 HG2 ... 10 THR10
> > 150 HD1 ..... 11 LEU11
> > 168 HE2 .... 12 GLN12
> > 226 HH1 ... 16 ARG16
> > 259 HD2 ... 18 LEU18
> > 279 HD1 ... 20 LEU20
> > 281 HD2 .. 20 LEU20
> > 294 HD1 ... 21 LEU21
> > 296 HD2 ... 21 LEU21
> > 306 HG2 ... 22 ILE22
> > 308 HG1 ... 22 ILE22
> > 310 HD1 ... 22 ILE22
> > 365 HD2 ... 25 LEU25
> > 397 HG1 ... 27 ILE27
> > 430 HG1 .. 30 ILE30
> > 445 HD1 ... 31 LEU31
> > 578 HE1 ... 40 GLU40
> > 601 HD1 ... 42 ASP42
> > 718 HG2 ... 51 ILE51
> > 847 HG1 ... 59 VAL59
> > 861 HG2 ... 60 VAL60
> > 900 HG2 ... 63 THR63
> > 926 HG2 ... 65 VAL65
> > 974 HD1 ... 69 ASP69
> > 1037 HG2 ... 73 ILE73
> > 1039 HG1 ... 73 ILE73
> > 1041 HD1 ... 73 ILE73
> > 1063 HG1 ... 75 VAL75
> >
> > Being new to these procedures, could you please indicate how to fix  
> > the issue?
> >
> > Thanks
> >
> > francesco pietra
> >
> >
> >
> >
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> 


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