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@1@H that hydrogen. No words enough to thank you. francesco --- Eric Pettersen <pett@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@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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