Subject: Re: Chimera model (km) formatting
From: Thomas Goddard
Date: Nov 14 11:06 AM



Hi Kyle,

I think the problem getting Sparky and Chimera to agree on atom names
is that the PDB file format is wrong. The PDB format specifies exactly
which columns atom names, coordinates, ... must go in. And Chimera will
not read the file properly if these rules are not followed. With the
format you gave in your email Id expect to not even load those atoms.

Here are your example PDB file lines compared to a PDB file from the PDB:

(Yours)
ATOM 24 H1 G 1 3.089 -4.841 -0.387 0.00
0.00 H
ATOM 25 H8 G 1 -0.669 -5.816 -0.733 0.00
0.00 H

(From 1FAV.pdb)
ATOM 6 CG1 ILE A 2 15.259 13.322 -12.257 1.00 60.89 C
ATOM 7 CG2 ILE A 2 17.479 12.582 -11.282 1.00 61.68 C


So I suggest reformatting your PDB lines as:

ATOM 24 H1 G 1 3.089 -4.841 -0.387 0.00 0.00 H
ATOM 25 H8 G 1 -0.669 -5.816 -0.733 0.00 0.00 H

Also test whether Chimera is reading this right by starting Chimera
separately and opening the PDB file and hovering the mouse over individual
atoms which will show their full atom names.

Tom

From: Kyle L. Brown kyle.l.brown@...
To: sparky@...
Subject: Chimera model (km) formatting
Date: Sat, 12 Nov 2005 13:00:30 -0600

I am trying to use the chimera model extension for viewing potentially bad
restraints with sparky. Ive got both programs running with each other, but
I seem to have a formatting problem with my pdb and could use some advice.

Im currently working on a small piece of DNA. When using sparky, I will
assign peaks in the following manner:

Group = G1 Atom = H1
Group = G1 Atom = H8

The peak list seems to recognize the G1 as a residue and a number and will
separate them for me as follows:

H1 1 H8 1 ...etc

In my pdb files these entries look like

ATOM 24 H1 G 1 3.089 -4.841 -0.387 0.00
0.00 H
ATOM 25 H8 G 1 -0.669 -5.816 -0.733 0.00
0.00 H

However, once I have sparky and chimera running, If I click on the peak I
get the standard error message, No PDB atom for G1H8 G1H1.

I think the problem is with my pdb because if I load a properly formatted
restraint file, I get the same message. Could someone offer some advice or
possible things I should try. I dont think this is a problem with atom
name translation because H8 and H1 match my pdb perfectly. I think it has
to do with the residue and number registry, but all Ive tried to date
didnt work.

Thanks in advance
Kyle