[Chimera-users] water display problem

Eric Pettersen pett at cgl.ucsf.edu
Fri Jun 28 10:32:50 PDT 2013


Hi Inhee,
	Due to column-width limits, PDB files can only contain 100,000 atoms and/or 10,000 residues while still conforming to the PDB standard.  Your file has way more than that and the numbers are running into the columns to the right.  While this isn't so bad for the atom numbers, since the column immediately to the right is simply supposed to be blank, the column to the right of residue numbers is reserved for residue insertion codes.
	The long and the short of it is that Chimera will not parse this file in the way you would like it to, and you get what you see.  I'll try to put some additional smarts into the PDB parser to try to get such a file to show as intended, but it could be awhile.  There are already some such tricks in there.  For instance, if the large atom numbers had used the column to the left instead of the column to the right then they would have been processed since Chimera treats an "ATOM 1" (for instance) record as if it were an ATOM record with 100,000 added to the serial number.

--Eric

                        Eric Pettersen
                        UCSF Computer Graphics Lab
                        http://www.cgl.ucsf.edu

On Jun 26, 2013, at 5:56 PM, inhee park <ipark.c at gmail.com> wrote:

> Is there a xyz coordinate range limit or a residue numbering limit in Chmiera for display?
> 
> I tried to display all atoms in the PDB file using chimera version 1.8.
> As shown in the attached figure, not all waters were displayed.
> If I loaded the same PDB file using other programs such as vmd or maestro,
> all waters were correctly displayed.
> FYI, I also attached the PDB file.
> 
> Thank you for your help.
> _________
> inhee park
> <water_disply.png><wat_tleap.pdb.zip>_______________________________________________
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