[Chimera-users] writing out part of a PDB

Elaine Meng meng at cgl.ucsf.edu
Wed Mar 31 17:34:19 PST 2004

  Hi Shuanghong,
Question (1), surface problem:

I don't think the problem where nothing happens when you type the 
command "surface" has been reported.  Sometimes there is a delay 
while the surface is being calculated, but it shouldn't be terribly 
long.  Problems have been reported in some cases, but they generally
cause some sort of error message.

To register a problem more formally, you could send mail to
chimera-bugs at cgl.ucsf.edu and be sure to include what version of
Chimera and what kind of computer you are using, and what structure(s)
cause the problem.

Question (2), writing out part of a PDB file:

If you are on a **non-Windows** system, you can use the command
"pdbrun" to save just the atoms that are displayed.

You could display only the atoms you want by first selecting
what you want to measure the distance to.  Then, use Select...Zone...
to select all the atoms in the region you want to write out.
Then the command "show sel" will undisplay the rest of the stuff.
(Or, instead of selecting you could do it all in one command, for example
  show :212.a za<4.5
for all atoms within 4.5 A of any atom in residue 212 of chain A.
Specifying zones in the command line is described in the manual page
on atom specification, which is listed in the Basic Functions index.)

Next, use pdbrun (see man page using the command "help pdbrun"), for
   pdbrun nouser cat > myzone.pdb

Pdbrun literally sends the information for only the displayed atoms
in their displayed positions to another command, in this case "cat"
to send the information to the file myzone.pdb.  If you want the coordinates
to be the same as in the original file, first use the command "reset."

The command "save" (or File... Save Session As... ) doesn't save coordinates,
only how they are positioned/colored/displayed, etc.  In fact, restarting
a saved session will use the original input file(s) for coordinates.
The command "write" (same as the function "write PDB" in the Model Panel)
saves coordinates into a file.  However, these will save the entire coordinates
whether displayed or not.

If you are on **Windows** the only way I can think of is to actually
delete the atoms/bonds you don't want to write out ("delete" command or
Actions... Atoms/Bonds... delete).  For example, when only what you want
to write out is displayed,
  delete @/!display
actually deletes the other stuff.  Subsequently, a file created with
"write" would only contain the atoms/bonds that had not been deleted.
I hope this helps,
Elaine C. Meng, Ph.D.
Computer Graphics Lab and Babbitt Lab
meng at cgl.ucsf.edu

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