Hi Sabuj, The save dialog does not allow for what you want. Do you think it's something that people in general would want to do, or is it fairly specific to something you're doing? You can do what you want using the command line with a mixture of the 'write' and 'system' commands:

write relative 0 1 /usr/tmp/x ; system egrep -v ^HELIX|^SHEET| ^CONECT /usr/tmp/x > out.pdb

which will write model 1 relative to model 0 into out.pdb.

Now, I'm guessing you are going to do this repeatedly or you wouldn't have bothered asking on the list about it. You can reduce the above into a much shorter command using 'alias' and save that alias into a file that the command line reads at startup so it is always available. Here's the alias that redefines the above as the command 'minsave':

alias ^minsave write relative $1 $2 /usr/tmp/x ; system egrep -v ^HELIX|^SHEET|^CONECT /usr/tmp/x > $3

With the above alias, "minsave 0 2 xyz.pdb" will write model 2 relative to model 0 into the file xyz.pdb. If you put this alias into ~/.chimera/midasrc or into ~/.chmidasrc (changeable using the Midas preference category) then the alias will always be available.

--Eric

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

On Dec 19, 2005, at 10:59 AM, Sabuj Pattanayek wrote:

Hi,

I was wondering how it might be possible to not include the CONECT, RIBBON, HELIX, or SHEET keywords in a pdb when saving from the save pdb file dialog?

It can be done using "pdbrun nouser cat | grep -v HELIX | grep -v SHEET" ...etc but I can't save the pdb model relative to another model on the screen using that command.

Thanks, Sabuj Pattanayek _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users