[Chimera-users] how to not include CONECT, RIBBON, HELIX, SHEET keywords in a pdb when saving from the pdb file dialog

Eric Pettersen pett at cgl.ucsf.edu
Mon Dec 19 12:04:26 PST 2005

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 Pettersen
                         UCSF Computer Graphics Lab
                         pett at 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  
> ...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 at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

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