VMD-L Mailing List

From: Leonardo Trabuco (ltrabuco_at_ks.uiuc.edu)
Date: Fri Dec 21 2007 - 14:35:16 CST

Dear Amaury,

Thanks for the patch, I will incorporate it soon. And thanks for your
suggestions as well. One thing that I would like to add is the ability
to selectively plot salt bridges within VMD, but I never got the time to
do it. Maybe next year... ;-)

Best,
Leo

On Fri, Dec 21, 2007 at 10:31:07AM -0500, Amaury Pupo Meriño wrote:
> Hello everybody:
> I am processing in a TCL script thousands of structures (one by one) and among
> many others things I'm calculating salt bridges of a given selection using
> the saltbr plugging.
> The first problem arises when saltbr can not find any residues adequate to
> form salt bridges in the given selection, two typical error messages can
> appear:
>
> *No oxygen of acidic amino acid residues were found in the given selection.
> *No nitrogens of basic amino acid residues were found in the given selection.
>
> You have to catch these errors, or the script get stopped, and then set the
> number of salt bridges to zero in the selection. But, there is a problem
> here. I am generating a log file, and then I parse this file searching for
> some residues of interest. I am doing something like this:
>
> if{[catch "saltbr -sel $a_selection -writefiles no -log a_log_file.log"
> error_line]==1} {
> do something
> } else {
> do other thing
> }
>
> but, when saltbr exits with an error it DOES NOT close the log file. After a
> while the scripts stop with an error: too many open files.
>
> You can check this problem inside vmd, do the following:
>
> **
>
> set sel [atomselect top "a_selection_text"] ;# This selection doesn't have
> oxygen of acidic amino acid residues or nitrogens of basic amino acid
> residues
> set f [open a_file.txt w]
> puts $f
> close $f
>
> saltbr -sel $sel1 -writefiles no -log a_log_file.log
>
> set f [open a_file.txt w]
> puts $f
> close $f
>
> **
>
> You will see fileid from the first put and file(id+1) from the second.
>
> I checked inside saltbr.tcl and solved this problem, closing the log file
> before raising the error message. I send the diff file as an attachment.
>
> To the salbr authors: please, could you fix this?. And, have you consider that
> saltbr could return an atom index list, just like measure contacts and
> measure hbonds do?. It will be really nice.
>
> Thanks for this great plugging and for the super VMD.
> Best regards.
>
> --
> Amaury Pupo Meriño
> Centro de Inmunología Molecular.
> Cuba.
> Linux user #394752
> Phone: 2717933 (219)
> Jabber: amaury_at_jabber.biocomp.cigb.edu.cu
> amaury_at_softwarelibre.cu
> amaury.pupo_at_gmail.com
> Skype: amaury.pupo
> *****************************
> Mice LOVE Bioinformatics :-)
> ***************************** 

-- 
Leonardo Trabuco, Ph.D. student
Theoretical and Computational Biophysics Group
University of Illinois at Urbana-Champaign