From: chandrakala gowda (chandrakala.gowda_at_gmail.com)
Date: Fri Feb 07 2014 - 14:48:28 CST

Dear Maxim and Axel,

Thank you very much for solving the issue..

The code works now. I now understand better.

best wishes,

Chandrakala

On Feb 7, 2014, at 5:23 PM, Maxim Belkin <mbelkin_at_ks.uiuc.edu> wrote:

> Hi Chandrakala,
>
> When you measure dihedral, you have to specify molecule by adding 'molid $mid' at the end of ‘measure' command. Otherwise it gets atom indices and analyzes top molecule.
>
> Maxim
>
>
> On Feb 7, 2014, at 10:08 AM, chandrakala gowda <chandrakala.gowda_at_gmail.com> wrote:
>
>> I need to measure dihedral angle of a particular segment
>> of several calculated protein models.
>>
>> My code as follows
>>
>> #==To load the pdb files==#
>>
>> set filelist [glob *.pdb]
>> foreach file $filelist {
>> mol new $file waitfor all
>> }
>>
>> #== to measure the dihedral of each file that is loaded==#
>>
>> foreach mid [molinfo list] {
>>
>> set Ncax [ atomselect $mid "segid B and resid 1 and name CAX" ]
>> set Ncay [ atomselect $mid "segid B and resid 1 and name CAY" ]
>> set Ncaz [ atomselect $mid "segid B and resid 1 and name CAZ" ]
>> set Ncbg [ atomselect $mid "segid B and resid 1 and name CBG" ]
>> set ind1 [ $Ncax get index ]
>> set ind2 [ $Ncay get index ]
>> set ind3 [ $Ncaz get index ]
>> set ind4 [ $Ncbg get index ]
>>
>> set xdihed [ measure dihed [list $ind1 $ind2 $ind3 $ind4]]
>> puts $xdihed
>> }
>>
>> #===#
>> But the code does not really work. It gives me the same value for the dihedral angle always.
>> which in reality is not the case. when I measure for each molecule the dihedral angle is different.
>> when i use the code for a single molecule
>>
>> 177.88656616210938
>> 177.88656616210938
>> 177.88656616210938
>> 177.88656616210938
>> 177.88656616210938
>> 177.88656616210938
>> 177.88656616210938
>> 177.88656616210938
>>
>> please could anyone point out if there is something wrong in the code.?
>