VMD-L Mailing List

From: Francois Martz (francois.martz_at_icsn.cnrs-gif.fr)
Date: Thu Mar 15 2012 - 04:51:54 CDT

Hi,

I'm using VMD 1.8.7. There isn't any problem in the mol2 files.
But it seems that the problem come from my VMD script itself, since
between multiples running, errors are not reproducible.
Wrong lines are changing.
But if I manually copy/paste my script for one mol2 which is failing, in
VMD terminal, the final pdb is correct.

I am wondering if the problem doesn't come from the "no closing" file at
the end of each step.
Adding 'mol delete 1' or 'unset in_heme' at the end of foreach loop
doesn't change anything.
Here's my script:

"
set in_prot [mol new 3EBS.pdb]
set sel_in_prot_heme [atomselect $in_prot "serial 3313 or serial 15038
or serial 15043 or serial 15054 or serial 15062"]

set file_list [glob -type f *.mol2]

foreach mol_file $file_list {
    set in_heme [mol new $mol_file]
    set sel_heme_to_sup [atomselect $in_heme "serial 13 or serial 3 or
serial 4 or serial 39 or serial 33"]
    set sel_heme_to_move [atomselect $in_heme "all"]

    set transformation_matrix [measure fit $sel_heme_to_sup
$sel_in_prot_heme order {1 2 0 4 3}]
    $sel_heme_to_move move $transformation_matrix
    $sel_heme_to_move writepdb out3_$mol_file.pdb
}
"

Thanks you,

Martz François.

John Stone a écrit :
> Hi,
> Which version of VMD are you using? I wonder if there's something
> amiss with the mol2 plugin in your VMD installation, in terms of the
> data it originally read in. I don't expect the PDB plugin to do anything
> unusual on writing a new file. If you query those atoms with an atom
> selection right after loading your mol2 file, do those fields look correct,
> or do they exhibit the same problem that you see in the PDB?
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Wed, Mar 14, 2012 at 06:15:22PM +0100, Francois Martz wrote:
>
>> Dear all,
>>
>> I have done a simple script to superimpose multiple (45) mol2 files on
>> the same structure.
>> To save results as pdb files it uses 'writepdb' command for each input
>> mol2 files.
>>
>> But in 28 of the 45 pdb, few (between 2 and 4 on 51) lines are wrong
>> (like here the ATOM 21 line):
>>
>> ATOM 19 H19 5202X**** -18.490 3.871 -9.493 0.00
>> 0.00
>> ATOM 20 C20 0 X 0 -20.028 4.492 -8.167 0.00
>> 0.00
>> ATOM 21 N21 -237X-251643850 -20.577 4.610 -6.911 0.00 0.00
>> ATOM 22 C22 62 X 62 -21.760 5.291 -7.080 0.00
>> 0.00
>> ATOM 23 C23 0 X 0 -21.961 5.607 -8.475 0.00
>> 0.00
>>
>> It can be fixed by replacing '-251643850' by '0'.
>> But since I have to compute multiple files, I would like to understand
>> why 'writepdb' generates this, taking into account that all input mol2
>> files, are generated by one of my script and are equally formatted.
>>
>> Thanks you,
>>
>> Martz François.
>>
>
>