VMD-L Mailing List

From: Akshay Bhatnagar (akshaybhatnagar2790_at_gmail.com)
Date: Thu Nov 05 2015 - 18:25:59 CST

Thank you very much Sir, I will try this immediately.

With Regards
Akshay Bhatnagar
PhD Student
BITS Pilani Hyderabad Campus

On Fri, Nov 6, 2015 at 5:54 AM, Tristan Croll <tristan.croll_at_qut.edu.au>
wrote:

> Yes, but you can easily do it in a script.
>
>
>
> set usepdb true
>
> set standardnames {ALA LEU … (put all the standard amino acid names here)}
>
>
>
> foreach testname $resnames {
>
> if { [lsearch $standardnames $testname] == -1 } {
>
> set usepdb false
>
> }
>
>
>
> If { $usepdb} {
>
> Whatever you want to do with your pdb files
>
> }
>
>
>
>
>
> *From:* Akshay Bhatnagar [mailto:akshaybhatnagar2790_at_gmail.com]
> *Sent:* Friday, 6 November 2015 10:19 AM
> *To:* Tristan Croll
> *Subject:* Re: vmd-l: Query for eliminating proteins with unusual amino
> acids
>
>
>
> Hello Sir
>
>
>
> Thank you very much for the reply. But i have around 5600 pdb's i cannot
> manually do this for all these pdb files.
>
>
> With Regards
>
> Akshay Bhatnagar
>
> PhD Student
>
> BITS Pilani Hyderabad Campus
>
>
>
>
>
> On Fri, Nov 6, 2015 at 3:58 AM, Tristan Croll <tristan.croll_at_qut.edu.au>
> wrote:
>
> Hi Akshay,
>
>
>
> Probably the easiest way to do this is to take advantage of the fact that,
> to VMD, “protein” is anything that contains atoms named C, N, CA and O –
> which should catch all non-standard amino acids as well. So if you do:
>
>
>
> set sel [atomselect top protein]
>
> set resnames [lsort –unique [$sel get resname]]
>
>
>
> … then all you have to do from there is a simple check of $resnames
> against a list of standard amino acid resnames.
>
>
>
> Cheers,
>
>
>
> Tristan
>
>
>
> *From:* owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] *On
> Behalf Of *Akshay Bhatnagar
> *Sent:* Thursday, 5 November 2015 3:46 PM
> *To:* vmd-l_at_ks.uiuc.edu
> *Subject:* vmd-l: Query for eliminating proteins with unusual amino acids
>
>
>
> Hello everyone
>
> I have around 5600 pdb files downloaded from rcsb.org. I want to generate
> psf for all these files. For this i have already made a tcl script. But the
> psf generation stops whenever it encounters a pdb files that contains an
> amino acid other than the 20 essential amino acids. These amino acids are
> generally the post translation modified amino acids. I tried removing them
> using a perl scipt where i searched for pdb files that contain only 20
> essential amino acid and HOH, but this has resulted in only 2 pdb files (it
> is removing all the pdb files that contains ligands and drug molecules
> also). I want to know is there any identifier through which i can remove
> only the post translated modified amino acids.
>
>
>
> With Regards
>
> Akshay Bhatnagar
>
> PhD Student
>
> BITS Pilani Hyderabad Campus
>
>
>
>
>