On Fri, Nov 12, 2021 at 11:15 AM amirhossein taghavi <
taghavi.amirhoss...@gmail.com> wrote:
> Hi Xiang-Jun,
>
> Sorry to bother. I meant if I can do the same thing you have done with
> DSSR pro with free version of x3dna-dssr, as I am getting some error
> messages:
>
No, as made clear in my prev
Hi Xiang-Jun,
Sorry to bother. I meant if I can do the same thing you have done with DSSR
pro with free version of x3dna-dssr, as I am getting some error messages:
x3dna-dssr -i=model.pdb --frame-pair=last -o=model1-ref-last.pdb
Processing file 'model.pdb'
total number of nucleotides: 26
[e] no m
Hi Amir,
Please have a look at the announcement "No more grant funding for
3DNA/DSSR" (
http://forum.x3dna.org/site-announcements/no-more-grant-funding-for-3dnadssr/)
on the 3DNA Forum. DSSR results are reproduced, period.
Best wishes,
Xiang-Jun
--
Xiang-Jun Lu (Ph.D.)
Email: xiang...@x3dna.org
Hello Dr. Xiang-Jun Lu,
Thanks a lot for your help. The model you have duplicated is exactly what I
am looking for (checked it with VMD). Unfortunately I do not have access to
DSSR-Pro. Is there any way that I can reproduce your procedure with
x3dna-dssr?
I need to create different numbers of dupl
Dear Blaine,
On Fri, Nov 12, 2021 at 10:14 AM Mooers, Blaine H.M. (HSC) <
blaine-moo...@ouhsc.edu> wrote:
> Hi Xiang-Jun Lu,
>
> Thanks for proving me wrong. Congratulations on your duplicated model!
> Please share the commands that you used with DSSR to generate the
> duplicated helix.
>
The du
-users@lists.sourceforge.net
Subject: Re: [PyMOL] [EXTERNAL] create a 26 bp RNA from a 13 bp system
Message: 1
Date: Thu, 11 Nov 2021 01:21:47 +
From: "Mooers, Blaine H.M. (HSC)"
mailto:blaine-moo...@ouhsc.edu>>
To: amirhossein taghavi
mailto:taghavi.amirhoss...@gmail.com>
Hello Prof. Blaine,
Thanks a lot for the detailed explanation. The model is out of MD
simulations with the box information.
I will try the workflow you suggested.
I very much appreciate your help.
Best regards,
Amir
On Wed, Nov 10, 2021 at 8:21 PM Mooers, Blaine H.M. (HSC) <
blaine-moo...@ouhsc.
Hi Amir,
No, not automatically. Your RNA is very distorted from
the standard A-form. I doubt any modeling program
can accurately extend such a distorted helix. Maybe
someone else will prove me wrong.
Your RNA does not have the expected
doughnut cross-section of the A-form when
viewed down the
