Thanks Ben,
is there a way to avoid that an insertion from becoming a curious loop
like the one shown at the top in the figure?
I’m trying to relax the system using MD but maybe I can avoid it during
modeling.
Best,
Marco
Il 22/10/2024 01:26, Modeller Caretaker ha scritto:
> On 10/21/24 2:28 AM, Marco Sette via modeller_usage wrote:
>> I have obtained five models of a protein with Modeller and I am
>> analyzing them in relation to the wt. There are of course small
>&…
[View More]gt; deviations, and such differences affect some physical properties. In
>> your opinion, should I analyze the separate models or I can take the
>> average structure? In NMR, people often use an average structure so I
>> wonder if it makes sense in the modelling field.
>
> Normally we look at the individual models. If you do want to average
> the structures, I would recommend you at least relax the final
> structure. One way to do that is to use AutoModel.cluster() as per
> https://urldefense.com/v3/__https://salilab.org/modeller/10.5/manual/node71…
> which does a basic conjugate gradients minimization.
>
> Ben Webb, Modeller Caretaker
--
Dr Marco Sette, PhD.
Department of Chemical Sciences and Technology
University of Rome, "Tor Vergata"
via della Ricerca Scientifica, 00133, Rome, Italy
e-mail: sette(a)uniroma2.it
Tel.: +39-0672594424
--
Questa email è stata esaminata alla ricerca di virus dal software antivirus Avast.
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[View Less]
Hi all,
I tried to use modeller10.4 to build a homology model for a peptide, which contains a D-Ala. Here the following steps I did:
1: in modlib/top.lib, Copy topology entry of L-Ala, then change
From
IC N C *CA CB 1.4592 114.4400 123.2300 111.0900 1.5461
IC N C *CA HA 1.4592 114.4400 -120.4500 106.3900 1.0840
To
IC N C *CA CB 1.4592 114.4400 -123.2300 111.0900 1.5461
IC N C *CA HA 1.4592 114.4400 …
[View More]120.4500 106.3900 1.0840
Save as DAL
1. In modlib/top_heav.lib, I copied the topology entry for L-Ala and modified it similarly.
2. Added 'DAL' information into modlib/resty.lib.
Despite following these steps, when I ran Modeller10.4, the D-Ala in the peptide appeared identical to L-Ala. Could someone please advise on what might be causing this issue?
Thank you so much.
Wu
[View Less]
A new version of Modeller, 10.6, is now available for download! Please
see the download page at https://salilab.org/modeller/ for more information.
If you have a license key for Modeller 9 or 10, there is no need to
reregister for Modeller 10.6 - the same license key will work. (It won't
do any harm to reregister if you want to, though!)
10.6 is a minor update that adds support for Python 3.13, and modifies
the behavior of Alignment.append_sequence() to make it easier to
construct …
[View More]multiple-sequence alignments containing chain breaks.
If you encounter bugs in Modeller 10.6, please see
https://salilab.org/modeller/10.6/manual/node10.html for information on
how to report them.
Note: you are receiving this email either because you subscribed to the
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Ben Webb, Modeller Caretaker
--
modeller-care(a)salilab.org https://salilab.org/modeller/
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[View Less]
Dear all,
I have obtained five models of a protein with Modeller and I am
analyzing them in relation to the wt. There are of course small
deviations, and such differences affect some physical properties. In
your opinion, should I analyze the separate models or I can take the
average structure? In NMR, people often use an average structure so I
wonder if it makes sense in the modelling field.
Thanks a lot for your help,
Best,
Marco
--
Dr Marco Sette, PhD.
Department of Chemical …
[View More]Sciences and Technology
University of Rome, "Tor Vergata"
via della Ricerca Scientifica, 00133, Rome, Italy
e-mail:sette@uniroma2.it
Tel.: +39-0672594424
[View Less]
