October 2024 - modeller_usage

Fwd: Average the models
by Marco Sette 24 Oct '24

24 Oct '24

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 >> 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. www.avast.com

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D-Ala
by Xiaosa Wu 22 Oct '24

22 Oct '24

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 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

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Modeller 10.6 release
by Modeller Caretaker 22 Oct '24

22 Oct '24

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 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 modeller_usage mailing list, or you provided this address when you requested a Modeller license and you ticked the "notify me of new releases" box. In the latter case, if you no longer wish to receive announcements of new Modeller releases, simply unsubscribe from the modeller_announce mailing list, or reply to this email and let us know. Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org https://salilab.org/modeller/ Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage

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Average the models
by Marco Sette 21 Oct '24

21 Oct '24

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 Sciences and Technology University of Rome, "Tor Vergata" via della Ricerca Scientifica, 00133, Rome, Italy e-mail:sette@uniroma2.it Tel.: +39-0672594424

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