- modeller_usage - salilab.org

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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model different regions of a protein
by José Xavier 10 Sep '24

10 Sep '24

Dear Modeller users, I'm new here.. so sorry if this is an already answered question. I want to model a protein but the better template doesn't show ~50 aminoácids in its sequence. Is it possible to model the protein based on this template and only the region of ~50 residues based on another template? Thank you for your help Xavier

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Fwd: Error in modeller 10.5
by Victor Eduardo Rojas Pérez 04 Sep '24

04 Sep '24

---------- Forwarded message --------- De: Victor Eduardo Rojas Pérez <victor.rojas.03(a)alu.ucm.cl> Date: mar, 3 sept 2024 a las 13:11 Subject: Error in modeller 10.5 To: Modeller Caretaker <modeller-care(a)salilab.org>, < modeller_usage(a)salilab.org> Dear All, Along with greeting them cordially. I have the following error using modeller 10.5. in linux operating system. I have added the restyp RTN, retinal with % symbol in the restyp.lib file in the modlib folder but I still have this error. What else could I do to solve this error. Thank you. mod10.5 align1.py Could not find platform independent libraries <prefix> Could not find platform dependent libraries <exec_prefix> Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>] 'import site' failed; use -v for traceback Traceback (most recent call last): File "align1.py", line 56, in ? a.make() # do homology modeling File "/usr/lib/modeller10.5/modlib/modeller/automodel/automodel.py", line 141, in make self.homcsr(exit_stage) File "/usr/lib/modeller10.5/modlib/modeller/automodel/automodel.py", line 611, in homcsr aln = self.read_alignment() File "/usr/lib/modeller10.5/modlib/modeller/automodel/automodel.py", line 572, in read_alignment aln.append(file=self.alnfile, align_codes=codes) File "/usr/lib/modeller10.5/modlib/modeller/alignment.py", line 82, in append allow_alternates) _modeller.ModellerError: read_al_375E> Unknown residue type,position,sequence: % 334 1 -- * Víctor E. Rojas Pérez, Msc.* *Estudiante Doctorado en Biotecnología Traslacional * * Universidad Católica del Maule * *Facultad de Ciencias Agrarias y Forestales* *e-mail: victor.rojas.03(a)alu.ucm.cl <victor.rojas.03(a)alu.ucm.cl>* -- * Víctor E. Rojas Pérez, Msc.* *Estudiante Doctorado en Biotecnología Traslacional * * Universidad Católica del Maule * *Facultad de Ciencias Agrarias y Forestales* *e-mail: victor.rojas.03(a)alu.ucm.cl <victor.rojas.03(a)alu.ucm.cl>*

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Using frcmod+off non-standard residue in modeller.
by Pedro Guillem 15 Aug '24

15 Aug '24

Hello, I'm using Modeller to mutate only. I was wondering how hard it would be to mutate any position into a non-standard residue. I have my residues in Amber format (frcmod+off), and I read that I must create the definitions in CHARMM (RST) format, so modeller understands its topology+charges,etc. I also have a PDB file and PRMTOP with the non-standard residue. How hard would it be to make this work in Modeller?. Has anybody done it before? I see that ParmED (for example) can import the Amber files and generate RST files from them, but I didn't fully understand how many files I must modify in modeller, or whether I should use the BLK option, but it is not very well documented how to do so. Thanks in advance for any info on this. Pedro

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help at second script
by Junyi.FENG＠gustaveroussy.fr 23 Jul '24

23 Jul '24

Hi, While I was running the second script which is called compare.py and is the following: from modeller import * env = Environ() aln = Alignment(env) for (pdb, chain) in (('1jfw', 'A'), ('4ogr', 'D'), ('4or5', 'C'), ('3o6l', 'C'), ('3mi9', 'C'), ('1tbc', 'A'), ('1tiv', 'A')): m = Model(env, file=pdb, model_segment=('FIRST:'+chain, 'LAST:'+chain)) aln.append_model(m, atom_files=pdb, align_codes=pdb+chain) aln.malign() aln.malign3d() aln.compare_structures() aln.id_table(matrix_file='family.mat') env.dendrogram(matrix_file='family.mat', cluster_cut=-1.0) I recieved the following message and I don't know what to do. You can find many useful example scripts in the examples\automodel directory. It is recommended that you use Python to run Modeller scripts. However, if you don't have Python installed, you can type 'mod10.5' to run them instead. C:\Program Files\Modeller10.5>cd bin C:\Program Files\Modeller10.5\bin>cd Modeller_test C:\Program Files\Modeller10.5\bin\Modeller_test>mod10.5 compare.py 'import site' failed; use -v for traceback Traceback (most recent call last): File "compare.py", line 10, in ? aln.malign3d() File "C:\Program Files\Modeller10.5\modlib\modeller\alignment.py", line 348, in malign3d edit_file_ext) _modeller.ModellerError: fit2xyz_296E> Number of equivalent positions < 3: 0 Please, help me.

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help at second script
by FENG Junyi 23 Jul '24

23 Jul '24

Hello, While I was running the second script which is called compare.py and is the following: from modeller import * env = Environ() aln = Alignment(env) for (pdb, chain) in (('1jfw', 'A'), ('4ogr', 'D'), ('4or5', 'C'), ('3o6l', 'C'), ('3mi9', 'C'), ('1tbc', 'A'), ('1tiv', 'A')): m = Model(env, file=pdb, model_segment=('FIRST:'+chain, 'LAST:'+chain)) aln.append_model(m, atom_files=pdb, align_codes=pdb+chain) aln.malign() aln.malign3d() aln.compare_structures() aln.id_table(matrix_file='family.mat') env.dendrogram(matrix_file='family.mat', cluster_cut=-1.0) I recieved the following message and I don't know what to do. You can find many useful example scripts in the examples\automodel directory. It is recommended that you use Python to run Modeller scripts. However, if you don't have Python installed, you can type 'mod10.5' to run them instead. C:\Program Files\Modeller10.5>cd bin C:\Program Files\Modeller10.5\bin>cd Modeller_test C:\Program Files\Modeller10.5\bin\Modeller_test>mod10.5 compare.py 'import site' failed; use -v for traceback Traceback (most recent call last): File "compare.py", line 10, in ? aln.malign3d() File "C:\Program Files\Modeller10.5\modlib\modeller\alignment.py", line 348, in malign3d edit_file_ext) _modeller.ModellerError: fit2xyz_296E> Number of equivalent positions < 3: 0 Please, help me. Thank you very much. Best regards J_FENG

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Issues with incorporating ligands in multichain protein
by Kyle- richard Dawson 17 Jun '24

17 Jun '24

Hi there, I am trying to model a multichain protein (homodimer) using 2 templates. I have two issues, Currently my .pir file looks like this >P1;seq1 sequence:seq1:1:A:1224:A:::: xxxx/ xxxx* >P1;template1.pdb structureX:template1.pdb:40:A:651:B:41:B:648:xxxx/xxxx* >P1;template2.pdb structureX:template2:3:B:291 :B::Thermus thermophilus HB8:1.45:xxxx/-------/ >P1;template2.pdb structureX:template2:3:B:291 :B::Thermus thermophilus HB8:1.45:-------/xxxx* Firstly, my template 1 I am using both chain A and chain B, they have slightly different missing residues in the template but thats fine.For template 2 I cant put them under the same header, modeller doesn't seem to understand that I want to use chain B of template 2 for both chain A and B of my target so I specified it separately - it seems to work fine though with this setup. Unfortunately when I try add HETATM information ".." at the end of my target and template 1 and 2 gaps "--" for template 2 modeller says the whole sequence is out of alignment suddenly. I have specific HETATM=true in my script so it reads that part fine. My alignment looks like this but does not work? Am I missing some obvious? >P1;seq1 sequence:seq1:1:A:1224:A:::: xxxx../ xxxx..* >P1;template1.pdb structureX:template1.pdb:40:A:651:B:41:B:648:xxxx../xxxx..* >P1;template2.pdb structureX:template2:3:B:291 :B::Thermus thermophilus HB8:1.45:xxxx--/---------/ >P1;template2.pdb structureX:template2:3:B:291 :B::Thermus thermophilus HB8:1.45:---------/xxxx--* RegardsKyle

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