- modeller_usage - salilab.org

Fwd: model structure of IDP regions
by Priya Dey 25 Nov '20

25 Nov '20

From: "Priya Dey" <pdey(a)chemistry.du.ac.in> To: "modeller usage" <modeller_usage(a)salilab.org> Sent: Tuesday, November 24, 2020 3:37:57 PM Subject: model structure of IDP regions espected sir/ madam i want to model the unmodelled region of an intrinsically disordered protein region. I have tried the basic modelling tutorial with the total sequence of idpr 1mvf and the coordinate of the ordered region of the 1mvf idpr. But the final modelled structure generated have only the coordinate of the ordered one. Please guide me, so that i can find the all region coordinates of the modelled structure of 1mvf. Thanking you Priya dey Research Scholar Department of Chemistry University of Delhi

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MODELLER modelling of a single chain
by Austin Varela 25 Nov '20

25 Nov '20

Hello, I have a PDB file containing a complex composed of 2 proteins interacting. I wish to perform homology modelling of one of these proteins and leave the other one fixed. I have been able to do the modelling of the one protein of interest, however I am not sure how to have MODELLER include the fixed protein in the final PDB outputs as all my current outputs only contain the modelled protein. Is this some option I can modify on running MODELLER? Or would I have to align the new structures to the old one and somehow merge files to reintroduce the other protein. Thanks for the help! Austin -- Austin Varela University of Rochester - Class of 2020 BS Computational Biology & BA Data Science Computational Biology Researcher in the Werren Lab

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multi-chains: modeled separately or jointly?
by Amin Zia 25 Nov '20

25 Nov '20

Hi List, In multi-chain modeling, I am wondering if the alignment and modeling algorithms take into account multiple chains and their spatial locations concurrently or just simply model each chain separately and then combine the results. Related to this, is the dope score assessment a sum of scores for chains in these cases (in which case, it's assumed the statistics are measuring two independent models), or the correlation of chains are considered in the statistical assessment? Thank you in advance Amin Zia, Stanford Immunology

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Mismatch between residues of alignment and pdb
by Sunidhi 30 Oct '20

30 Oct '20

I downloaded the pdb_95.pir files, updated on May 14th 2020, from here <https://salilab.org/modeller/downloads/pdb_95.pir.gz>. I used the tutorial <https://salilab.org/modeller/tutorial/basic.html> to model one chain of a protein. I downloaded the pdb structure from RCSB-PDB. No changes done from my side in either files. Firstly, I was receiving an error " No atoms were read from the specified input PDB file, since the starting residue number and/or chain id in MODEL_SEGMENT (or the alignment file header) was not found; requested starting position: residue number " 1", chain " "; atom file name: 1r42A.pdb". I manually changed the chain id from blank to A and another error popped up stating that initial residue isn't matching, so I changed the initial residue from 1 to 19 and the error got resolved. Now, another error is there and isn't getting resolved anyhow. " After running model_single.py, I am getting the following error - _modeller.ModellerError: read_te_290E> Number of residues in the alignment and pdb files are different: 596 655 For alignment entry: 1 1r42A ". Ideally the pdb_95.pir file should have the same info as pdbs, yet this is popping up. Attaching the alignment section of the stated structure and the PDB is 1r42. Kindly can anyone help me in debugging what the exact issue is. I've been on it since days now. The alignment file has 596 residues while the pdb is supposed to have the same number because it has not been tampered with. Where it is going wrong? How can this be resolved? The alignment section of stated structure - >P1;1r42A structure:1r42A: 19:A: 596: :::-1.00:-1.00 ------------------STIEEQAKTFLDKFNHEAEDLFYQSSLASWNYNTNITEENVQNMNNAGDKWSAFLKE QSTLAQMYPLQEIQNLTVKLQLQALQQNGSSVLSEDKSKRLNTILNTMSTIYSTGKVCNPDNPQECLLLEPGLNE IMANSLDYNERLWAWESWRSEVGKQLRPLYEEYVVLKNEMARANHYEDYGDYWRGDYEVNGVDGYDYSRGQLIED VEHTFEEIKPLYEHLHAYVRAKLMNAYPSYISPIGCLPAHLLGDMWGRFWTNLYSLTVPFGQKPNIDVTDAMVDQ AWDAQRIFKEAEKFFVSVGLPNMTQGFWENSMLTDPGNVQKAVCHPTAWDLGKGDFRILMCTKVTMDDFLTAHHE MGHIQYDMAYAAQPFLLRNGANEGFHEAVGEIMSLSAATPKHLKSIGLLSPDFQEDNETEINFLLKQALTIVGTL PFTYMLEKWRWMVFKGEIPKDQWMKKWWEMKREIVGVVEPVPHDETYCDPASLFHVSNDYSFIRYYTRTLYQFQF QEALCQAAKHEGPLHKCDISNSTEAGQKLFNMLRLGKSEPWTLALENVVGAKNMNVRPLLNYFEPLFTWLKDQNK NSFVGWSTDWSPYA------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- --------------------------------------------------------------------------- ------------------------------------------------------------------------* Kindly help. Thanks and Warm Regards Sunidhi Center for Computational Biology Indraprastha Institute of Information Technology (IIIT <https://www.iiitd.ac.in/>) New Delhi 110020 India

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Consctruct a model with different templates' height
by Miguel Lacerda 28 Oct '20

28 Oct '20

Hi, Is it possible to build a model setting different heights for the templates, say , according to template similarity or other parameters? Regards, Enviado do Correio<https://go.microsoft.com/fwlink/?LinkId=550986> para Windows 10

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Modelling missing N-terminal residues
by Aathithya Diaz 23 Oct '20

23 Oct '20

Dear team, How to model the missing N-terminal residues (Residue number: 1-16) from the protein structure? My PDB structure consists of residues beginning from residues number 17. We tried modeling the structure using advanced modelling. When the missing residues were given in the loop refine step, there occurred an error stating, "The region cannot be found on the template" Is there any way you could help us in modelling the missing residues from the N-terminal? Thanks in advance Aathithya D SASTRA University Thanjavur

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Building missing atoms using MODELLER
by Zeineb Si Chaib 16 Oct '20

16 Oct '20

Dear Modeller users, I have a PDB file with missing atoms and residues. I would like to build the missing atoms only without touching the rest. I tried to build an alignment file where the sequence of the template is the same as the target and without putting any gaps (since I don't want to build any missing loops/residues). My alignment file looks like this: >P1;4xfa_atom_temp structureX:4xfa_atom: 5 :A:+186 :A:::-1.00:-1.00 ELLKPRTLADLIRILHELFAGDEVNVEEVQAVLEAYESNPAEWALYAKFDQYRYTRNLVDQGNGKFNLMILCWGE GHGSSIHDHTDSHCFLKLLQGNLKETLFDWPDKKSNEMIKKSERTLRENQCAYINDSIGLHRVENVSHTEPAVSL HLFSPPFDTCHAFDQRTGHKNKVTMTFHSKFGIRTP* >P1;4xfa_atom structureX:4xfa_atom: 5 :A:+186 :A:::-1.00:-1.00 ELLKPRTLADLIRILHELFAGDEVNVEEVQAVLEAYESNPAEWALYAKFDQYRYTRNLVDQGNGKFNLMILCWGE GHGSSIHDHTDSHCFLKLLQGNLKETLFDWPDKKSNEMIKKSERTLRENQCAYINDSIGLHRVENVSHTEPAVSL HLFSPPFDTCHAFDQRTGHKNKVTMTFHSKFGIRTP* Next, I am using the automodel class to build the missing atoms. I am using the following script: *from* modeller *import* * *# Load standard Modeller classes* *from* modeller.automodel *import* * *# Load the automodel class* log.verbose() *# request verbose output* env = environ() *# create a new MODELLER environment to build this model in* *# directories for input atom files* env.io.atom_files_directory = ['.', '../atom_files'] a = automodel(env, alnfile = 'alignment.ali', *# alignment filename* knowns = '4xfa_atom_temp', *# codes of the templates* sequence = '4xfa_atom') *# code of the target* a.starting_model= 1 *# index of the first model* a.ending_model = 1 *# index of the last model* a.make() It seems that Modeller built the missing atoms (4) but I am ending up with a new model that has fewer atoms than the original one (1512 vs 1558) although they both have the same number of residues. Any idea where could be the problem? Is my approach correct? I would appreciate your help with this. Best, Zina

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Sequence difference between alignment and pdb:
by Arnau PC 05 Oct '20

05 Oct '20

Hello, I have been using Modeller a few times for simple approaches but, currently, I have to face a more complex problem. I have the crystal structure of my template (740 residues, PDB: 4J0M) and I want to model three putative homolog sequences coming from a different organism. In that sense, the putative protein sequences are 1100 residues long, so I can only model the region that it locally matches with my template. For this reason, I have to use a local alignment (Smith-Waterman algorithm) between the target and the template and you may imagine which kind of problems I have to face when trying to run Modeller with this alignment: as it is a local alignment, there are multiple positions in the pdb file that have been skipped in the alignment so I have to remove those atoms from the pdb file one by one. Additionally, there are missing positions in the crystal template so I have to remake the alignment (deleting from the template fasta file these residues) each time I find missing atoms in the pdb, plus removing the atoms in the pdb file that do not match with the local alignment. I am pretty sure there is a more intelligent and practical solution to this problem since I have to do this for more than 700 residues and it can take hours for only one model. Since I am a new Modeller user and I have only used it for simple purposes, any help you can provide it would be very appreciated. Thank you very much for your attention and sorry for the inconvenience.

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External Source Sequence Alignment
by Li,Haoxi 05 Oct '20

05 Oct '20

Dear Modeller Users, Hope this email finds you well! I have a question about building homology models with sequence alignments coming from external sources (BLAST, PROMALS3D, etc). Since PIR format alignment files are usually not provided by these sources, do I need to manually construct the file based on the alignment I have? Are there any other ways? Thank you so much! Best wishes, Haoxi

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loop.py
by Jeff Reneker 24 Sep '20

24 Sep '20

Following the example in “Refining an existing PDB file” I want to “refine a region of an existing PDB file without comparative modeling.” The first thing I want to do is to get the loop.py script in the examples to work for any other structure. The only change I made is in this block of code from loop.py where I substitute 6aa0 for 1fdx as follows: m = MyLoop(env, inimodel='1fdx.B99990001.pdb', # initial model of the target sequence='1fdx', # code of the target loop_assess_methods=assess.DOPE) # assess loops with DOPE # loop_assess_methods=soap_loop.Scorer()) # assess with SOAP-Loop m = MyLoop(env, inimodel=‘6aa0.pdb', # initial model of the target sequence=‘6aa0', # code of the target loop_assess_methods=assess.DOPE) # assess loops with DOPE # loop_assess_methods=soap_loop.Scorer()) # assess with SOAP-Loop Then, I copy the 6aa0.pdb file to the appropriate directory. This is the error message at the tail end of the output: Traceback (most recent call last): File "loop.py", line 35, in <module> m.make() File "/usr/lib/python3.6/dist-packages/modeller/automodel/loopmodel.py", line 37, in make self.build_seq(self.inimodel, 1) File "/usr/lib/python3.6/dist-packages/modeller/automodel/loopmodel.py", line 169, in build_seq atmsel = self._check_select_loop_atoms() File "/usr/lib/python3.6/dist-packages/modeller/automodel/loopmodel.py", line 398, in _check_select_loop_atoms atmsel = self.select_loop_atoms() File "loop.py", line 18, in select_loop_atoms return selection(self.residue_range('19:', '28:')) File "/usr/lib/python3.6/dist-packages/modeller/coordinates.py", line 329, in residue_range start = self.residues[start]._num File "/usr/lib/python3.6/dist-packages/modeller/coordinates.py", line 259, in __getitem__ (self.offset, self.length, self.suffix)) File "/usr/lib/python3.6/dist-packages/modeller/util/modutil.py", line 23, in handle_seq_indx int_indx = lookup_func(*args) File "/usr/lib/python3.6/dist-packages/modeller/coordinates.py", line 323, in _indxres raise KeyError("No such residue: %s" % indx) KeyError: 'No such residue: 19:' So, I’m not sure what the deal is because that’s how new I am to Modeller. Thanks, JR.

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