October 2020 - modeller_usage

Query regarding the modelling of a particular set of residues in a protein
by Sruthi Sudhakar 20 Jan '21

20 Jan '21

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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

2 1

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

2 1

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

2 1

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.

2 1

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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