Hello Sourav,

First of all, please Check the active form of the protein (monomer or dimer or trimer). e.g. some protein exists in dimeric/tetrameric form, however only monomeric/dimeric form is active for instant. This information you can easily get from the enzymes belonging to the same family.

If really the homotrimeric form is active then simply you can generate homotrimeric form using modeller. The model will be constructed based on your input file if you specify it as a trimer then you will end up with trimer and so on.

If you are using modeller then define different subunits/chains of the template as well as the target in the input alignment with the "/" character:

Else you can use other servers like Swiss-Model, HHPred.

Good luck

Gaurao

Dear Sourav,

You can follow the tutorial given in the below link to build multi-mer protein model with the help of modeller.

https://insilicoengine.blogspot.it/2017/06/how-to-use-modeller-to-build-dimer.html

Dear Sourav,

If I am able to understand correctly you are trying to model a structure for a human homotrimeric protein using CryoEm structure from mouse @ 91% sequence id.

1. Can you mention the resolution of CryoEm structure and what is the state (active/inactive) of the structure in mouse. If it is the active active then you will need to validate if the protein in mouse functions as a monomer.

2. Once, established with that, you can proceed with two options:

• Use modeller to generate a homotrimer of your protein using multi-chain scripts from modeller package. This is possible as you have a homotrimer and therefore the sequence remains same.
• You can generate a monomer using modeller and then try to dock the three monomeric replicates together as a trimer. HADDOCK gives promising results with such an approach.

Thanks Tarun...I already followed your second opinion; that is generation of monomer by modeller. but there one problem is arised. i have a only one template. so upon running of basic tutorial.. i made alignment file like this, (where tseq1 is single template file)

from modeller import *

env = environ()

aln = alignment(env)

for (pdb, chain) in (('tseq1', '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)

That time it was failed to run by showing the following error

"ValueError:too many values to unpack" .

can you tell me where is the problem?

Hi Sourav,

As I can see from your code, it is trying to unpack string elements in a tuple to var (pdb, chain). However, in python will treat a string as a list of characters if not mentioned otherwise. This is causing the error "too many values to unpack" i.e the actual value in pdb and chain is 't' and 's' resp. rest of the string is not being able to unpacked.

You need either a tuple of tuple or a list. This can be achieved by precising strings 'tseq1', 'A' as [('tseq1', 'A')] - a list of strings. Alternatively, (('tseq1', 'A'), ))- a tuple of tuples. I would recommend to use a list.

I hope this helps.

Thank you Tarun. i will try this a bit later.