Building missing residues in PDB structure as loop regions using PyMol

This tutorial will guide you to a step by step procedure of building or constructing annotated missing residues in a PDB structure as loop regions by using the Build Tool in PyMol, and subsequent refinement of the built loop by the ModLoop feature (loop modelling routine) in Modeller web server.

[@pedromazim3372]

Very useful guide, helped a lot. Thank you Mr.

[@ilgaztastekil6633]

Very nice explanation, thank you very much!

[@venkatanagarajue8196]

Thank you Shayon

[@sanjanaroychowdhury4254]

THANK YOUUUUUUUUUUU :')))))))))))))))))))))))

[@saquibali5043]

Even after filling the gap in between the protein sequence, I am getting broken lines in my structure. How to fix it?

[@fahmidazamanirin]

Thanks a lot to make videos on PyMol. Can you show the hoogsteen pairing at 54-57th bases in tRNA (1ehz) by PyMol?

[@shayonbh_molmod]

Please have a look at this PyMol plugin which can represent RNA in Hoogstein base pairs pymolwiki.org/index.php/Dssr_block. Hope it works for you. Thanks!

[@fahmidazamanirin]

@@shayonbh_molmod Thanks for sharing the link 👍

[@dianaolivera8132]

Hello Sir!
Thanks for the tutorial!
What happen if I have more than 20 missing residues in my protein, all of them in both terminal regions (22 a.a. in N terminal and 34 in the C terminal). Modeller does not accept too many residues. How can I minimize the protein?
Thank you!!!

[@SAG993]

Thank you very much. Could you let me know, how I can do this when missing resides are in the middle of protein?

[@joydipbarua3647]

Hello, you are doing grate. Actually I wanted to ask you just add missing and refine B chain, but how it is joined with the chain A,C and D? Because the original pdb structure has A,B,C and D chain which protein you taken in this tutorial.

[@shayonbh_molmod]

If you wish to retain rest of the chains (like A, C an D in this case), please do not delete/remove them in the first place and just build your missing residues with the other chains intact. Thanks!

[@ikponwmosaobaseki3645]

Thanks what if u have missing residue that is not at the C and N termina

[@shayonbh_molmod]

If you have missing residues in a segment other than the termini, you can still use the Build tool to add those residues from N -> C in the missing segment, that is "bond" the carboxyl of the residue before the start of the missing segment to the amino of the first residue of the missing segment, then at the end of the segment, bond the carboxyl of the last residue of the missing segment to the amino of the residue after the end of the missing segment.

[@chukyfreak994]

hello sir, i want to ask, if in chains B there is not example CYS B but in there is CYS B in missing residues, so my quesions is can CYS A or CYS E, become a imitate structure? thank you sir..... i hope you can answer this, thank you sir

[@harindurajapaksha6034]

Hii.. hope your doing well. If you have the time can you also make a video on using modeller for homology modeling and also on how to refine the models made by modeller or swiss model ? thank you very for your time.. Be safe.

[@shayonbh_molmod]

Hi, please have a look for SWISS-MODEL th-cam.com/video/kfMpOnnBjP8/w-d-xo.html

[@harindurajapaksha6034]

thank you very much..
it would be really helpful if you can make a video on how to refine a protein structure made by swiss model or modeller. In the past i have made several models that fails tests like ProSA, Errat, Verify3D. if you can make such video that on how to refine a homology model, that would be really beneficial to the scientific community as such quality knowledge is hard to come by..
thank you.

[@shayonbh_molmod]

@@harindurajapaksha6034 okay perfect! will try to do one using Modeller Python scripts

[@harindurajapaksha6034]

@@shayonbh_molmod thank you very much

[@ikponwmosaobaseki3645]

Please how can I use my prepared protein now for normal node analysis

[@shayonbh_molmod]

Unrelated to the tutorial, but please have a look: thegrantlab.org/bio3d_v2/tutorials/normal-mode-analysis#:~:text=Normal%20mode%20analysis%20(NMA)%20is,2015).

[@keyajoshi3965]

How to build a alpha helix at C-terminal by adding in the missing residues?

[@shayonbh_molmod]

Once you have the info on the sequence of missing residues, just keep "building" residues one by one from Build > Residues > Helix

[@hanstsahnang4533]

Hello Sir, thanks very much for this tutorial. after building up the missing residues can you also perform minization of the whole protein to have a more stable structure or we need to absolute treat the loop with modloop.

[@shayonbh_molmod]

Yes you can directly go for minimisation without loop refinement.

[@agathacindy8038]

Hello sir, thank you for the tutoral.I have built 9 missing residues at n-terminal at chain A, but when i uploaded it to modloop, it always says failed to produce any output models.. i am very confused because i have uploaded the correct pd file and entered the right loop selection.. have you encounter this problem before, sir?

[@shayonbh_molmod]

Not really, but I know that modloop limits number of residues to model to 14, which in your case is less - so I am not sure what's going on, unless your could please copy and paste the exact error.

[@muhammadshahab1421]

In my case the missing residues are miss in center what is the procedures to do this

[@shayonbh_molmod]

If you have missing residues in a segment other than the termini, you can still use the Build tool to add those residues from N -> C in the missing segment, that is "bond" the carboxyl of the residue before the start of the missing segment to the amino of the first residue of the missing segment, then at the end of the segment, bond the carboxyl of the last residue of the missing segment to the amino of the residue after the end of the missing segment.

[@GeneMania2024]

Sir, is it necessary to validate proteins secondary structure using Prochek after loop refinement?

[@GeneMania2024]

How to add atoms on missing residues?