Homology modeling using Modeller - Tutorial for beginners (Part 1)

[@salmabassem9868]

Hi, thanks for the video! Is the .pir file a general file and can be used for any query or is it specific and needs to be modified? thank you!

[@FarhanHaqj]

pleasure. PIR file can be used for any query. You can download it from the MODELLER website or from the top comment in this video!

[@salmabassem9868]

@@FarhanHaqj Thank you!

[@dinhthuan-thien8048]

salilab.org/modeller/supplemental.html You can check the updated file from here

[@KC-hd3wi]

@@dinhthuan-thien8048 Thank you!!

[@randebuu1]

dude you are a genius, i was struggling with bioinformatics and you explained it in the best way possible in 20 mins thanks a lot!

[@krishanuchoudhury7943]

Thanks!! But could not understand about pir file

[@독일사는윤미]

As a final step of this video, I run the modller writing 'mod10.1 build_profile.py' However, I got the error massage 'can not open logfile build_profile.log: permission denied.' what can I do for that? Actually, I am using Modller 10.1 version and previously, I couldn't save the build_profile.py after modifying the text 'file=querysequence.ali.' Therefore, I went to the security settings of the file and enable access all the permissions and I could save this modified file.

[@navyadarling4555]

There is no pinned comment here and I am not getting how to dowload pdb_95pir ?can u please explain with clarity

[@F.EmreBora]

Dear Farhan, I got "Cannot open file pdb95.pir: No such file or directory" error and I couldnt find to fix this error, can you help me?

[@anjhere]

Very informative video sir. But how do I get the FASTA sequence of a protein in an insect (like you did in 6:19) from NCBI when its not listed in there. What does that mean?

[@dannieel1327]

Hi, sir please tell me how did you save the PIR file? Was it saved like you did for other pdb files or whole pir and python files(from Basic Modeling) are needed to be copy paste all together? In addition, all the saved files are only 5 in total(4 pdb files +querysequence) for me and not 6.

[@gasgatt]

yeaah!! How is it appear this file pdb_95.PIR ???

[@louissjoel]

Hi sir, I followed all of your steps up until "mod (my version is 10.4) build_profile.py" and then i got this error message: 'import site' failed; use -v for traceback Traceback (most recent call last): File "build_profile.py", line 10, in ? chains_list='ALL', minmax_db_seq_len=(1, 40000), clean_sequences=True) File "C:\Program Files\Modeller10.4\modlib\modeller\sequence_db.py", line 72, in read minmax_db_seq_len) IOError: openf______E> Cannot open file pdb95.fsa: No such file or directory not sure what to do with this or how to fix it, would you be able to help me out? Thanks a lot :)

[@olegdoom]

Same here. What did you do to overcome this?

[@Gauravkumar-ze2wq]

Hi Farhan, I Hope you are doing well, and thanks for such an informative video. I am facing a problem, after installing the Modeller 32 or 64, I am not getting the modeler file in the Bin file. Can you help me with this issue?

[@hanstsahnang4533]

Hi, thanks very much for this tutorial can you do a tutorial on how to build missing amino acids residues from pdb structures please.

[@munsifshad8283]

how to do alternative template modelling or modelling for specific loop conformations?

[@Sulbee]

Farhan bhai if I have four chains in a protein, how do I prepare a sequence file? Do I copy paste the fasta file for all chains and then put an asterik at the end or make 4 individual text files for each chain?

[@armichaudhary8445]

Hii my modeller version is 10.1 I am building profile by >mod10.1 build_profile.py but it is showing that command not found mode10.1 I am in bin libraray of modeller.

[@FarhanHaqj]

update your system first $ sudo apt-get update $ sudo apt-get upgrade then try again $ mod(modeller version) space build_profile.py

[@Sulbee]

I'm getting this error: 'import site' failed; use -v for traceback

[@nagalambikabiradar1297]

Hello Farhan. Thanks for the video. I am not able to convert txt file to .ali file, COuld you tell me how to resolve this issue?

[@hnnn2341]

In RCSB , pdb format download option is not available. I downloaded pdb format-like files (tar.gz). When I unzip this compressed file , there are 2 pdb files with name pdb-bundle1 and pdb-bundle2 . Both the files are same. I'm confused whuch file is corect file to use. Anyone can guide me?

[@baharehdabirmanesh9570]

Hi When choosing your pdb files, You selected the highest identity ones but did not mentioned anything about their low Query coverage.

[@sharanyamukherjee1161]

Kindly let us know how to download the pdb_95 pir file. Thanks in advance!

[@farzanehsamandar1035]

Thank you so much for this perfect video. My question is when I typed mod10.2 build_profile.py, this error showed up: in ALIGN_CODES(i) was not found in the alignment file!! Could you please tell me what I should do?

[@saikulkarni7867]

hello sir, after giving my command its showing this what should i do ? Cannot open logfile build_profile.log: Permission denied

[@FarhanHaqj]

Save your folder somewhere else other than C drive. Then Run all the commands!

[@saikulkarni7867]

@@FarhanHaqj i saved it in dekstop how to run now? Any commands for that?

[@_qurrota]

Thank you for your video. Can i use modeller if the missing residue more than ten?

[@atkuriparabandarpopyakter798]

How can i get the pdb_95 pir file??

[@eyaberrais2686]

Same qtion

[@eugenioferrario4810]

PIR file is missing! The only thing you didn't explain is the problem

[@sunidhibhatt9920]

Hello sir, I have a query!! The protein I'm working with doesn't show enough similarity after running BLAST. So, how can I get a suitable template to run modeller? Kindly help!!! Best wishes

[@FarhanHaqj]

What is the percentage? If it is around 60% than it is good.

[@sunidhibhatt9920]

@@FarhanHaqj Sir, it's 34% only

[@sunidhibhatt9920]

When I'm running PDB BLAST it doesn't show any similarity but on running NR BLAST it's coming 34%

[@侯大]

@@sunidhibhatt9920 I have the same problem. I get for templates, just 1 have high similarity and coverage. 3 templates have 30%-40% similarity and low coverage

[@FarhanHaqj]

Why dont you guys go for methods like threading (I-Tasser etc.)

[@dianaolivera8132]

Hi Sir! Many thanks for the video! I saw I have a similar issue in the comments about the last running instruction. I run the modller writing 'mod10.1 build_profile.py' However, I got the error massage "FATAL ERROR: Cannot open file build_profile.py: No such file or directory" But the file is in the folder. Do you know if there's anything I can do? Thanks!

[@FarhanHaqj]

update your system first $ sudo apt-get update $ sudo apt-get upgrade then try again $ mod(modeller version) space build_profile.py

[@Tarekamerica]

How do I convert file to ALI? It keeps still saying it is saved as .txt, any help will be greatly appreciated. Thank you!

[@concept1994]

If its not converting. Open basic example file, copy it and paste your sequence

[@kamilahnazmi705]

Hi sir. I want to ask if it is possible to not run this in bin file? Instead, I saved all the files in folder at Dekstop and use cd command. Will the outcome be the same? Thank you for the video.

[@FarhanHaqj]

its always good to run in the bin folder because all the other required files must be there by default

[@kamilahnazmi705]

@@FarhanHaqj thank you sir for you reply. i have another question. i replicated methodology from a research article and it turns out the protein structure i obtained is very different but it has the same amino acid sequence with the expected result. is there any way i can improve my result? thank you again

[@parmitachawley9850]

I am not able to edit the file name of query sequence in build_profile.py file. please help. it is showing message as " you do not have permission to open this file. see the owner of the file or administrator to obtain permission.

[@FarhanHaqj]

You can try again by changing the directory. Save the folder in Desktop or go to the security settings of your file and enable access all the permissions.

[@samansohail902]

Can u please guide me regarding query sequence file whenever i try to save it in ali format it saves in text document format i am following each nd every step but still the same

[@FarhanHaqj]

ALI format option is given when you save the file. I am not sure where you are facing the problem.

[@shantanukhatri007]

Look if its windows you can just google changing file format.

[@muhammadshahab1421]

Make a vedio about missing residues

[@dimascarballotorres7585]

I have problems with mod9.25 command. I don't know why my computer can't read it. I need your help!!!

[@FarhanHaqj]

Please recheck your modeller version and make sure you are in the correct directory(probably where the modeller folder is present in your system) while running this command.

[@dimascarballotorres7585]

@@FarhanHaqj Thanks for your advice.

[@dikshakumari4469]

can we install modeller in our laptop and do all this stuff in laptop

[@FarhanHaqj]

yes

[@takimsarker929]

Very nice interpretation. please make the part 2 soon.

[@FarhanHaqj]

Thanks. Sure

[@gasgatt]

It's an amazing video, I learned a lot. But i have a question, because I'm using the version 10.2. and there isn't the file Modeller inside the bin, so in the first moment I copied the basic-example zip, copied the build_profile.py inside this archieve to put to my new file that I create to put my proteins, but when I edited it, changing the name of my file.ALI, I can not save, it appears a message tht my permission is denied. Anyone can help me?

[@gasgatt]

It was only because the file wasn't in the USERS, and yes on the files and programms. =)

[@sharanyamukherjee1161]

First of all, I would start replying to you by thanking you! I implemented this idea of yours and extracted the "build_profile.py" file from the example zip file. However, I also faced the same issue while editing the file. Thereafter, I downloaded Notepad++, and edited the same in Administrator mode. See if this works for you.

[@urwatilwusqa8303]

Assalam o Alikum Sir! I'm unable to update the build_profile.py file, it keeps on saying "[Errorno 13] Permission denied"... I also changed the security setting but that didn't work... Can you help in this regard????

[@FarhanHaqj]

Please check comments. The issue is addressed couple of times.

[@hnnn2341]

Sir I couldn't find build_profile.py?

[@FarhanHaqj]

please check the pinned post

[@archanabhati111]

Sir, while editing build_profile.py It is showing .... permission denied.. Plz help me with it

[@FarhanHaqj]

permission denied errors are mostly because of modeller version issue. System maybe not supporting this modeller version

[@archanabhati111]

@@FarhanHaqj Sir, what will be the recommended version for windows 10?

[@FarhanHaqj]

Version 9.21 should be working for windows 10. You can try again by changing the directory. Save the folder in Desktop or go to the security settings of your file and enable access all the permissions.

[@qaiserfatmi]

Indeed very helpful

[@FarhanHaqj]

gracious :)

[@mohamadzulkefleesabri3790]

thank you sir for your help

[@bhartimittal5569]

From where did you get ...95.pir file

[@FarhanHaqj]

Please check the pinned comment of this post

[@RupeshKumar-mq4eu]

What is actually pdb_95.pir file

[@FarhanHaqj]

This file is used to search for possible templates having known pbd structures against your protein of interest.

[@nazmussakibshuvo4292]

Where is your pinned comment?

[@FarhanHaqj]

Somehow its removed. What is your question.

[@nazmussakibshuvo4292]

@@FarhanHaqj Can you help me in this regard😔 it is occured at the time of alignment in homology modelling by modeller. It shows the information that i am given below. 'import site' failed; use -v for traceback Traceback (most recent call last): File "alignment.py", line 6, in ? aln.append(file='querysequence.ali', align_codes='querysequence') File "C:\Users\User\Modeller10.1\modlib\modeller\alignment.py", line 82, in append allow_alternates) _modeller.ModellerError: read_al_373E> Protein specified in ALIGN_CODES(i) was not found in the alignment file; ALIGN_CODES( 2) = querysequence. (Note: I download the Fasta format of my protein several time from NCBI. so i think there is a less chance of my protein to be wrong. Thanks in advance.

[@alizanirmal2028]

95_pir file?? ​@@FarhanHaqj

[@uzairmarwat4539]

thank you

[@saeedraza]

👍👍👍

[@enasastiata3315]

وعليكم السلام ورحمه الله وبركاته

[@samansohail902]

C