At final plot_profiles script, where do you obtain the template.profile archive from? Following the steps I only obtained the query.profile, I don't know if I'm clear.
template is the best possible hit that you need to select from the generated model previously in the last step of model generation. The name of the file is just query sequence B99990005.pdb. Don't get confused
@@FarhanHaqj The message I received is the following: Traceback (most recent call last): File "C:\Modeller9.24\EhVps26\plot_profiles.py", line 33, in template = get_profile('1bdmA.profile', a['1bdmA']) File "C:\Modeller9.24\modlib\modeller\alignment.py", line 490, in __getitem__ ret = modutil.handle_seq_indx(self, indx, File "C:\Modeller9.24\modlib\modeller\util\modutil.py", line 25, in handle_seq_indx raise KeyError(indx) KeyError: '1bdmA' In past scripts I substituted '1bdmA' for the name of my own files. But particularly in my files I don't find the equivalent file to '1bdmA.profile' . How can I obtain it?
@@dianaa.valencia3910 Ahan. You are doing some mistake while uploading a template file. Please go to the gnu plot documentation available on the website and try to follow the steps carefully. Good luck !
The only issue I'm facing is to prepare the template.profile We have the query.profile which was created in the build.py step. But I'm confused how to prepare the template.profile as it is required in plot_profiles.py
@ Farhan Haq I tried so many times but always it shows error in compare.py step. I have done same steps that you did but still it shows error. Please help me out.
@@FarhanHaqj Traceback (most recent call last): File "compare.py", line 10, in ? aln.malign3d() File "E:\Modeller10.1\modlib\modeller\alignment.py", line 348, in malign3d edit_file_ext) _modeller.ModellerError: fit2xyz_296E> Number of equivalent positions < 3: 2 It is showing this .. although I have done the same steps that you did.
@@FarhanHaqj from modeller import * env = Environ() aln = Alignment(env) mdl = Model(env, file='t1', model_segment=('FIRST:A','LAST:A')) aln.append_model(mdl, align_codes='t1A', atom_files='t1.pdb') aln.append(file='querysequence.ali', align_codes='querysequence') aln.align2d(max_gap_length=50) aln.write(file='querysequence-t1A.ali', alignment_format='PIR') aln.write(file='querysequence-t1A.pap', alignment_format='PAP') Can you please help me out to find error in line 7 please.?
Hi!! The videos are amazing but I have a problem. I am getting this error after running the command alignment.py read_al_373E> Protein specified in ALIGN_CODES(i) was not found in the alignment file; ALIGN_CODES( 2) = querysequence I know that this question was asked before but I don't understand the answer about loading another file. Please can you help me with this? Thank u so much!!
#Thank you for your helpful video. I am a beginner and I have a problem when comparing 2 templates. My compare.py file is : env = Environ() aln = Alignment(env) for (pdb, chain) in ('3rze', '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) #And then the error that I received: Traceback (most recent call last): File "compare.py", line 5, in ? for (pdb, chain) in ('3rze', 'A'): ValueError: too many values to unpack #I try to fix this error but it seems to be invalid. I hope you can help me. Thank you so much!
AOA sir how are you? Sir, I have tried to use modeller to generate a model for my query sequence of SARS-CoV 2 E-protein. Sir, I chose three models which are (1) B99990005.pdb having a molpdf of 378.85013, DOPE score of -5237.88574, and GA341 score of 0.95393 (2) B99990003.pdb having a molpdf of 421.25500, DOPE score of -4757.49756, and GA341 score of 1.00000 (3) B99990002.pdb having a molpdf of 391.71848, DOPE score of -4841.44629 and GA341 score of 0.99953 but i'm bit confused that among these three models which one would be the best model for further analysis so please clarify my confusion? Thank You!
I am unable to install metaplotlib. When I try to install metaplotlib in cmd prompt, it shows python was not found. run without arguments ... could not find python while following point no. 26 of the description.
I am getting this error when I try to execute build_profile.py: Traceback (most recent call last): File "build_profile.py", line 4, in ? env = Environ() NameError: name 'Environ' is not defined I am using the tutorial files so I don't understand what is happening, can you help me? Thanks!
Dear Dimas Have you imported these two library modules? (import pylab) (import modeller) If the problem still persists, please attach the snapshot of your error
I am getting this error after running the command alignment.py read_al_373E> Protein specified in ALIGN_CODES(i) was not found in the alignment file; ALIGN_CODES( 2) = query Please can you help me with this
It is an amazing video, thanks a lot. Besides, I have a little problem because in the final to evaluate my model, in the first line to the file plot_profiles.py there is a phrase: IMPORT 'PYLAB', but it can not be read or run in the sequence. What is pylab?
Don't use the code "mod10.2 plot_profile.py" instead use only "plot_profile.py". Alternatively, run the python file directly from IDLE as shown in the video. Also Pylab is matplotlib only.
@@FarhanHaqj But my guide has told me to use modeller to model the receptor ADGRG3 with the template PDB ID 7d77. If I don't use compare.py and go ahead with the alignment program, would that be fine?
Please help me to solve the problem 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.)
sir I am getting this error with compare.py: File "compare.py", line 10, in ? aln.malign3d() File "C:\Users\vinay\Modeller10.3\modlib\modeller\alignment.py", line 348, in malign3d edit_file_ext) _modeller.ModellerError: fit2xyz_296E> Number of equivalent positions < 3: 2
At final plot_profiles script, where do you obtain the template.profile archive from? Following the steps I only obtained the query.profile, I don't know if I'm clear.
template is the best possible hit that you need to select from the generated model previously in the last step of model generation.
The name of the file is just query sequence B99990005.pdb.
Don't get confused
@@FarhanHaqj The message I received is the following:
Traceback (most recent call last):
File "C:\Modeller9.24\EhVps26\plot_profiles.py", line 33, in
template = get_profile('1bdmA.profile', a['1bdmA'])
File "C:\Modeller9.24\modlib\modeller\alignment.py", line 490, in __getitem__
ret = modutil.handle_seq_indx(self, indx,
File "C:\Modeller9.24\modlib\modeller\util\modutil.py", line 25, in handle_seq_indx
raise KeyError(indx)
KeyError: '1bdmA'
In past scripts I substituted '1bdmA' for the name of my own files. But particularly in my files I don't find the equivalent file to '1bdmA.profile' . How can I obtain it?
@@dianaa.valencia3910 Ahan. You are doing some mistake while uploading a template file. Please go to the gnu plot documentation available on the website and try to follow the steps carefully. Good luck !
@@FarhanHaqj Thank you very much.
I faced the same stuff. Did you solve the problem?
16:25 isnt 2nd one the lowest score ?
Thanks a bunch..... Really helpful 😁
hello Sir,thank you for the course... I have a question ,how can we convert an alignement file (fasta form) to PIR file
Why my modeller is not preparing files after traceback of build profile?
I'm sorry how is t1A is the most closely related? can you explain please?
Where is this t1.profile file how to generate it please explain
The only issue I'm facing is to prepare the template.profile We have the query.profile which was created in the build.py step.
But I'm confused how to prepare the template.profile as it is required in plot_profiles.py
we need to evaluate template as well
Facing problem in script 3 it says line 7, in? Line 82, in append allow-alternate unknown residue type, position,sequence: 75 2 how to fix it?
how did you overcome this
@ Farhan Haq
I tried so many times but always it shows error in compare.py step. I have done same steps that you did but still it shows error. Please help me out.
What is the error?
@@FarhanHaqj Traceback (most recent call last):
File "compare.py", line 10, in ?
aln.malign3d()
File "E:\Modeller10.1\modlib\modeller\alignment.py", line 348, in malign3d
edit_file_ext)
_modeller.ModellerError: fit2xyz_296E> Number of equivalent positions < 3: 2
It is showing this .. although I have done the same steps that you did.
@@technicalknowledge2296 some mistake in preparing input file
check/debug the line once again that is mentioned in the error
@@FarhanHaqj from modeller import *
env = Environ()
aln = Alignment(env)
mdl = Model(env, file='t1', model_segment=('FIRST:A','LAST:A'))
aln.append_model(mdl, align_codes='t1A', atom_files='t1.pdb')
aln.append(file='querysequence.ali', align_codes='querysequence')
aln.align2d(max_gap_length=50)
aln.write(file='querysequence-t1A.ali', alignment_format='PIR')
aln.write(file='querysequence-t1A.pap', alignment_format='PAP')
Can you please help me out to find error in line 7 please.?
@@technicalknowledge2296 hey i am facing similar error. were u able to solve it back then?
I want to create homology model for homotrimeric protein . Please guide me the steps
Hi!! The videos are amazing but I have a problem. I am getting this error after running the command alignment.py
read_al_373E> Protein specified in ALIGN_CODES(i) was not found
in the alignment file; ALIGN_CODES( 2) = querysequence
I know that this question was asked before but I don't understand the answer about loading another file.
Please can you help me with this? Thank u so much!!
I am also getting same error. Please give solution to this
I was also getting the same error but its resolved now did ull get resolved with it?
@@parmitachawley9850
I was also getting the same error but its resolved now did ull get resolved with it?
#Thank you for your helpful video. I am a beginner and I have a problem when comparing 2 templates. My compare.py file is :
env = Environ()
aln = Alignment(env)
for (pdb, chain) in ('3rze', '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)
#And then the error that I received:
Traceback (most recent call last):
File "compare.py", line 5, in ?
for (pdb, chain) in ('3rze', 'A'):
ValueError: too many values to unpack
#I try to fix this error but it seems to be invalid. I hope you can help me. Thank you so much!
Hello, Thank you for the informative tutorial; I wondered what the differences between a GUI like EasyModeller and Modeller are?
EasyModeller is just a better user interface for Homology Modeling. No difference to my knowledge
@@FarhanHaqj thank you for your reply
Hello, Thanks for this tutorial. How can I make .profile file for template?
we need to evaluate template as well
AOA sir how are you? Sir, I have tried to use modeller to generate a model for my query sequence of SARS-CoV 2 E-protein. Sir, I chose three models which are (1) B99990005.pdb having a molpdf of 378.85013, DOPE score of -5237.88574, and GA341 score of 0.95393 (2) B99990003.pdb having a molpdf of 421.25500, DOPE score of -4757.49756, and GA341 score of 1.00000 (3) B99990002.pdb having a molpdf of 391.71848, DOPE score of -4841.44629 and GA341 score of 0.99953 but i'm bit confused that among these three models which one would be the best model for further analysis so please clarify my confusion? Thank You!
Where can I get the script text document?
Hello did you find the script text document, I cant find it either
@@harrisazmi2472 No bro! I have done the Homology modelling through a web server called Swiss Model
build_profile.log file is not generated after entering mod10.2 build_profile.py
what should I do now?
we need to evaluate template as well as model
I am unable to install metaplotlib. When I try to install metaplotlib in cmd prompt, it shows python was not found. run without arguments ... could not find python while following point no. 26 of the description.
Your python is not installed properly
@@FarhanHaqj If such is the case then how would the other files generated using python script?
thanks.
I am getting this error when I try to execute build_profile.py:
Traceback (most recent call last):
File "build_profile.py", line 4, in ?
env = Environ()
NameError: name 'Environ' is not defined
I am using the tutorial files so I don't understand what is happening, can you help me? Thanks!
Solved! I just installed the new version of Modeller and it worked.
Good job!
How can I open the PAP file, sir?
for generating plot u r using folder modeller and u r doing tutorial in modeller1? so sry but very confusing..
I have problems with last run, in the second line . How can I fix??
Dear Dimas
Have you imported these two library modules?
(import pylab)
(import modeller)
If the problem still persists, please attach the snapshot of your error
@@FarhanHaqj how can I import these two library modules?
My computer can't open files .bin. What program do you recommend me downland?
You can open all the files used here in notepad++
@@FarhanHaqj Okay. Thanks
you mentioned that the minimum DOPE value is for fifth model sir. But you have selected third model for evaluation. Please let me know about this.
Maybe slip of tongue. I have selected the correct model 3 (B9999003.pdb) having minimum dope score (-35614.78516) for further evaluation
@@FarhanHaqj is it maximum dope value? In your video model 2 show minimum dope value
I am getting this error after running the command alignment.py
read_al_373E> Protein specified in ALIGN_CODES(i) was not found
in the alignment file; ALIGN_CODES( 2) = query
Please can you help me with this
You are loading the wrong protein file
@@FarhanHaqj I am also getting same error. but I followed same protocol as shown in video. please solve this?
@@parmitachawley9850 Is your problem solved sister? i have been facing same kind of problem.
@nazmus yes problem solved. In my queeysequence file I did not changed the name of protein. So it was unable to read it.
@@nazmussakibshuvo4292 yes solved. Change the name of protein in the querysequence file.
It is an amazing video, thanks a lot. Besides, I have a little problem because in the final to evaluate my model, in the first line to the file plot_profiles.py there is a phrase: IMPORT 'PYLAB', but it can not be read or run in the sequence. What is pylab?
Don't use the code "mod10.2 plot_profile.py" instead use only "plot_profile.py". Alternatively, run the python file directly from IDLE as shown in the video. Also Pylab is matplotlib only.
how can i get scripts files too much confusion created
Hello did u find the script files
U can get them at modeller tutorial itself
I have a problem when I open build_profile.log. It doesn't show all this information. What was my mistake?
Your code isn't running properly. And it will take alot of time to generate a complete file. Or you should wait or recheck the code and input files.
@@FarhanHaqj Okay!!! Thanks!! Your videos are amazing and useful.
@@dimascarballotorres7585 Thank you
If we just want to model out query sequence with a single template, do we need to use the program compare.py?
no need to use a modeller if you have a single template and a query sequence.
You can do it with Pymol
watch my PYmol video tutorial
@@FarhanHaqj But my guide has told me to use modeller to model the receptor ADGRG3 with the template PDB ID 7d77.
If I don't use compare.py and go ahead with the alignment program, would that be fine?
Yes
@@FarhanHaqj pls attach the link for this particular tutorial of PYmol
Please help me to solve the problem
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.)
Hi I am getting the same error will you help me out
sir I am getting this error with compare.py:
File "compare.py", line 10, in ?
aln.malign3d()
File "C:\Users\vinay\Modeller10.3\modlib\modeller\alignment.py", line 348, in malign3d
edit_file_ext)
_modeller.ModellerError: fit2xyz_296E> Number of equivalent positions < 3: 2
What can I do sir?
hi vinay, i am facing similar error, were you able to solve it back then? how did you do it ?
Sir can we do modelling in moduller without template?
no
t1A file does it get automatically created?
Yes. The output file is generated by running the code.
I have query.. I tried so many times but always fatal error occurs...can you help about this?
At which step?
How can I know which template is the best?
You can find it in the first part of the video ruclips.net/video/Zb98mmfnsvg/видео.html