The Zhang Lab Message Boards

Back in May I submitted a TACOS run but never got a result back. Run ID: TACOS95A-TACOS95B

Today, I submitted a SPRING run and several hours later returned the following error.

An error has occured for target S0984A-S0984B
SPRING job has failed

Please report to zhanglabs web forum.
For Developer:When error resolved delete user email addresss file and rerun it

Any help in resolving these issues would be appreciated.

Noitat Paxe

The X-ray structures of a protein has two chains (A, B) which forms after a proteolytic cleavage step of a single chain. i want to model proteins which have a single continuous sequence. However, I want to input the FASTA sequence as two separate chains A and B. How do I input the sequence?
Inputting a continuous single chain gives incorrect active-site due to conformational change after cleavage.

When getting the I-TASSER results, is there a way to search a specific residue in the protein structure?

Is it possible for a 30 sequence long amino acid sequence in a protein to have a coil structure without alpha or beta sheets as predicted by ITASSAR.Should I have to further validate structure given by ITASASAR?

When submitted the whole protein structure sequence two missing loops are modelled as loops(two coils). But when loops are provided alone they have alpha helix and beta sheet structures. Why is that?

Dear colleagues,

I recently submitted a protein sequence to I-TASSER for modeling. This protein comes from two crystal structures: its N-terminal part is a global protein, and its C-terminal is a helix. I wish to input the pdb IDs of both crystal structures into I-TASSER's "Specify template without alignment" option, but this option seems to accept only one pdb ID, so I input the pdb ID of the helical protein as the template. Strangely, in all models generated by I-TASSER, the helical part is not a helix, but a loop. I wonder whether I missed something during my operation?

Thank you in advance.

Hi,

I have been using I-TASSER tool and I think it’s great, well done.
I was wondering though, what each color means and I couldn’t find this information in any publication. For example, in the attached model, what does each color mean? Same question for the thick and thin parts of the structure, what do they represent?

This is the protein of interest: https://www.rcsb.org/structure/6h7d

Any help would be highly appreciated

Best regards

Dear all,

Could you tell me how to delete the jobs I submitted to the I-TASSER server?

Thank you.

I'm working with a protein that has two functions: 1) an annotated function confirmed by AA sequence and a crystal structure, etc.; and, 2) a putative moonlighting function that is completely different from the annotated function.

When I use iTasser, obviously all of the best hits are related to the annotated function based on the previously solved CS.

Is there a method to make iTasser omit all structures related to the annotated function so it allows me to explore candidate models for the moonlighting function?

Just as an example, imagine my annotated function is "DNA ligase" and I'm trying to explore the possibility that this protein can also behave as a "transpeptidase" under certain circumstances. Can I set the parameters so none of the hits have anything to do w/ DNA ligase? Can I also add a keyword such as "transpeptidase" for the hits?

thanks

Hello,

I am working on a protein, the crystal structure of which was resolved. In the sequence, there is a 9-residue loop at the C termini. However, the structure of the loop is not resolved. (In PDB file, these residues are missing.) Thus, I would like to run de novo loop modeling to create the loop. The problem is the loop is an outage loop, only one side of the loop is constrained. Is it possible to use rosetta to make the loop? Could you please share with me a similar tutorial or course specific for this kind of loop? Thank you.

Best regards,

Hi

I submitted the sequence at the I-TASSER On-line Server and the ID for my job S486621. I didn't receive the result yet . This seems unusually slow compared to my previous submissions , I was wondering whether something had gone wrong with my submission .and I tried multiple time this week with different sequence but it is not working. can you help me please.

Thank you!

Hi!

I am trying to run the standalone I-TASSER suite in a HPC cluster. Java is installed (OpenJDK Runtime Environment (build 1.8.0_161-b14)) and supposed to be located in /usr/bin/java (at least that is what I got from "which java" command). However, when I run I-TASSER, I constantly receive this error:

Error: /usr/bin/java does not exist.
Please check if -java_home was correct

Moreover, in the error log I have:
which: no java in (/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/ibutils/bin:/home/myuser/.local/bin:/home/myuser/bin).

What I am doing wrong? I know Java is there... Is there something I can do for fixing it?

Thank you very much in advance for your help. Have a nice day!

Thread for questions about acceptable input file format for BindProfX.

Hello, I recently ran Job Q4933 and it executed successfully. I tried to to use the same ligand on another receptor and I consistently get Job was finished with error.
An error found in the submitted ligand strucutre.
Please check if the ligand has correct file format and chemical structure.

I then ran as a control the same input that I used for Job Q4933. The new Job Q4957 unfortunately finished with the same error namely Job was finished with error.
An error found in the submitted ligand strucutre.
Please check if the ligand has correct file format and chemical structure.

I have checked the ligand geometry in PyMol 2.2.3 and its chemical composition with ChemDraw 16.0. The .sdf file (PDB file appended) is interpreted correctly by both PyMol and ChemDraw.

I would appreciate any assistance on how to solve this problem.

Hello,

My name is Joseph. I downloaded the Linux version of BindProfX onto my computer (CentOS 6.0). In the "bin" directory, I made a directory called "test", saved 1A22.pdb as "complex.pdb", and placed "complex.pdb" and "mutList.txt" into the "test" directory. Per the readme file, I ran the following commands:

./get_final_score.py test

./get_final_score.py /get_final_score.py /home/hayek27/Downloads/bin/test

and get the following output:

Traceback (most recent call last):
File "./get_final_score.py", line 38, in
from module.pdb2fasta import pdb2seq # convert pdb to fasta
File "/home/hayek27/Downloads/bin/module/pdb2fasta.py", line 26, in
from fixMSE import code_with_modified_residues
File "/home/hayek27/Downloads/bin/module/fixMSE.py", line 59
'ALA', 'VAL', 'PHE', 'PRO', 'MET', 'ILE', 'LEU', 'ASP', 'GLU', 'LYS',

Any help you can offer would be most appreciated.

Best,
Joe

There are some errors when I submit the task of QUARK. I don't get the e-mail as the information mentioned, which causes my unavailability for the result . Please help me about where I can get my result of QUARK, thank you very much!

I would like I-TASSER to predict protein structure. However, it's a protein working in chloroplast. There should be a signal peptide in the N-terminal of the protein. Do I need to cut the signal peptide off before I use I-TASSER to predict the protein structure? Thanks in advance!

Hello, since am new and just started using I-Tasser.

Quick question about the possibility to run multiple protein sequences on i-Tasser online? or are there any software related can possibly does this?

Thanks in advance.

Hi,

Could you please provide information related to deposition of homology modeled protein structure in any of the databases.
I have generated two protein structures using I-Tasser and wish to deposit it in any of the database.

Thanks,
Prashantha

Hello

I recently sent several jobs to SAXSTER (job codes: S1046 and S1047). For S1046 the top model is in good agreement with the crystal structure of the protein and the shape and P(r) profile of the experimental data.

For S1047, all the models show smaller Dmax compared to the experimental (Dmax ~265). Model #9 show the right shape but again the Dmax is too small. Is it possible to generate models with the right Dmax?

Thanks in advance
Ruth

I have taken 3456 proteins (used for 'Deepcon covariance') and tried the implementation of ResPRE on my CNN model of architecture depth = 32.

I got an accuracy of 74.7 for covariance calculations, also similar 74.6 for precision calculations. I am not sure why I am not able to get better prediction(as per the claim of the ResPRE paper).

I used the default option for weight calculation while using the 'calNF_ly'.
a. Is there a specific normalization value that gives high prediction?

b. ResPRE specifically mentions that precision values were higher than covariance values when tested on DNCON2 protein dataset. Can you throw more insight in to this?

Hi,
Has the I-Tasser suite been updated with LOMETS2? If not when can we expect the update?
Is LOMETS2 available for download?

Thanks

I uploaded an amino acid sequence, but the predicted secondary structure amide bond is formed by dehydration condensation of the ahpla-amino group with the carboxyl group. Is there any way to build a model of peptide fragments linked by isopeptide bonds?
Thanks

Hi,
I like the results that you provide. I got a question. Is it possible to download the image (3D) and paste it in ppt? Is it possible to spin the image?

Thank you

The predicted structure model 1 (attached) has a strange line going across... which doesn't look like a protein structure to me. Could you help advise what might have caused it please, and if it's an artifact how might we get around it?

Job ID: S477807

Thanks so much and best regards,
Koi

Hi,

I haven't fully understood on what basis the models predicted by I-TASSER is categorised on.

The confidence is measured by the C-Score as stated, so I had a query in one of the sequences I'd sent to I-TASSER for prediction. In the image attached, the C-Score for Model1 is -1.76 whereas the C-Score for Model2 in 1.72. As the Model2 has a higher C-Score, do I need to choose Model2 as the best-predicted model by I-TASSER? Even the C-Score values differ by a very small number, there is consdierable difference in the structure between both the models.

Could someone help me out on this?

Thank you for your time!
Ahish M Sujay

Hi guys I'm trying to use QUARK fragment library for use as decoys in MR with AMPLE in ccp4-online.
The result zipper folder however only contains the 5 final models.
Any idea where I can find the decoys?
Thank you very much.

best,
Shengyang

Dear Administrator,

I've currently got a problem with the pair3.dat file and Illegal division by zero. I've attached my STDOUT output from running I-TASSER (v5.1) belwo. I've also attached a .tar.gz file containing the temporary files generated by I-TASSER. Would you please let me know what I could do to fix this problem please? Thank you in advance.

Your setting for running I-TASSER is:
-pkgdir = /home/z3371724/Tara/I-TASSER/I-TASSER5.1
-libdir = /srv/scratch/z3371724/I-TASSER
-java_home = /apps/java/8u45/
-seqname = example2
-datadir = /home/z3371724/Tara/I-TASSER/I-TASSER5.1/example2
-outdir = /home/z3371724/Tara/I-TASSER/I-TASSER5.1/example2
-runstyle = gnuparallel
-homoflag = real
-idcut = 1
-ntemp = 20
-nmodel = 5
-light = false
-hours = 50
-LBS = false
-EC = false
-GO = false

1. make seq.txt and rmsinp
Your protein contains 143 residues:
> example2
MYQLEKEPIVGAETFYVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLA
LQDSGLEVNIVTDSQYALGIITQWIHNWKKRGWPVKNVDLVNQIIEQLIKKEKVYLAWVP
AHKGIGGNEQVDKLVSAGIRKVL
2.1 run Psi-blast
2.2 Predict secondary structure with PSSpred...
2.3 Predict solvent accessibility...
2.4 run pairmod
2.4.1 Use all templates
submit threading jobs first and run pair during threading
3.1 do threading
start gnuparallel threading PPAS
start gnuparallel threading dPPAS
start gnuparallel threading dPPAS2
start gnuparallel threading Env-PPAS
start gnuparallel threading MUSTER
start gnuparallel threading wPPAS
start gnuparallel threading wdPPAS
start gnuparallel threading wMUSTER
Illegal division by zero at /home/z3371724/Tara/I-TASSER/I-TASSER5.1/example2/PPAS_example2 line 354.
Illegal division by zero at /home/z3371724/Tara/I-TASSER/I-TASSER5.1/example2/dPPAS_example2 line 356.
Illegal division by zero at /home/z3371724/Tara/I-TASSER/I-TASSER5.1/example2/dPPAS2_example2 line 355.

Hello Dear,

How are you?. I hope you are doing well.
I have a question please, I am trying to compare between 2 pdp file, One I got from protein data bank websit and the other one from I-taaser software both of them for the same protein. But I do not know why I got more number of atom from I-TASSER one . I tried to remove all water atoms but the number still different. I am attaching some of them to have a look.
Thank you very much in advance for your time and your help.
Your feedback is highly appreciate it.

Best regards,
Shada

Hi,
Do you have an online service that can introduce a sulfur atom to a cysteine residue of a protein and analyze the structural changes induced by the addition of that atom?