The Zhang Lab Message Boards

I was trying to run LOMETS2 locally in my workstation. During the threading 3.1 stage it started running CEthreader. When it executed the command for hhsearch I got the following error message:

Error in /vol1/software/citasser/1.0/contact/DeepMSA/bin/hhsearch: could not open file '/vol1/software/citasser/1.0/lib/CE/pdb.hhm

The problem can be related to the following line in the script file for CEthreader (LM2CEthreader_5l4qA)

$hhsearchdb="$libdir/CE/pdb.hhm";

and the following system command is generating the error message

system("$hhsuite/bin/hhsearch -i initial.hhm -d $hhsearchdb -o hhsearch_initial.out -glob -mapt 0 -z 20000 -Z 30000 -b 20000 -B 30000 -v 0")

However pdb.hhm file is indeed present under the correct library folder (i.e. CE subfolder). I checked the pathname and permission settings of the pdb.hhm as well as the folders that contain this file. Nothing is wrong with that. This can be related to a database naming error. I tried to rename the pdb.hhm as pdb_hhm.ffdata and used

$hhsearchdb="$libdir/CE/pdb";

database argument but it didn't work (giving a similar error message). I will appreciate if you can help me to resolve this problem.

I submitted a job at i-tasser. The predicted 3D models do not have same secondary structure elements as listed under "Predicted Secondary Structure."
I am unable to understand this discrepancy. Can you please help me in this regard. The link of the job is given below.
https://zhanglab.dcmb.med.umich.edu/I-TASSER/output/S609759/

I submitted for I-tasser on 19042021, and I received notification email on 24042021.
but when I accessed web server, there is no result.
So, I may have to waiting or the model finished, but I could not retrieve?
Sincerely

We are moving to a new forum:
https://zhanglab.dcmb.med.umich.edu/forum/
You are welcome to make your posts on the new forum.

This forum is formally closed now!

Thank you for your support!!

--The I-TASSER Team

Hello,

I am also trying to search for ligands on BioLip, but the server is not working. Every time I submit my search I am told that there is an internal server error.

Best Regards,
Andy Garcia

Hello,

Is there anyway to get PDB files for more than just the top 5 complexes reported in the ligand binding sites portion of the I-TASSER output?

Best Regards,
Andy Garcia

Dear Zhang Lab Team,

I was trying to run the standalone version of the IonCom. I believe I have the correct setup including I-TASSER5.1 and the libraries but do not have any troubleshooting skills or that much experience coding.
Upon running IonCom I received:
(base) mascheier@123:~$ IonCom_standalone/run_IonCom.pl
job: P3B
begin new job
PDB2Seq failed

Any ideas where to start resolving the issue?

Hello,

I'm using SPRING to predict the structure of my PPIs, but I find that the outcome pdb file of SPRING only contains C-ahpha of each residue.
Is that result of SPRING by default? Can I get the complete structure containing all the atoms of residues?

Thanks for any information.

How to evaluate whether the predicted protein structure can be used for molecular docking in drug screening?

Dear BioLIP developers,
I recently found that the downloadable file "ligand_2020-09-2.tar.bz2" is erroneous, and its contents cannot be extracted. I would like to ask whether there is a chance for replacing it with a correct one in the near future.

Best wishes,
George

Hi all,
Your service has been really useful for my research, thank you!
I was wondering the images I receive in the email versus when I click the link are designed differently. What is the 'style' I receive in the email and how can I choose this option when I click the link, as this would my preferred way to view the proteins? The attached pictures are the same protein, but the style is different, what style is the 'pink email' structure?
Hope this makes sense, feel free to contact me for any clarification.
Kind regards,
Siobhán

Greetings,

I would like to run Threpp offline to predict structures of a large number of PPI, but the package.zip downloaded from Threpp page seem to be used to recognize PPI rather than predict the structure.

If it is possible for the offline package of Threpp to enter two sequences and return pdb format models, like Threpp online server does?
The service URL: https://zhanglab.ccmb.med.umich.edu/Threpp/

Thanks very much.

Hello there,
I have a question regarding the processing timeline. I have submitted a job on 3/25/2021 with ID: S605053. The protein sequence is 1500 aa. and I included a PDB file and cross-link data as well. When I checked the job status since April 5th, it indicates: Expected time for the result is approximately 10hrs. I would like to know if something went wrong and killed the job or due to a long sequence, it is normal to take that much time.

Thank you very much for your amazing tool; I have been using it for two years now!

Kia

Hi,
I submitted the below 5 jobs over 2 months ago and they are still waiting or have not been submitted. Can you let me know how to get them to run or when the ThreadomEX server will be running again?
T12382391e55
T12383d52b40
T12384d3f88d
T12385ce421c
T12364193444

Kind regards,
Sarah

Hello everyone:

I was trying to upload a sequence to the DeppMSA server, but the following error appeared: Internal Server Error
The server encountered an internal error or misconfiguration and was unable to complete your request.

Do you have any information about it?
Thank you

Hi,
let me start by stating I am not a programmer, so my software/script related troubleshooting skills are limited.
I am currently in the process of establishing the C-I-TASSER suite (v1.0) on a freshly set-up local machine and ironed out a fair amount of errors and deprecated behavior warnings I got returned while running the example sequence that comes with the install files (mostly missing software/package dependencies or related to the requirement of particular versions of such).

I finally got stuck in step 3.1 though (running the 11 threading programs). Here all threading programs seem to complete successfully with an output but the flavors of the CEthreader (CEthreader, mCEthreader, eCEthreader) do not.

The error for each is similar:

Error in /home/ihi/C-I-TASSER-1.0/contact/DeepMSA/bin/hhsearch: could not open file '/home/ihi/ITLIB/CE/pdb.hhm'
Illegal division by zero at /home/ihi/C-I-TASSER-1.0/example/CITCEthreader_example line 418.
Error in /home/ihi/C-I-TASSER-1.0/contact/DeepMSA/bin/hhsearch: could not open file '/home/ihi/ITLIB/CE/pdb.hhm'
Illegal division by zero at /home/ihi/C-I-TASSER-1.0/example/CITmCEthreader_example line 390.
Error in /home/ihi/C-I-TASSER-1.0/contact/DeepMSA/bin/hhsearch: could not open file '/home/ihi/ITLIB/CE/pdb.hhm'
Illegal division by zero at /home/ihi/C-I-TASSER-1.0/example/CITeCEthreader_example line 417.
FORTRAN STOP
only 8 threading programs have output, please check threading programs

The pdb.hhm file is indeed at the right path and I am somewhat at a loss why hhsearch cannot process it. It seems not corrupted and I can easily peak into that monster of a file with e.g. -head. Any idea what might be the issue or what specific information I could provide to get to the bottom of this?

Kind regards,
Robert

Hello,
A week ago , I sent in a sequence to inferred three dimensional structure and which was supposed to run in 64 hours.
It still has not finished, however!
Because now I urgently need this prediction result as the result of my graduation thesis.
I would be very grateful of you could look into the matter as soon as possible.
Best,
Ruan Yanwei

Greetings I having problems with the script ./download_lib.pl, it gives me the following error: System call failed: at ./download_lib.pl line 102., have anyone know how to solve this?

Thanks in advance.

Hello!
What names should directories and files of UniRef90 and Metaclust libraries have? Run-srcipt doesn't see those ones after automatic installation.

Greetings,
I submitted a job about 10 days ago, it was suposed to be conclude in 60 hours... the job number is cS603708 .
Cordially

Hello there,

I used the LOMETS server for prediction of a recombinant protein (180 AA) attached with a 20 AA-long peptide tag, of which the secondary structure is unknown.
The mature protein structure of the 180 AA-protein is published and served as template. The predicted structure was matching quite well my expectations: The mature region was overlapping with the template, as expected, and the attached 20 AA-long protein tag was exposed outwards.

I was wondering, how the prediction was done. I guess the mature region was modelled by protein threading, right? Was the unknown peptide sequence modelled by ab initio folding? And were both prediction combined afterwards?

Which method is usually used for ab initio folding and does it include total energy minimization?

And thank you for the development of the great tools!

Best regards,
Fab

Hello Zhang Lab!
Regarding the ResPRE paper, I have some questions. Hope to get your answer. Thank you very much!
1. What is the meaning of "L/10 L/5 L/2 L" in Table 2? How are they calculated?

Hello,

In January, I sent in a sequence to COACH for analysis which was supposed to run in 24 hours.

It still has not finished, however!

The job ID is CH057847.

Would you please look it over?

Best,
Peter

Hi everyone,
I recently submitted a protein sequence to I-TASSER (233 residues long), and just got the modeling results. Unfortunately, even though I got the usual five models and suggested structural analogs, I did not get any C scores or estimated TM score for my top model. Has this happened to anyone before? I use I-TASSER frequently and have never had this problem before.
Thanks

Dear scholar, hello.
Thank you for answering my questions.

My question is how many features does resnet use during training?
I saw "ResPRE directly uses the precision matrix as input feature" in the paper. But I also saw that at the beginning it said "Potentials at each position pair were then utilized as training features,"
I have some doubts, what features are used in the training process?

Looking forward to your answers, sincerely thank you! !

Few days ago I had submit a sequence, and received a fantastic results. Then I want to continue, the I-TASSER warning that I had submit the same sequence. It may related to the sequence I submitted latter had only one amino acid residue difference from the former. Do you know how to deal with it? I submitted this question for several days, but no one replied. Can you give me a response? Thanks.

Good morning, I'm running a structure in itasser and another in quark but none of these tools has yet returned the results. Itasser said that in 60 hours it would be ready but more than 72 hours have already passed. What can I do to know the status of my jobs?

jobs ID: S572987 AND QA12487

Regards.

Dear Zhang Lab Team：

I meet a problem in 5.1 do clustering that cp: cannot stat ‘./closc*.pdb’: No such file or directory cp: cannot stat ‘./combo*.pdb’: No such file or directory
.It have try download source code of SPICKER (i.e.,spicker.f) http://zhanglab.ccmb.med.umich.edu/SPICKER/ and put the spicker.f at the directory I-TASSERmod. gfortran -static -O3 -ffast-math -lm -o spicker45d spicker.f（there are a 0 Kb file gfortran under directory I-TASSERmod），delete all result and re-run the I-tasser， but it still not create the pdb files, I don‘t know how to fix it.

Your setting for running I-TASSER is:
-pkgdir = /mnt/nfs_storage9/zhangsiyu/local/app/I-TASSER/ITLIB/I-TASSER5.1
-libdir = /mnt/nfs_storage9/zhangsiyu/local/app/I-TASSER/ITLIB/I-TASSER5.1/ITLIB
-java_home = /usr
-seqname = seq.fasta
-datadir = /mnt/nfs_storage9/zhangsiyu/local/app/I-TASSER/data/Heim_UBC+
-outdir = /mnt/nfs_storage9/zhangsiyu/local/app/I-TASSER/data/Heim_UBC+
-runstyle = serial
-homoflag = real
-idcut = 1
-ntemp = 20
-nmodel = 5
-light = true
-hours = 1
-LBS = false
-EC = false
-GO = false

1. make seq.txt and rmsinp
Your protein contains 158 residues:
> seq.fasta
MIVIRLYRDIINKVNKISTDDFLLANEMQLVFDKQLNFEPVRDNLKQWKGYVGTIEDTEI
PIFANVYIQDGFPDVPPFVDITPKVNHPNVDEDGTLSMRLLAEWEPRYHIYQVMIDIKQL
FINVPAKTYKTKIKKPKEEQRYTGLPRATIPVRTLTQV
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
2.4.2 running pair ................
FORTRAN STOP
30000 6379375 total lib str & residues
number of observations 18.78456 1406813.
pair done
3.1 do threading
start serial threading PPAS
/tmp/zhangsiyu/ITseq.fasta
/mnt/nfs_storage9/zhangsiyu/local/app/I-TASSER/data/Heim_UBC+/PPAS_seq.fasta
hostname: ubuntu-32
starting time: Wed Oct 7 18:24:46 HKT 2020
pwd: /tmp/zhangsiyu/ITseq.fasta

Dear Zhang Lab Team,

I submitted my protein structure onto the COACH server for ligand binding site prediction on September 30, 2020. The job id assigned to this submission is CH056273. I checked in the queue list and saw that the job was expected to be finished in about 15 hours. However, a week has been passed without any result yet. Can you please help me to check the reason of this delay? Any help from you for making the job to be finished is very much appreciated.

Regards,

Minh Nguyen

Hi there,

I have a short question: Can I input a template structure with a modified LYS residue such as LYR (LYS+RET) to both the server and the 5.1 suite versions of I-TASSER ? will it then be also teated correctly as the modified residue during the geometry determination?

I'm asking because a paper by Nikolaev et al. 2018 (https://pubs.acs.org/doi/10.1021/acsomega.8b00721) seems to claim that, at least at the time it was published, this resulted in problem for the residue orientations around the LYR region when they used your software.
I was wondering if this has been addressed ever since.

FYI: An example of a PDB with LYR: https://www.rcsb.org/structure/6EID

Thanks in advance !