The Zhang Lab Message Boards

Hi, I'm interesed in NeBcon.
I followed the readme.txt in NeBcon but encountered some problems. The download links in the script download_db.sh are not available and some problems occur as I use nebcon.pl. The problems are as follow:

copy and install SPcon at local .........
tar: data/ur90/uniref90.03.phr: Wrote only 1536 of 10240 bytes
tar: data/ur90/uniref90.03.psi: Cannot open: No space left on device
tar: data/ur90/uniref90.05.psd: Cannot open: No space left on device
tar: data/ur90/uniref90.02.psd: Cannot open: No space left on device

Are these errors result from the missing databases in download_db.sh ?
Thanks.

Hi Everyone,
What are the probable options for prediction 3D structure, if homology modeling is inadequate in prediction protein 3D structur? and What is the accuracy rate of the chosen method compare to homology modeling?

Hello,

When I get to 4.1 I get this error:

4.1 run simulation
run 14 serial simulations
run simulation job 1 / 14
Error: bzip2: Can't open input file rep*.tra: No such file or directory.
.
.
.
run simulation job 14 / 14
Error: bzip2: Can't open input file rep*.tra: No such file or directory.
5.1 do clustering
No. of trajectory files:0
cp: cannot stat 'model*.pdb': No such file or directory
cp: cannot stat 'cscore': No such file or directory
cp: cannot stat 'lscore.txt': No such file or directory
cp: cannot stat 'rst.dat': No such file or directory
cp: cannot stat 'rep*tra*.*': No such file or directory

What can I do to try and fix?
Thanks

Hi,
most probably because of /tmp being used as the top level temporary directory in the I-TASSER suite, I am getting "No space left on device" messages. This might also be the probable reason for COACH to fail. Is the only way to change this directory from /tmp to /scratch is manually changing the "/tmp" to "/scratch" in all the perl scripts ? Or is there a keyword/option that can be used to designate /scratch as the top level temporary directory. It seems that the former approach is the only one possible at the moment since only runLOMETS.pl has a -tmptop (top temporary directory) option.
Thanks,
ambarishnag.

Hi,
after installing I-TASSER, I ran `download_lib.pl -P true -B true -N true` successfully.

When I run `ls` in the ITLIB directory, I get the following directories:
Bfactor BPOCKET CNT DEP dotProfiles Enzyme GO ligand map MTX nr PDB PSSM receptor SIG stride summary

Next, I run runI-TASSER.pl with -LBS true -EC true -GO false options.

However, COACH fails to work and I am copying the final lines from my out_COACH_model1 file.
There is a line that says "There is something wrong in between the query PDB file and sequence file. -1000 != 0", what does this mean ? I am not providing any pdb file as input and the only input I am providing is a file called seq.fasta.
What am I missing and how do I fix these issues ?
Your help will be greatly appreciated.
Thanks,
ambarishnag.

Following are lines from out_COACH_model1:

run JSD...

=============== COFACTOR starts ================
run CF_sequence1_model1...
Hostname: xxxxxx
Started : Mon Jan 27 00:31:55 MST 2020

Path : /tmp/anag/CH_sequence1_model1

loading libraries...
All the library files were read. Starting COFACTOR predictions at 0.001
There is something wrong in between the query PDB file and sequence file. -1000 != 0
ending time: Mon Jan 27 00:31:57 MST 2020

=============== COFACTOR ends ==================

=============== TM-SITE starts ================
run TM_sequence1_model1...
Hostname: xxxxxx
Started : Mon Jan 27 00:31:59 MST 2020

Path : /tmp/anag/CH_sequence1_model1

run JSD...
JSD_coach.dat missed

=============== TM-SITE ends ===================

=============== S-SITE starts ================
run SS_sequence1.pl locally
Hostname: xxxxxx
Started : Mon Jan 27 00:31:59 MST 2020

Path : /tmp/anag/CH_sequence1_model1

run JSD...
JSD_coach.dat missed

=============== S-SITE ends ==================
COFACTOR LBS prediction fails
TM-SITE fails
S-SITE fails
COACH exit, pleach check
COACH done

protein of my interest have 390 amino acid. It shows only 22 % similarity to nearest pdb structure. but ab initio allows modelling of 200 residues. Suggest me a solution to model this protein

Hi, I am currently comparing the similarity of protein contact map. I'm interested in CEthreader.
Now, I have serveral protein sequences ( in fasta format). I have read the introduction of CEthreader but I am not certain how I can get the results I need. Can anyone tell me the main steps? The result I need is the similarities between any pairs of the input fasta.

Thank you very much!

Is that serious?

Attaching full output:

Your setting for running I-TASSER is:
-pkgdir = /opt/itasser
-libdir = /db/ITLIB
-java_home = /usr
-seqname = cterm
-datadir = /home/user/Projekty/pa2504/cterm
-outdir = /home/user/Projekty/pa2504/cterm
-runstyle = serial
-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 95 residues:
> cterm
YARRCFVTRRVIDEGKAVGYLYREAPEEENDSGWRLMAGDESDDYMNTAGTTAYVSLGSV
LNADDSILPLLDAPPGRAFERLADGSFIEVQGPEG
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 ................
30000 6379375 total lib str & residues
number of observations 16.97411 459573.9
pair done
3.1 do threading
start serial threading PPAS
/tmp/user/ITcterm
/home/user/Projekty/pa2504/cterm/PPAS_cterm
hostname: lelezor
starting time: pon, 20 sty 2020, 15:51:50 CET
pwd: /tmp/user/ITcterm
running zalign .....
ending time: pon, 20 sty 2020, 15:54:24 CET

start serial threading dPPAS
/tmp/user/ITcterm
/home/user/Projekty/pa2504/cterm/dPPAS_cterm
hostname: lelezor
starting time: pon, 20 sty 2020, 15:54:25 CET
pwd: /tmp/user/ITcterm
running zalign .....
ending time: pon, 20 sty 2020, 15:59:26 CET

start serial threading dPPAS2
/tmp/user/ITcterm
/home/user/Projekty/pa2504/cterm/dPPAS2_cterm
(END)At line 447 of file ppa1.f
Fortran runtime error: Bad real number in item 4 of list input

What are the last two columns in the seq.dat file from I-TASSER output and what do they signify ?

Hi All,

I installed the iTasser onto my linux box and am running my first simulation.

I have gotten two different errors so far...

At line 447 of file ppal.f
Fortran runtime error: Bad real number in item 4 of list input

and

At line 1074 of file zal33.f
Fortran runtime error: Bad real number in item 4 of list input

Are these common?

Thanks!

Chad

Hello

How long QUARK server spend to finish de novo modeling for a 200 aminoacid protein?

Thanks

To whom it may concern,
I have a question regarding the ranking system of the model structures for a given I-TASSER output folder.
Five model structures are obtained per run and both in the result web page and in the downloaded "cscore.txt" file, the model structures are ranked inaccordingly with the C-score. For example, the structure with the highest C-score may rank below a structure with lower C-score.
I would like to know if this ranking has a meanning, or if I should base my further work on the model structure with the highest C-score, regardless of its ranking.
I attached a screenshot of the "cscore.txt" file in which the model structures are ranked, along with their C-scores etc. In the text, I highlighted the sentence that confused me a bit.

Thank you in advance for your help,

Best regards,
Mehmet Erguven.

I used online server I-TASSER-MR to solve the structure of my protein on 30th Dec. 2019, and now it is still job waiting. Is it running? Could you please help me sort out what is happening?

I do not find my job ID. Here is the link to my job: https://zhanglab.ccmb.med.umich.edu/I-TASSER-MR/output/T1093xBqh3/index....

Thank you for your assistance.

Hello,

is there a standalone CLI version of STRUM? Preferably even a conda package or a docker container for it?
I would like to use it for a nf-core (nf-co.re/) nextflow pipeline and therefore need a packaged build (for many reasons, one of which is reproducibility).

Thank you very much!
Best

Greetings,
I submitted the jobs PD103357 and PD103358 several weeks ago and they have not finished yet. Is there any problem with the server?

Sincerely,

Greetings, I submitted the jobs PD103357 and PD103358 several weeks ago and they have not finished yet. Is there any problem with the server?

Sincerely,

Merry Christmas！
I run ResPRE service on the ZhangLab website. Here are the results returned. But I don't understand what is the meaning of d1, d2?
Thank you！
PFRMAT RR
TARGET
AUTHOR ResPRE
REMARK The full prediction can be viewed at https://zhanglab.ccmb.med.umich.edu/ResPRE/output/RPC136
METHOD contact prediction by deep residual neural networks
MODEL 1
EDPEVLFKNKGCVACHAIDTKMVGPAYKDVAAKFAGQAGAEAELAQRIKN
GSQGVWGPIPMPPNAVSDDEAQTLAKWVLSQK
i j d1 d2 p
3 74 0 8 0.9964910000
3 77 0 8 0.9961920000
6 74 0 8 0.9949530000
44 75 0 8 0.9915450000
3 73 0 8 0.9878440000
.....

Dear The Zhang Lab:
Hello！I encountered a problem while running the program of ResPRE.Just like the error message in the attached picture.
RuntimeError: unexpected EOF, expected 95827 more bytes. The file might be corrupted.
Is the model wrong? How do I get down to the right model?My pytorch version is 1.3.0. It is higher than 0.3.0 used in the paper, so I slightly modified the code to read the model.

Dear all,

I sent two jobs to the EvoDesign server some weeks ago and when I come back to the job page it says it is still running. What might be the cause of that? Could you please help me sort out what is happening?

The id's are PD103342 and PD103339

Thank you very much for your attention!

Good day

I have submitted protein and ligand for docking in bsp-slim. I got the ligand sdf file from pubchem. However all my results always comes back with error message of the ligand is not correct structure. Please advise. I attach the ligand file I used recently.

Message I get back reads as follows:

Job Status
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.

Below is the ligand structure I got from Pubchem:

4091
-OEChem-12021915113D

20 19 0 0 0 0 0 0 0999 V2000
-1.5155 -0.3600 -0.0790 N 0 0 0 0 0 0 0 0 0 0 0 0
0.7170 0.2154 -0.8185 N 0 0 0 0 0 0 0 0 0 0 0 0
-0.6602 1.8744 -0.1620 N 0 0 0 0 0 0 0 0 0 0 0 0
2.9005 -0.4475 -0.3361 N 0 0 0 0 0 0 0 0 0 0 0 0
1.5201 -0.0296 1.4348 N 0 0 0 0 0 0 0 0 0 0 0 0
-1.2978 -1.7839 -0.3082 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.7800 0.0051 0.5511 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.5260 0.5926 -0.3455 C 0 0 0 0 0 0 0 0 0 0 0 0
1.6419 -0.0664 0.0634 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.6868 -1.9541 -1.2008 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.2427 -2.3145 -0.4674 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.7919 -2.2289 0.5541 H 0 0 0 0 0 0 0 0 0 0 0 0
-3.4061 -0.8696 0.7568 H 0 0 0 0 0 0 0 0 0 0 0 0
-3.3495 0.6744 -0.1018 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.5980 0.5078 1.5067 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.5953 2.0901 0.1923 H 0 0 0 0 0 0 0 0 0 0 0 0
3.6259 -0.6688 0.3371 H 0 0 0 0 0 0 0 0 0 0 0 0
3.1387 -0.5194 -1.3192 H 0 0 0 0 0 0 0 0 0 0 0 0
0.6520 0.2314 1.8892 H 0 0 0 0 0 0 0 0 0 0 0 0

I am currently working on GPCR homology modeling and I'm new to it.I use ModRefiner for minimization on the structure,but I do not have a reference structure.So,I want to ask:1.What is reference structure?Does it refer to my model sequence in fasta or a second structure? 2.Can I still use ModRefiner for minimization on the structure without a reference structure.If the answer is YES,will it affect my outcome?
Look forward to your helpful reply.Thank you.

I calculated a sequence of MSA files using the HHblits tool described in the ResPRE paper. The sequence name is d102ma_.
My problem is that the MSA file I get is different from the one in the example （T0759-D1.aln）provided.
What can I do to make my MSA file the same as that provided in the paper（T0759-D1.aln）?

The T0759-D1.aln file the paper provided is like this：
VVIHPDPGRELSPEEAHRAGLIDWNMFVKLRSQE
VVIHPDTGRELSPEEAHRVGLIDWNMFVKLRSQE
VVIHPDTGRELSPEEAHRAGLIDWNMFVKLRSQE
VVIDPDTGRELSPEEAHRAGLIDWKMFVKLRSQE
S----------STPTRHGAGLIDRAMFDRLRGQE
...............

The MSA result d102ma_.hhr obtained by using d102ma_ via hhblits is like this：
Query d102ma_ a.1.1.2 (A:) Myoglobin {Sperm whale (Physeter catodon) [TaxId: 9755]}
Match_columns 154
No_of_seqs 752 out of 845
Neff 7.12999
Searched_HMMs 1849
Date Mon Nov 25 00:54:27 2019
Command hhblits -i ./seq/d102ma_.fa -d ../src/uniclust30/uniclust30_2018_08
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 sp|P10060|HBB1_SPHPU Hemoglobi 100.0 6.1E-54 2.3E-59 318.3 0.0 145 2-148 2-146 (146)
2 tr|A0A1K0GUW6|A0A1K0GUW6_PONAB 100.0 7.7E-54 2.6E-59 324.1 0.0 145 2-148 48-192 (192)
3 sp|P81024|HBAD_MELGA Hemoglobi 100.0 7.1E-52 2.9E-57 308.9 0.0 140 2-148 1-141 (141)
4 tr|L8HU81|L8HU81_9CETA Unchara 100.0 1.9E-50 6.2E-56 293.3 0.0 145 2-148 3-151 (151)
5 tr|H3B4U9|H3B4U9_LATCH Cytoglo 100.0 1.1E-48 4.1E-54 296.8 0.0 153 1-153 17-172 (179)
6 tr|A0A1I7Q446|A0A1I7Q446_CHICK 100.0 3.2E-48 1.1E-53 284.0 0.0 137 1-148 7-143 (143)
7 tr|A0A146ZNV6|A0A146ZNV6_FUNHE 100.0 4.7E-47 1.6E-52 285.6 0.0 143 1-148 47-189 (189)
8 tr|H3A6U9|H3A6U9_LATCH Unchara 100.0 2.1E-46 7E-52 297.7 0.0 145 2-148 149-304 (304)
...............

Thank you！

Hello,

My run S505561 has not completed with the submission date being 2019-11-19.

Thanks

I am Rafat Ali PhD scholar at Jamia Millia Islamia University. I have a protein sequence of 2074 aa long but there is a limit in I-Tasser of 1500 aa sequence length. So, I want to ask you how can I go for the model this protein structure of 2074 aa sequence.

I am doing structural modelling of some sequences using I-TASSER suite but its taking more than two days. I want to finish ii early, can anyone suggest me how to set the time for short period of time that I can set.

I intend to analyze a large number of proteins, how can I prepare the file to put on i-TASSER? In this case, I should copy the FASTA from each protein but how can I save (in what format) in case what type of document should I save to add the data to i-TASSER?

Greetings. I would like to know the procedure and equations used to calculate the average accuracy of the top L/5 long-range contact predictions of the different methods described on the NeBcon research, as I am currently trying to reproduce these results, but so far I only got prediction accuracies for each protein I have as input.

There is an executable file under 'bin' path named calNf_ly.
I have added this file to the environment variable and given the highest permissions.
But I still can't run the command.
Error message show: 'calNf_ly' is not an internal or external command, nor is it a runnable program or batch file.
My operating system is windows10. Is this file not working in windows environment?
How can I run this file?

Thank you！
--Terence

Hello,

My run S504154 has not completed with the submission date being 2019-11-08.

Thanks

Hi there, is there any estimation of how long CEThreader to finish a job?
I've sent 2 proteins sequences 10 days ago and no results yet, thanks!
Pablo