The Zhang Lab Message Boards

hi all
many thanks for your helpful work and structure prediction.

I m contact you because when l download the PDB of model1 and open it with chimera, but there are some differences; for example the strands predicted (and as l expected ) should be 11, in the small generated 3d model are 11 but in the pdb only 9.

do you think is a chimera problem or something related to the pdb file?

thanks again
federica

Hi everyone

I modeled my protein on I TASSER and then tried to refine it on the modrefiner right on the desktop (the web version is unavailable). However, I get the following message: "PDB file can not be opened" (in this case, the protein I just modeled). Has anyone had a similar problem, and if so, any suggestions on how to resolve it? Both structures (the model and the template) are in PDB format. The command line I used was the same as indicated in the program's documentation. (./mcrefinement data_dir bin_dir ini_name ref_name ran_num)

Best regards

I am having an error as seen below. Would very much appreciate any assistance in finding the bug. Obviously it is somewhere in my seq.fasta or input PDB. The zip of the directory is attached.

4.1 run simulation
init.dat is wrong!!!!! 1 - 4gzkA ne HIS MUSTER
init.dat is wrong!!!!! 1 - 4gzkA ne LEU MUSTER
You have 2 errors in your input files. Please fix these problems before you run TASSER

There are problems with your input files
Please check before simulation

The command run was:

runI-TASSER.pl -libdir /n/shared_db/I-TASSERLib -seqname seq.fasta -restraint4 protein.pdb -nmodel 2 -datadir .

The seq.fasta is:

MREIVHLQAGQCGNQIGAKFWEVISDEHGIDPTGTYHGDSDLQLERINVYYNEATGGKYVPRAVLVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKEAESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVVEPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCLRFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDAKNMMAACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRGLKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVSEYQQYQDATAEEEGEFEEEAEEEVA

After reviewing the form, I saw a prior issue was related to 'invidible characters'. So I ran this python line to print out all the characters:

python -c 'print list(open("seq.fasta").read())'

hi,
I had submitted two protein sequences for the structure prediction. But I am unable to see that predicted pictures, as they contain no image file opening that model file. All the PDB files are opening except this predicted structure ones which are GIF files.

Hi,
I want to predict the homology of 6vsb.pdb which is about spike protein in covid 19. because the original pdb file has some missing pieces. I have the problem to use I-Tasser to predict this protein. this protein has 3 chains in unique sequence. all 3 chains in this multi chains protein have the same sequence. I do not know what should I do to receive completed homology structure which contains all chain in one pdb file.
I submitted only one sequence with the 6vsb.pdb template. I do not know if I receive all chains or only one chain.
Could you please help me with this? I saw the complex homology for spike protein in your site. but 6vsb.pdb is different with this.
can I predict each chain separately and then assemble them for getting the structure containing all chains?

Please help me with this, I really need your help as soon as possible.

I attach the original pdb file which have some missing pieces and its sequence.

Many thanks

Mohammad

I was able to get the standalone pipeline working with the example dataset as far as Step 7, but it fails looking for some files that were not a part of the downloads. The files include 4ly7A.pdb, 4zcnB.pdb, 3bb9B.mtx among a few others with different extensions but the same prefix.

The pipeline creates over 100 files up to this point, but fails at the end in that 7th step. It's very similar to the error noted here https://zhanglab.ccmb.med.umich.edu/bbs/?q=node/4486 but I see there was no resolution to that error and I got a bit disheartened.

We tested the data produced versus data we submitted online and it varied enough that we are hoping the differences will be due to Step 7 not completing.

I'm running this on CentOS 7 with gnuparallel, the system has 88 threads and 384GB of RAM.

Any help would be appreciated, thanks in advance!

The following total binding energy values were generated for a protein complex using EvoEF2 BuildMutant and then ComputeBinding. One mutation was applied for each run. These are partial list of all different combinations, such as L351A, L351D, etc.

L351L -52.27
G352G -52.27
K353K -55.31
G354G -52.27
D355D -52.15
F356F -52.15
R357R -51.66

My question is why some of the values are different than others while these mutations make no change to the protein?

I appreciate very much the modesl you provided for a 64 aac caseinmacropeptide.
I am a new user of quark, not working in protein modeling. I would like to know the following:

1- what criteria I have to use in order to select between the five models you provided.

2- What is the probability of the model on describing the real structure.

3- The caseimacropeptide is the 64 C-terminal part of K-casein. Can I match the model with this K-casein derived peptide?

4- Also I would like to know the location of N-terminal aac.

5- Is it possible to show all aacs location ?.

Thank you very much

I submitted job T1187kwDV8 yesterday around noon (Eastern time). It's been 24h and status keeps showing: job-waiting. please, advise.

Is the MR server currently accepting job submissions?

Jorge

Dear I-TASSER developers，
I am using the standalone I-TASSER5.1 to do modeling of some proteins. However, an error occurred during the running of example protein. A threading program 'Env-PPAS' seems not to work as expected. The error log file 'err_Env-PPAS_example' reported that 'At line 697 of file zal3.f\nFortran runtime error: No such file or directory\n'. The following is what I used as the parameters:

Your setting for running I-TASSER is:

-pkgdir = /path/to/itasser/I-TASSER/I-TASSER5.1
-libdir = /path/to/itasser/I-TASSER/I-TASSER5.1/ITLIB
-java_home = /path/to/java/jdk1.8.0_181
-seqname = example
-datadir = /path/to/itasser/I-TASSER/I-TASSER5.1/example
-outdir = /path/to/itasser/I-TASSER/I-TASSER5.1/example
-runstyle = parallel
-homoflag = real
-idcut = 1
-ntemp = 20
-nmodel = 5
-light = false
-hours = 50
-LBS = false
-EC = false
-GO = false


Additionally, I checked the template script 'Env-PPASmod' under the directory of I-TASSERmod. It seems that no parameters are explicitly specified for zal3 program, so we don't know exactly what files are missing for running this program.

Looking forward to hearing from you. Thank you a lot!

Regards,

Hi,
I had a minor problem in downloading the Models results of I-TASSER, I was curious about the difference between the downloaded PDB structure and the resulting page structure. Could you please figure out my problem?
Thanks.

Dear Zhang lab team,
I am using CI TASSER for the first time. I submitted my job the previous week and got the link https://zhanglab.ccmb.med.umich.edu/C-I-TASSER/output/CIT508 to check status. But the status still remains the same 'the sequence has been submitted and in processing'.
I wanted to know whether I have submitted the job correctly and when can I expect a result or how can I retrieve the results.

K Sindhu

The tarball is empty when uncompressed.

Dear I-TASSER developers,
Thanks much for the great software. We are trying to run I-TASSER5.1 on HPC cluster using slurm. We encounter a few issues:
1 We want to use shared public readable folder for the library. Because the folder is not writable by regular users, the software got permission error, like: cp: cannot stat ‘/shared_database/I-TASSERLib/PDB/list’: Permission denied
2 We have 32 CPUs on each computer on our cluster, but the software is only using one CPU. Is it possible to add an option to let user decide the number of CPU to use?
3 The sync command does not work well with our file system. If you can make sync optional, for example add an option in the command to disable it, it would be great. For now we created a script called sycn and put in the same folder as the software, so that the original sync command is overridden:
echo sleep 2 > I-TASSER5.1/sync; chmod +x I-TASSER5.1/sync

Please suggest.
Best,
ldong

Dear I-TASSERS developers and users,
we are using I-TASSER for the modelling of a difficult membrane protein for which we have found some indication about the secondary structure in the literature.
We tried a first modelling using I-TASSER and we found that the secondary structure prediction done by the server is not in complete agreement with the experimental results found in literature.
We then tried to specify the secondary structure by using the "Specify secondary structure for specific residues." option, but the results are very similar to the previous run.
Are we doing something wrong?

Thanks in advance for you help.

Hi,

I can only see the C-score of model 1 and not of model 2-5 for https://zhanglab.ccmb.med.umich.edu/I-TASSER/output/S531294/
Please help.

Kind regards.

Dear all,

I submitted a sequence of my desired protein via I-TASSER. My protein is a homodimer protein but the pdb file that is generated has just one chain. Is there any way to make a homodimer pdb file with the current file or I should submit a sequence including both chains to I-TASSER?
Best,
Hossein

I am receiving index out of bounds errors and a divide by zero error when running runI-TASSER.pl. Here is the command line and console output:

===============================================
time /media/sf_D_DRIVE/home/bill/I-TASSER5.1/I-TASSERmod/runI-TASSER.pl -libdir /media/sf_D_DRIVE/home/bill/ITLIB -seqname orf8 -datadir /home/bill/covid-19/orf8 -runstyle gnuparallel -java_home /home/bill/anaconda3

Your setting for running I-TASSER is:
-pkgdir = /media/sf_D_DRIVE/home/bill/I-TASSER5.1
-libdir = /media/sf_D_DRIVE/home/bill/ITLIB
-java_home = /home/bill/anaconda3
-seqname = orf8
-datadir = /home/bill/covid-19/orf8
-outdir = /home/bill/covid-19/orf8
-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 121 residues:
> orf8
MKFLVFLGIITTVAAFHQECSLQSCTQHQPYVVDDPCPIHFYSKWYIRVGARKSAPLIEL
CVDEAGSKSPIQYIDIGNYTVSCLPFTINCQEPKLGSLVVRCSFYEDFLEYHDVRVVLDF
I
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
Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: Index 66 out of bounds for length 66
at d.a(d.java)
at d.main(d.java)
Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: Index 66 out of bounds for length 66
at c.a(c.java)
at c.main(c.java)
Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: Index 101 out of bounds for length 101

It looks like my job I submitted on 2020-04-07 is completed but I did not get an email and I have lost my key for my ITASSER ID S531529. Help! sah202@pitt.edu

I recently submitted an order to SPRING for two fusion proteins. These two fusion proteins should interact at with each other at two different sites. The SPRING results looked very clean and the models looked as would be expected on PDB. However, the generated models only provided the protein complex threading results for one of the two interaction sites between the two molecules (ie basically half of each submitted sequence was omitted in the modeling results). When I submitted an order to TACOS to model the full domains of each molecule, the nice protein interaction modeling obtained from the SPRING results completely disappeared. (Although there was one TACOS model which came somewhat close to modeling the second protein-protein interaction site).

Am I missing something here? Should the threading results and protein complexes found in SPRING be similar to the results for TACOS? Or is there some way for my order to include this constraint in TACOS (or PDB template, like with I-TASSER)?

Thank you very much for your time and effort!

Hi,
when trying to download the results tarball, S530462_results.tar.bz2, the file size is 46 byte only, with noting inside but a small binary file. Could you please fix this issue?
Thank you.

Dear Zhang lab,

Thank you for providing this resource. I submitted an I-Tasser job on 3/11/2020 and it has still not completed. I understand that your server is likely experiencing an increase in submissions, but is this a normal wait time or is there something wrong with the submission?

job id: S525942

Best,
Stephanie

Hi,
This is the link for the predicted structure:
https://zhanglab.ccmb.med.umich.edu/I-TASSER/output/S526507/
However, it doesn't show any of the TM-score or C-score for any of the predicted structures. Can you help me find out why, please?
Many Thanks,
Batool

The tarball for job ID S530697 is empty - can you please advise?
thanks!

My local installation of I-TASSER seems to ignore -restraint1/2/3/4 as an input option (it is not listed in the summary when the job is submitted.) Also, the optional arguments list is confusing as to which restraint is appropriate for which option.
-restraint1 links to I-TASSER/option1.html
-restraint2 links to I-TASSER/option4.html
-restraint3 links to I-TASSER/option2.html
-restraint4 links to I-TASSER/option3.htmlrestraint provided, run

Thanks,
Vish

Dear all,

is there a way to make a programmatic submission to C-Quark (using curl, Python, a web service, or any other means)? I have tried to find this information on the web and in this forum, but with no success. Any help is welcome.

Kind regards, Carlos Oscar

My I-TASSER job id S523880 is displaying nan errors for all models and numbers
C- Score shows nan and the estimated TM and RMSD for all models also display nan.

Could you please help me with this issue?

hello. I am an undergraduate student working on a protein structure prediction research project and I used LOMETS servers to predict my protein. This is my first project using computational biology. So, my questions are, why there is no TM-score or C-score for the full-length models? how would I know the best model to use for further analysis? and are the full-length models already refined? do I need to use ModRefiner and validate the structure predicted?.

Is it possible to predict structures for cyclic peptides? These peptides are end-on-end cyclised and not with disulphide bridges.