Cport give error

I submitted the protein but it gives the following error

traceback (most recent call last):
File “/home/enmr/services/CPORT/cgi/cport.py”, line 91, in
webform = cgi.FieldStorage()
File “/usr/lib64/python2.7/cgi.py”, line 507, in init
self.read_multi(environ, keep_blank_values, strict_parsing)
File “/usr/lib64/python2.7/cgi.py”, line 636, in read_multi
environ, keep_blank_values, strict_parsing)
File “/usr/lib64/python2.7/cgi.py”, line 509, in init
self.read_single()
File “/usr/lib64/python2.7/cgi.py”, line 646, in read_single
self.read_lines()

Could be an issue with your input PDB file… Did you try with say a standard PDB file from the PDB database?

Where is your file coming from?

Hi, I do not think there is a problem with the file because for the test I gave previous PDB structures and also standard PDB files from the PDB database and gave this error again.

PDB structures predicted by I-TASSER.

Just checked the server and submitted a job. No issues…

The problem must reside in your input data.

Thanks, but my problem is not solved and even with the PDB structures it gives the same error.:pray::pray:

Without more info it is impossible to help you…

Describe exactly what you are doing and provide the input data

I have used cport before and given this predicted structure with I-TASSER (attach file) and it gave me the following residues

Cport balanced

Predicted residues (active residues in HADDOCK):
1, 2, 3, 6, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19,
20, 21,

Surrounding residues (passive residues in HADDOCK):
4, 5, 8, 9,

Thank you for using CPORT

But now I give the same structure or new structures (predicted by I-TASSER) give an error
model1.pdb (21.8 KB)

To reproduce the problem we also need the sequence alignment

I have several epitopes and I want to determine the best order of them like the following article

Exploring NS3/4A, NS5A and NS5B proteins to design conserved subunit multi-epitope vaccine against HCV utilizing immunoinformatics approaches

I was done the following steps

1-GPGPG was added to each epitope, and the 3D structures were predicted by I-TASSER.

2- The active and passively interacting residues of structures were determined using CPORT (http://alcazar.science.uu.nl/services/CPORT/).

3- Compatibility of the interaction of every individual epitope to the others was analyzed by the Guru interface of the HADDOCK server (https://alcazar.science.uu.nl/services/ HADDOCK2.2/haddockserver-guru.html). This step was followed by refinement using the HADDOCK refinement interface (HADDOCK Refinement Interface).

Until now I have not had any problem. But now, unfortunately, my work is incomplete because it does not accept any structure from I-TASSER

The epitope sequence of previous 3d structure: >seq NYYAEYYATGASTAGKGPGPG

(I have not done the alignment)

This epitope is of the fimbrial protein of A. baumannii with the following sequence

tr|B0V4C0|B0V4C0_ACIBY Putative fimbrial protein (Pilin) OS=Acinetobacter baumannii (strain AYE) OX=509173 GN=ABAYE1856 PE=4 SV=1

MKKLALIAALSVVGIANAQAADGTITINGLVTDKTCDIVTPAGKDFTVTLPTVSKQTLAVAGDVAGRTPFQINLANCSQGKVATYFEPGATVDFNTGRLLNQDATGAKNVNVQLLGSNNNFIPVLAAGANGAQANSQWVDVAEGASADLNYYAEYYATGASTAGKVTTSVQYTIIYQ

I have several epitopes and I want to determine the best order of them like the following article

Exploring NS3/4A, NS5A and NS5B proteins to design conserved subunit multi-epitope vaccine against HCV utilizing immunoinformatics approaches

I was done the following steps

1-GPGPG was added to each epitope, and the 3D structures were predicted by I-TASSER.

2- The active and passively interacting residues of structures were determined using CPORT (http://alcazar.science.uu.nl/services/CPORT/).

3- Compatibility of the interaction of every individual epitope to the others was analyzed by the Guru interface of the HADDOCK server (https://alcazar.science.uu.nl/services/ HADDOCK2.2/haddockserver-guru.html). This step was followed by refinement using the HADDOCK refinement interface (https://bianca.science.uu.nl/haddock2.4/refinement/1).

Until now I have not had any problem. But now, unfortunately, my work is incomplete because it does not accept any structure from I-TASSER

The epitope sequence of previous 3d structure: >seq NYYAEYYATGASTAGKGPGPG

(I have not done the alignment)

This epitope is of fimbrial protein of A. baumannii with the following sequence

tr>B0V4C0|B0V4C0_ACIBY Putative fimbrial protein (Pilin) OS=Acinetobacter baumannii (strain AYE) OX=509173 GN=ABAYE1856 PE=4 SV=1

MKKLALIAALSVVGIANAQAADGTITINGLVTDKTCDIVTPAGKDFTVTLPTVSKQTLAV

AGDVAGRTPFQINLANCSQGKVATYFEPGATVDFNTGRLLNQDATGAKNVNVQLLGSNNN

FIPVLAAGANGAQANSQWVDVAEGASADLNYYAEYYATGASTAGKVTTSVQYTIIYQ

Try cleaning the i-Tasser PDB file with pdb_tidy from our PDB-tools server

Remove any “junk” from the iTasser PDB file, keeping only the ATOM and TER/END lines.

Thank you very much
my problem was solved
the Cport now accepts I-TASSER structures, similar to the past. :pray::pray: