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.
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. 