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I recently starting studying bioinformatics and have a question. I need to build a model of protein using Swiss-Model. First, I need to download a protein record from PDB (for example, 2HZI), then I must open PDB file using simple text editor. I know this usually requires biopython, but i don't use it yet. Now I'm trying to study how to build a model.

Swiss-model needs only one chain to build model, and I remove from file all extra information like AUTHOR,REMARK,HETATM etc. But Swiss-model still gives an error: "Sequence String contains illegal characters. Only letters and gaps allowed."

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    $\begingroup$ Welcome to the site @Badscience. Perhaps you haven't noticed but the site language is English. If you could translate your question into English we might be able to help. Please edit the question in English. About which program do you have a problem? I see Biopython and PDB mentioned but you might be trying to parse a file or using it to connect with another program. $\endgroup$
    – llrs
    Mar 19 '19 at 14:40
  • $\begingroup$ Thank you very much, @llrs. I'm sorry if i do some mistakes in this text. I am just starting to study bioinformatics and i have a problem. Today i download protein from PDB and try to build a model, using "Swiss-model" site, but this is requires work with PDB file, i don't use biopython yet, because i only try to understand how to build a model. I should delete excess information from PDB file, information like MODEL.ENDMDL,REMARK etc. But when i try to prepare file to modeling, i still face error: "Sequence String contains illegal characters. Only letters and gaps allowed". $\endgroup$
    – Badscience
    Mar 19 '19 at 14:56
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    $\begingroup$ please edit your question with the details of the comment and more: Which "Swiss-model" site? (add a url at least). What are you trying to build? A model of a protein, or a complex or something else? Could you add the text of the file you are uploading to that site? Also don't worry much about the English, we would help you improving it if we can. $\endgroup$
    – llrs
    Mar 19 '19 at 15:11
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As explained in the website the data introduced must be:

Format must be FASTA, Clustal, plain string, or a valid UniProtKB AC

So you need to paste just the protein sequence. Without seeing the data you paste I would guess that you don't use a valid plain string.

As Jonathan Moore explains below a FASTA format is:

>SEQUENCE_1 
MTEITAAMVKELRESTGAGMMDCKNALSETNGDFDKAVQLLREKGLGKAAKKADRLAAEG
LVSVKVSDDFTIAAMRPSYLSYEDLDMTFVENEYKALVAELEKENEERRRLKDPNKPEHK
IPQFASRKQLSDAILKEAEEKIKEELKAQGKPEKIWDNIIPGKMNSFIADNSQLDSKLTL
MGQFYVMDDKKTVEQVIAEKEKEFGGKIKIVEFICFEVGEGLEKKTEDFAAEVAAQL

(breaking the sequence in several lines is optional but usually done fore easy reading)

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  • $\begingroup$ I agree with this comment. Take a look at the FASTA format and present your protein in a text file in that format, like this: {>SEQUENCE_1 MTEITAAMVKELRESTGAGMMDCKNALSETNGDFDKAVQLLREKGLGKAAKKADRLAAEG LVSVKVSDDFTIAAMRPSYLSYEDLDMTFVENEYKALVAELEKENEERRRLKDPNKPEHK IPQFASRKQLSDAILKEAEEKIKEELKAQGKPEKIWDNIIPGKMNSFIADNSQLDSKLTL MGQFYVMDDKKTVEQVIAEKEKEFGGKIKIVEFICFEVGEGLEKKTEDFAAEVAAQL} $\endgroup$ Mar 20 '19 at 14:45
  • $\begingroup$ What they should be doing is overlaying the Swiss-Prot prediction against the real sequence data .... thats when things get harder $\endgroup$
    – M__
    Mar 21 '19 at 3:35

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