Hello,
I was wondering if there was a computational tool which I could use to read the amino acid sequence for PB ID: 3igm. I was considering using the FASTA format, but I received poor output from online functions.
I would appreciate all the help I can get!
Many thanks,
Micah L
I think fasta is the gold standard for writing amino acid sequences ... it is also the simplest, so I'm surprised you got poor results.
I'm guessing you're looking at a PDB file, in which case you can get the fasta file by going to the PDB website, looking for the 3igm entry, then selecting the "Sequence" tab and finally selecting the "Download FASTA File" button. This file will contain the amino acid sequence of the structure in the 3IGM.pdb file, which is not necessarily the sequence of the whole wild type protein (if a tag was used to purify the protein, then parts of it might be included in the sequence, some parts might not be visible in the structure or have been mutated and have therefore been omitted or altered). If you want the "standard" or wild type sequence, you'll need to look for it in a database like Uniprot or NCBI.
Interestingly, there's a problem some of the students I worked with had. If you're working with a PC (windows), the PDB website might give you a file called 3IGM.fasta.txt, which is a txt file and might not be recognised by certain programmes as a fasta file. You will need to change the name/file type to 3IGM.fasta or 3IGM.seq ... which is easy in Linux/Unix but not in windows. However, many programmes don't actually require you to upload a fasta file, they will let you paste the content of the txt file (which has been written in fasta format) into a window. Simply open the file with a word editor (notebook, word, etc..), copy the text and paste it into the window.
Thank you, Antonio, I will look over my procedures and revise them once I have a chance!
There are also some very simple scripts that can convert a PDB file to fasta format: see e.g. https://gist.github.com/jameslyons/00cad4f1ab6a49c2b3df (python), https://github.com/alexholehouse/pdb2fasta (python) or http://cupnet.net/pdb2fasta/ (bash).
Just to add to Antonio's answer...
In case you are handling multiple FASTA files (for multiple sequence alignment) and have problems because of ".fasta.txt", you could change ".fasta.txt" to ".fasta" by
Step 1 - going to DOS (type cmd.exe in Start, in older windows Start > Run > cmd.exe )
Step 2 - go to the folder with the files
cd FULL_FOLDER_PATH
Step 3 - rename files
ren *.fasta.txt *.fasta
This would rename all the ".fasta.txt" files to ".fasta"
Dear Micah,
My suggestion is Pymol, because you will can show 3D structure and amino acid, too.
https://www.pymol.org/
You can access the fasta sequence by modifying this link, changing the PDB ID
http://www.rcsb.org/pdb/files/fasta.txt?structureIdList=1N0R
http://www.rcsb.org/pdb/files/fasta.txt?structureIdList=3IGM
You can download the sequence easily from the console in linux doing something like:
wget http://www.rcsb.org/pdb/files/fasta.txt?structureIdList=3IGM -O 3IGM.fasta
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