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dssp-2.0.4-linux and dssp2ssd.py and mult-chains
- stevesei
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10 years 4 months ago #3070
by stevesei
dssp-2.0.4-linux and dssp2ssd.py and mult-chains was created by stevesei
Hello
I have a homodimer with each chain having 42 residues. My pdb file has both chains res 1-42, res 1-42 separated by "TER" commmand. When I make the dssp file using dssp-2.0.4-linux-i386, it docuements "2" chains with total resudes 84 at the top of the file. However, when it counts out residues it adds one call "!" making the final count 85 instead of 84. I corrected this by taking out the line "!" and renumberng residues in file to 84...
Then I use dssp2ssd.py and it tells me I have a total of 84 residues (correctly), but shows only one chain that is 84 residues long. Of course, this creates a problem when I use Martinize.py because the topology file and etc..thinks there is one chain 84 residues long.
Can someone help me?? My main concern is the dssp2ssd.py script..How can I make it recognize two chains..?
Thanks Steve
I have a homodimer with each chain having 42 residues. My pdb file has both chains res 1-42, res 1-42 separated by "TER" commmand. When I make the dssp file using dssp-2.0.4-linux-i386, it docuements "2" chains with total resudes 84 at the top of the file. However, when it counts out residues it adds one call "!" making the final count 85 instead of 84. I corrected this by taking out the line "!" and renumberng residues in file to 84...
Then I use dssp2ssd.py and it tells me I have a total of 84 residues (correctly), but shows only one chain that is 84 residues long. Of course, this creates a problem when I use Martinize.py because the topology file and etc..thinks there is one chain 84 residues long.
Can someone help me?? My main concern is the dssp2ssd.py script..How can I make it recognize two chains..?
Thanks Steve
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- djurre
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10 years 4 months ago #3087
by djurre
Replied by djurre on topic dssp-2.0.4-linux and dssp2ssd.py and mult-chains
I don't really understand the problem with the exclamation mark of dssp. However, the good news about the dssp2ssd.py script is: You don't need it if you use martinize.py If you give the option -dssp to martinize.py with the location of your dssp executable (-dssp /home/johndoe/dssp-2.0.4-linux-i386) that should work.
Unless of course there is actually something strange going on with this exclamation mark... A quick google suggests that it might mean that the backbone of your original pdb is incomplete.
Unless of course there is actually something strange going on with this exclamation mark... A quick google suggests that it might mean that the backbone of your original pdb is incomplete.
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- xavier
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10 years 4 months ago #3101
by xavier
Replied by xavier on topic dssp-2.0.4-linux and dssp2ssd.py and mult-chains
One potential solution to build the topology for the two proteins would be to make them separately. Being a dimer it might be symmetrical in which case the two topologies should be identical.
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- rjt
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3 years 7 months ago #8701
by rjt
Replied by rjt on topic dssp-2.0.4-linux and dssp2ssd.py and mult-chains
Hi,
Do you still have the dssp2ssd.py script? I am wondering if you could share it with me. Thanks!
Do you still have the dssp2ssd.py script? I am wondering if you could share it with me. Thanks!
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