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Chain break handling in martinize
- johnd
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4 years 10 months ago #8145
by johnd
Chain break handling in martinize was created by johnd
Hi,
I'm wondering do I properly indicate a chain break to martinize.py (v2.5 for reference)?
In the script, it says "# A chain may have breaks in which case the breaking residues are flagged" (L4617, v2.5). I assumed this would be interpreted based on the numbering.
I am using a structure that has residues 1-39 and 64-103.
I ran it through, but did not get any warnings. I also noticed that there are backbone bonds and angles between residues at the chain break.
Not entirely convinced it was working I added the -cb flag to charge the chain breaks, but I still got the same itp file, with no charges at the chain break residues.
I also tried adding a blank line, a TER between sections, and using different chain IDs before and after the break, which also gave the same itp file.
It's not really a huge deal to me since manually removing bonds/angles is not a big deal, I'm just wondering if there is a proper way to handle this.
Thanks,
John
I'm wondering do I properly indicate a chain break to martinize.py (v2.5 for reference)?
In the script, it says "# A chain may have breaks in which case the breaking residues are flagged" (L4617, v2.5). I assumed this would be interpreted based on the numbering.
I am using a structure that has residues 1-39 and 64-103.
I ran it through, but did not get any warnings. I also noticed that there are backbone bonds and angles between residues at the chain break.
Not entirely convinced it was working I added the -cb flag to charge the chain breaks, but I still got the same itp file, with no charges at the chain break residues.
I also tried adding a blank line, a TER between sections, and using different chain IDs before and after the break, which also gave the same itp file.
It's not really a huge deal to me since manually removing bonds/angles is not a big deal, I'm just wondering if there is a proper way to handle this.
Thanks,
John
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- tsjerk
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4 years 10 months ago #8146
by tsjerk
Replied by tsjerk on topic Chain break handling in martinize
Hi John,
In a PDB file, the break is inferred from a change of chain ID or from the presence of a TER statement. In a GRO file, the break is inferred from the CA-CA distance. I agree that more intelligent behaviour (checking residue IDs and even a SEQRES record) may be useful. This may come in Martinize 2 at some point.
Cheers,
Tsjerk
In a PDB file, the break is inferred from a change of chain ID or from the presence of a TER statement. In a GRO file, the break is inferred from the CA-CA distance. I agree that more intelligent behaviour (checking residue IDs and even a SEQRES record) may be useful. This may come in Martinize 2 at some point.
Cheers,
Tsjerk
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- johnd
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4 years 10 months ago #8147
by johnd
Replied by johnd on topic Chain break handling in martinize
Hi Tsjerk,
Odd that both of those options did not work. Maybe it's a bug?
Regardless, thank you for your comments and the information.
Cheers,
John
Odd that both of those options did not work. Maybe it's a bug?
Regardless, thank you for your comments and the information.
Cheers,
John
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- tsjerk
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4 years 10 months ago #8148
by tsjerk
Replied by tsjerk on topic Chain break handling in martinize
Can you send me the structure, the log from martinize you get and the output?
T.
T.
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- johnd
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4 years 10 months ago #8152
by johnd
Replied by johnd on topic Chain break handling in martinize
Hi Tsjerk,
I did some extra testing today, and never got the functionality expected
-With just a resid to indicate a break, it was never recognized (expected, in tarball)
-Adding a TER to the pdb did not lead to a recognized chain break (when chain ID was blank (in tarball) or when chain ID was "A" (not in tarball))
-Using two different chain IDs did work (no TER), but did not make neutral termini at the breaks, regardless of if the -cb flag was on (in tarball). I think it was treating the structure as two separate proteins instead of the same protein with a break
I don't know what I did wrong yesterday to not have using two IDs work.
Link to tarball: 1drv.ms/u/s!Ajk4FaEBTv0_lFk06xe1AHJH37ut?e=6gi5in
Let me know if the link doesn't work.
Cheers.
John
I did some extra testing today, and never got the functionality expected
-With just a resid to indicate a break, it was never recognized (expected, in tarball)
-Adding a TER to the pdb did not lead to a recognized chain break (when chain ID was blank (in tarball) or when chain ID was "A" (not in tarball))
-Using two different chain IDs did work (no TER), but did not make neutral termini at the breaks, regardless of if the -cb flag was on (in tarball). I think it was treating the structure as two separate proteins instead of the same protein with a break
I don't know what I did wrong yesterday to not have using two IDs work.
Link to tarball: 1drv.ms/u/s!Ajk4FaEBTv0_lFk06xe1AHJH37ut?e=6gi5in
Let me know if the link doesn't work.
Cheers.
John
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