assign_chain_ID_in_mktrj()

[Former user]

Hi,

I performed NMA and I want o assign chain IDs to Calphas when generating traj. using mktrj(), so that I will not see these artificial bonds in pymol.

So,

trim.pdb(pdb = pdb.to.trim, "calpha")
mktrj (modes.APO, mode=7, file="test.pdb", resid=pdb.trim$atom$resid, resno=pdb.trim$atom$resno, chain=pdb.trim$atom$chain,  step=5.0)

But it does not work. Any suggestions very welcomed.

thank you

[Karol K]

Not able to edit previous post so little correction below:

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The code is:

pdb.trim <- trim.pdb(pdb = pdb.to.trim, "calpha")

mktrj (modes.APO, mode=7, file="test.pdb", resid=pdb.trim$atom$resid, resno=pdb.trim$atom$resno, chain=pdb.trim$atom$chain,  step=5.0)

Sorry for confusion. In a train…

[Xinqiu Yao]

Make sure pdb.trim contains distinct chain IDs. Also, you may add chainter=TRUE and try again.

[Karol K]

Indeed. pdb.trim did not contain labels for the first two chains thats way did not see them in the mktrj files. My bad.

Nevertheless, I am encountering a weird problem with my pdbs, which come from mktrj().

When I visualize mode trajectories in pymol or VMD, part of the structure is detached from the main structure, like 100 angstroms away, plus, these coordinates are deformed in a sense that they do not form a well structured structure. What I can see is a “blob”. The kind you see when you shift one of the columns in pdb.

I opened pdb files (produced by mktrj()) in text editor and I can’t see anything wrong with them. Formatting looks ok.

I will rerun with chainter=TRUE and check again, but I will find out in 2-3 days as these calculations will take 3 days, so meanwhile maybe you can narrow down a bit and point to something I should pay attention to?

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thanks

[Xinqiu Yao]

The mktrj() should be fine. What you have spotted most likely indicates an error in the NMA calculations. Do you mind to provide more detail how you did NMA?

[Karol K]

Hi,

So I got the recent results.

The problem with deformed coordinates appears to be solved. What helped was addition of chain labels and chainter=TRUE. I had more then 9999 atomic records in my pdb, but once I added termini and chain IDs, problem disappeared.

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You can close this ticket.

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THANK YOU.