Regarding RMSD/RMSF Plots and DCCM analysis

[Olivia Debnath]

Hello! I am working with two major proteins belonging to non-receptor tyrosine kinase family namely- Syk (PDB-ID: 1A81) and ZAP-70 (2OQ1). I do actively work with bio3d and have done DCCM, NMA and PCA analysis. How do I make sure it's all correct?! Can I fetch and modify the scripts for my own use? The problem is I don't understand what is the highest and lowest limit of Cij values while doing DCCM? I hope only the non-covalent interactions are considered. Also, are we doing it for the backbone C-alpha atoms or even the side chain interactions are included?

Most importantly, I am having a problem generating RMSD and RMSF graphs. From the RMSD histogram, it seems that the code is not identifying the core residues properly. How can I resolve the issue? We don't have a MD trajectory file for Syk- so, how do I perform the RMSD analysis from the PDB structure?

Looking forward to your kind reply,

Best regards, Olivia

[Lars Skjærven]

Hi Olivia,

How do I make sure it's all correct?! Basically by knowing what you're doing. Reading documentation, and writing tidy code is a good start. All functions in Bio3D are open source so you can easily take a peak at how they are written.

... highest and lowest limit of Cij values while doing DCCM dccm() outputs a matrix of NxN where N is the number of atoms (usually calpha atoms). max(cij) will give you the higest value, and min(cij) the minium. Note that you probably want to filter the cij matrix before doing this, e.g. through filter.dccm().

I hope only the non-covalent interactions are considered dccm() outputs all pairwise correlations, also for the pair (i, i+1). use the cmap argument to filter.dccm() to filter these out.

From the RMSD histogram, it seems that the code is not identifying the core residues properly. Please provide a running example so we can have a look. I don't understand the relationship between your RMSD histogram and core residues here.

how do I perform the RMSD analysis from the PDB structure. exactly what do you want to calculate RMSD on? you need two sets of coordinates to calculate RMSD.

[Lars Skjærven]

not a bug

[Olivia Debnath]

Respected Sir, Thank you so much for the reply. I am a beginner and I am trying my best to understand how the different functions are working. Actually, the codes written are without comments and so I need time to understand things properly.

In context to your reply, I want to ask how the values of cij will vary for different interactions and for different atoms (say, I want to consider all the non-covalent interactions of the backbone C-alpha atoms and exclude the side-chain interactions)? I want to know about the cutoff.cij values for these cases- are there any documentation about this?

After reading the documentation, I again did the RMSF plot and I am attaching the screenshot of the code used.

With best regards, Olivia

[Xinqiu Yao]

It is probably too late but there is no direct relationship between cij and physical interactions. Remember correlations are effect of overall interactions not just the two pairs under consideration. You need to play around with different cutoff.cij values and decide which one is the most suitable for your system. We have several issues discussing the same question. Please search and find relevant comments/suggestions.