REMARK 465

[Simon Brent]

Hi,

We would like to be able to label/render specific residues in a PDB structure based on chain ID:Residue Number combinations. Currently we are basing this on the internal numbering generated by PV but this does not appear to take into account missing residues in the structure (as detailed in REMARK 465) resulting in wrong placement of labels and rendering. Is it possible to render specific atoms on specific residues using chain identifier and PDB residue numbers?

Thanks.

[Marco Biasini]

PDB residue numbers and insertion codes are stored for each residue as num and insCode. To lookup a residue with a given residue number, you can use residueByRnum on the chain, e.g. structure.chain('A').residueByRnum(5) to get the residue with residue number 5. residueByRnum does not support insertion codes yet, so if you depend on insertion codes you will need to manually loop over the chain. We have recently added support for the sequential atom ids stored in the PDB files. They are stored for each atom as the serial property. You will need to update to master for this to work as this change is not yet included in any release.

I hope that helps

[Simon Brent]

Ok, thanks

[massinovitch]

Hello , you say : ' insertion codes you will need to manually loop over the chain'. How can I do this to color residues for chain by custom color code.

Thanks,

[Marco Biasini]

To implement a custom color operation, you can follow this guide. Inside the callback, instead of using atom properties, you can get back to the parent residue the atom belongs to by calling atom.residue(). Then it's up to you to map the the residue properties to the color. Does this answer your question? If not, could you elaborate what you are trying to achieve?

[massinovitch]

Hello, Thank you for your response. I succeeded to implement residues number coloration with this code : go.colorBy(color.uniform(codeColorResidue), go.select({chain:id, rnumRange: [numRes1, numResidue2]})); Cdt, Massinissa SEKHI 06.83.13.90.62 01.76.84.42.79 2017-02-23 5:51 GMT+01:00 Marco Biasini <[e-mail]>:

…

To implement a custom color operation, you can follow this guide <http://pv.readthedocs.io/en/v1.8.1/coloring.html#adding-a-new-color-operation>. Inside the callback, instead of using atom properties, you can get back to the parent residue the atom belongs to by calling atom.residue(). Then it's up to you to map the the residue properties to the color. Does this answer your question? If not, could you elaborate what you are trying to achieve? — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#152 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AK7N7Ht9IkrQrZRnXj8PP49p3Z6msBuXks5rfRA7gaJpZM4H6wGH> .

[massinovitch]

Hello, I want to color residues of one chain. I do it with this function : function colorstructuraletterpv() { viewer.forEach(function(go) { for (numChain in listColorResidues) { var listColorResiduesForChain = listColorResidues[numChain];// i get listColorResidues by file. for (numResidue in listColorResiduesForChain) { codeColorResidue = listColorResiduesForChain[numResidue]; var numResidueInt = parseInt(numResidue); go.colorBy(color.uniform(codeColorResidue), go.select({chain:numChain, rnumRange: [numResidueInt, numResidueInt]})); } } }); viewer.requestRedraw(); } but it take time considerable (>500 ms). is there another faster way to color just one chain in the structure by residues. thank you. Massinissa SEKHI 06.83.13.90.62 01.76.84.42.79 2017-02-24 9:49 GMT+01:00 Massinissa SEKHI <[e-mail]>:

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Hello, Thank you for your response. I succeeded to implement residues number coloration with this code : go.colorBy(color.uniform(codeColorResidue), go.select({chain:id, rnumRange: [numRes1, numResidue2]})); Cdt, Massinissa SEKHI 06.83.13.90.62 <06%2083%2013%2090%2062> 01.76.84.42.79 <01%2076%2084%2042%2079> 2017-02-23 5:51 GMT+01:00 Marco Biasini ***@***.***>: > To implement a custom color operation, you can follow this guide > <http://pv.readthedocs.io/en/v1.8.1/coloring.html#adding-a-new-color-operation>. > Inside the callback, instead of using atom properties, you can get back to > the parent residue the atom belongs to by calling atom.residue(). Then > it's up to you to map the the residue properties to the color. Does this > answer your question? If not, could you elaborate what you are trying to > achieve? > > — > You are receiving this because you commented. > Reply to this email directly, view it on GitHub > <#152 (comment)>, or mute > the thread > <https://github.com/notifications/unsubscribe-auth/AK7N7Ht9IkrQrZRnXj8PP49p3Z6msBuXks5rfRA7gaJpZM4H6wGH> > . >