normal Problem with mapping

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7 months 1 week ago #7966 by sot
Problem with mapping was created by sot
Hi all,
First of all, I tried reading the other posts in many topics that seemed right for this kind of question but found nothing of the matter. If for any case this question is covered elsewhere or should be posted on another category inform me so I can remove this particular post.
I have mapped (AA to CG) a series of similar molecules using backward.py with success. But in only one of the molecules and for only one bead I get a 1nm shift in the x-axis.
I am looking for hints on where might the problem be, or which part of the backward.py script reads the input files and makes the necessary transformations.
I know that my message is a bit general but this will help more in case a similar issue occurs.
Feel free to ask any questions and thank you all in advance.

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7 months 6 days ago #7970 by Pim
Replied by Pim on topic Problem with mapping
Hi,
It sounds very case specific - so it will be difficult to debug without the actual files. The 1 nm shift is in the output coordinates after 'forward' mapping, right?
As I understood it, backward converts your input coordinates to relative 'box coordinates', before transferring back at the end, so a 1 nm shift is strange. Is it 1.0000000 nm? Do you have strange atom names in your AA files that start with a letter that is not the element, maybe mass weighting is going weird?

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7 months 4 days ago #7971 by sot
Replied by sot on topic Problem with mapping
Hi, yes the problem occurs after forward mapping. It is exactly 1 nm (based on visual inspection and neighbour coordinates). There are actually some strange atom names in the file. I didn't know that this could affect the weighting.
If this works maybe it should be considered in the forum to write down a more detailed manual. Just an idea.
I will check and let you know how it goes.

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7 months 4 days ago #7972 by Pim
Replied by Pim on topic Problem with mapping
Considering the exactly 1 nm difference, weighting is probably not the problem, and I'm not entirely sure if it can even go wrong with strange names, but it's worth a shot I guess. I couldn't think of anything else to say :).

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7 months 2 days ago #7973 by sot
Replied by sot on topic Problem with mapping
Unfortunately this wasn't the case. Is it possible to know which part of the script makes the transformations? I've found that in the problematic bead is a single atom that is getting shifted. It is like the script is reading the coordinates wrong or that it makes a strange transformation.

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