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Messages - lukeczapla

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1
General discussions (Q&As) / Re: buggy rebuild
« on: June 24, 2017, 12:07:32 pm »
Thank you Xiang-Jun, that was exactly what I was looking to see.  A 5000 bp circular "mini-chromosome" with no proteins bound to it.  I will work to integrate PDBx/mmCIF into my work, UCSF Chimera definitely reads it in and I have to ask the guys at 3Dmol about loading it into the browser with their JavaScript viewer.  Do you have some special way to place the phosphates and sugar in rebuild?  I'd like to try to understand it better and see where it lines up for nucleosome-bound DNA that has a lot of slide.  I understand that you are more interested in the study of RNA structures in your research.

Thanks

2
General discussions (Q&As) / Re: buggy rebuild
« on: June 23, 2017, 10:49:08 pm »
Thank you.  I had to play tricks with reverse_stnd2() and the spacings in the PDB prints to make something that a viewer could read.  So if you could implement that support for the PDBx/mmCIF format, then I won't have to remove all the CONECT records for it to view properly.  It is well intentioned and I want to make a web system that can simulate and visualize these really long DNA molecules and include 3DNA in the pipeline.

Thanks again.


3
General discussions (Q&As) / Re: buggy rebuild
« on: June 23, 2017, 10:15:35 pm »
Ok I think I fixed it. I changed a line in reset_xyz() function to not reset the bp unless it's bigger than 99999.9 or -99999.99 and then it really is just changing to %8.2.  I should be good to go.


4
General discussions (Q&As) / Re: buggy rebuild
« on: June 23, 2017, 09:02:29 pm »
Believe me, if it was just changing a sprintf("%8.3f") to a sprintf("%8.2f") in your code, I would've done that already, I have the source.  But with this whole operation you're performing (following that warning you mentioned, which I did see), it is not so simple.  Therefore I just ended up writing my own code to rebuild double-stranded DNA.  Correct me if I'm wrong though, because I will go and change it myself if it's that simple.

Thank you

5
General discussions (Q&As) / Re: buggy rebuild
« on: June 23, 2017, 08:40:55 pm »
if it had a flag to handle big numbers using %8.2f or %8.1f and override what you believe to be the only "correct" way to write a PDB file, that'd make it compatible with the common applications that are used to visualize systems and generate images, which don't agree with you that that's the only correct way to format a number in a PDB file.  So it's not that it's wrong, it's just that it's not flexible with these larger datasets and the reality of using the product for research.


6
General discussions (Q&As) / Re: buggy rebuild
« on: June 23, 2017, 08:03:27 pm »
It's more than just the numbers, something's really going wrong with your code, here's the first nucleotide (which should be at the origin), and in v2.3 it's exactly the same:

REMARK    3DNA v2.1-2014mar25, created and maintained by Xiang-Jun Lu (PhD)
ATOM      1  C1'   A A   1    1962.0311187.0561104.807  1.00  1.00           C 
ATOM      2  N9    A A   1    1963.2191186.2081104.807  1.00  1.00           N 
ATOM      3  C8    A A   1    1964.5341186.6071104.807  1.00  1.00           C 
ATOM      4  N7    A A   1    1965.3871185.6121104.807  1.00  1.00           N 
ATOM      5  C5    A A   1    1964.5811184.4811104.807  1.00  1.00           C 
ATOM      6  C6    A A   1    1964.8791183.1081104.807  1.00  1.00           C 
ATOM      7  N6    A A   1    1966.1211182.6191104.807  1.00  1.00           N 
ATOM      8  N1    A A   1    1963.8421182.2421104.807  1.00  1.00           N 
ATOM      9  C2    A A   1    1962.5981182.7331104.807  1.00  1.00           C 
ATOM     10  N3    A A   1    1962.1901184.0001104.807  1.00  1.00           N 
ATOM     11  C4    A A   1    1963.2431184.8341104.807  1.00  1.00           C 



But it's fine, if you don't want to fix it, I can use my own code to rebuild the DNAs.  Most programs don't seem to support this XML format.  It's really a simple fix, just output 2 decimals, it will be properly read in Chimera, VMD, and 3Dmol.


7
General discussions (Q&As) / buggy rebuild
« on: June 23, 2017, 01:44:45 pm »
I tried to rebuild this structure (base-pair step parameters) and it comes out as junk.  The first base-pair is not even in the standard reference frame near the origin.  It does this in both v2.1 and v2.3.

command:

rebuild -atomic structure-5000bp-ID0-B0-1.dat out.pdb


Thanks
Luke Czapla

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Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.