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Author Topic: no nucleotide in some structures  (Read 2000 times)

Offline shuxiang

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no nucleotide in some structures
« on: February 11, 2019, 10:24:32 am »
Hi Xiang-Jun,

I'm using DSSR to analyze some structures and it showed there is no nucleotide was found. When I visualized these structures using pymol. I indeed saw nucleotides are there. For example (6CEV):

x3dna-dssr -i=6cev.pdb

Thanks. :)

Best,
Shuxiang

Offline xiangjun

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Re: no nucleotide in some structures
« Reply #1 on: February 11, 2019, 11:07:43 am »
By default, DSSR checked for ATOM/HETATM records with the alternative location (altloc) set either as space (most common) or 'A'. In PDB entry 6CEV, the DNA atoms have altloc as 'B'. That's why you do not see any results from a default DSSR run.

Try: x3dna-dssr -i=6cev.pdb --altloc=B

Best regards,

Xiang-Jun


Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

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Offline shuxiang

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Re: no nucleotide in some structures
« Reply #2 on: February 11, 2019, 11:41:21 am »
Thank you so much for the explanation and an option to solve my problem.

Best,
Shuxiang

 

Created and maintained by Dr. Xiang-Jun Lu [律祥俊], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.