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91
Dear Xiang-Jun, dear CTV team,

Attached to this post a screenshot of the page at URL http://innovation.columbia.edu/technologies/CU20391/ when i open it in Mozilla Firefox (tested on Linux and Windows 10) or Microsoft Edge (Windows 10).
Firefox version : 88.0.1 (but i had the same issue in past months with past versions)
Edge version : 91.0.864.37 (but same)


(Also notice the lack of HTTPS.)

Hope this helps,

Louis
92
RNA structures (DSSR) / Re: Incorrect topology assignment
« Last post by xiangjun on May 28, 2021, 09:52:45 pm »
Quote
Ok, I'll check these structures,

Please do. The more concrete examples, the better.

Quote
but it looks like our discussion goes beyond the canonical G-quadruplex structures (think in Webb da Silva's convention), hence the problems.

That is correct. Even 'canonical' G4 structures in the PDB have more complicated topologies than the Webb da Silva formalism allows. This is where DSSR can play a significant role: It can be used consistently on all G4s, and any "inconsistencies" are worth investigating further. Either DSSR needs to be improved (which I'd be delighted to do) or the structures themselves have some oddities (which is far more likely).

Quote
I look forward to the update if everything will be clearly explain in the publication. However, I hope that the "new convention" will be consistent with eg interpretations of CD spectra.

Do not expect to see a DSSR publication on G4 structures that have "everything clearly explained". For one thing, I have no idea on how a convention can "be consistent with eg interpretations of CD spectra". I simple do not have that expertise. Furthermore, the first DSSR paper dedicated to G4s may not be submitted/published anytime soon.

Quote
Unfortunately I am using the basic version of DSSR,  I have to think about buying the PRO version.

Hopefully, the DSSR Basic version and DSSR-G4DB have already been of some help to your project. If you decide to go for DSSR Pro, I may add an option that is tailored to your need.

There are many publications on structural analysis, annotations, and nomenclature of G4. If you find other free or more cost effective options, please let us know.

Best regards,

Xiang-Jun
93
RNA structures (DSSR) / Re: Incorrect topology assignment
« Last post by kogucior on May 28, 2021, 11:35:38 am »
Ok, I'll check these structures, but it looks like our discussion goes beyond the canonical G-quadruplex structures (think in Webb da Silva's convention), hence the problems.
I look forward to the update if everything will be clearly explain in the publication. However, I hope that the "new convention" will be consistent with eg interpretations of CD spectra.
Unfortunately I am using the basic version of DSSR,  I have to think about buying the PRO version.
94
RNA structures (DSSR) / Re: Color each block nucleotide at each locations
« Last post by xiangjun on May 27, 2021, 06:55:32 pm »
In PyMOL, type: help dssr_block, you will see the following usage info:

Code: [Select]
dssr_block [ selection [, state [, block_file [, block_depth [, block_color [, name [, exe ]]]]]]]
From the DSSR-PyMOL paper on NAR (https://doi.org/10.1093/nar/gkaa426), download the Supplementary PDF. Section 3.2 in on "The --block-color option". In PyMOL, you use block_color, as documented from help dssr_block.

Combined, you would do the following in PyMOL:

Code: Text
  1. # manual selection, named 'sele'; color any base red
  2. dssr_block sele, block_color='N:red'

PyMOL has a flexible selection engine you may want to get familiar with.

Best regards,

Xiang-Jun
95
RNA structures (DSSR) / Re: Color each block nucleotide at each locations
« Last post by spark159 on May 27, 2021, 02:41:46 pm »
Thank you so much for reply!

Here is example,

I made block image of pdb file:
x3dna-dssr -i=6rjg.pdb --blocview=png-c3 --block-file=wc-minor -o=6rjg.pml

I loaded pml file and I selected one nucleotide in pymol as figure I attached.
And type "color red, sele" to change the block color from blue to red.

But the block color (which I selected) is not changed, but I think the color of nucleotide embedded in the block is changed instead.
Do you have any suggestion to change the color of particular block of nucleotide which I selected?

Thanks
96
RNA structures (DSSR) / Re: Color each block nucleotide at each locations
« Last post by spark159 on May 27, 2021, 02:40:11 pm »
Thank you so much for reply!

Here is example,

I made block image of pdb file:
x3dna-dssr -i=6rjg.pdb --blocview=png-c3 --block-file=wc-minor -o=6rjg.pml

I loaded pml file and I selected one nucleotide in pymol as figure I attached.
And type "color red, sele" to change the block color from blue to red.

But the block color (which I selected) is not changed, but I think the color of nucleotide embedded in the block is changed instead.
Do you have any suggestion to change the color of particular block of nucleotide which I selected?

Thanks
97
Hi Louis,

Quote
I will discuss with my team, but yes, we may go for it.

Thanks!

Quote
If the CTV team wants more information on the problem, do not hesitate to ask me (i tried with different browsers, but nothing succeeds).

Yes, please provide screenshots and post them here. I've contacted the CTV support team, and they will view this thread.

Best regards,

Xiang-Jun

98
Hi Xiang-Jun,

Thanks for the copy-paste. I will discuss with my team, but yes, we may go for it.
If the CTV team wants more information on the problem, do not hesitate to ask me (i tried with different browsers, but nothing succeeds).

Louis
99
RNA structures (DSSR) / Re: Incorrect topology assignment
« Last post by xiangjun on May 27, 2021, 11:31:15 am »
Let's agree to disagree on this point for the time being. The directionality in each G-tetrad is specified unambiguously using either "Major-->WC" or "WC-->Major". The first G-tetrad directs the assignment of the four strands of the G-quadruplex.

Please check the descriptors of the other PDB entries I listed, specifically 2GKU, 2LOD, and 4U5M if not more, including groove widths. Let me know if the descriptors are "correct" in your option. Overall, the strands assignment and the corresponding +/- loop directions follow certain convention. I've added a switch in DSSR Pro to allow for both, as user desire. I've been in direct communication with Dr. Webba da Silva for several years. I may change the current default settings later, when a paper on G4 (including G4DB) is published.

Best regards,

Xiang-Jun


100
RNA structures (DSSR) / Re: Incorrect topology assignment
« Last post by kogucior on May 27, 2021, 10:56:19 am »
Quote
loop#1 type=propeller strands=[#1,#4] nts=1 C A.DC5
    loop#2 type=propeller strands=[#4,#3] nts=5 CACGA A.DC9,A.DA10,A.DC11,A.DG12,A.DA13
    loop#3 type=propeller strands=[#3,#2] nts=1 A A.DA17

I still have doubts about assigning strand numbers, e.g. loop #1 in my opinion occurs between strand #1 and #2. Until now I thought that the order of the strands is due to their relative arrangement in the space and that the counting starts at the 5'-end and goes counterclockwise.
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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.