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91
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
92
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

93
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
94
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


95
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.
96
RNA structures (DSSR) / Re: Incorrect topology assignment
« Last post by xiangjun on May 27, 2021, 10:31:12 am »
Hi,

Thank you very much for your feedback.

Technically, the assignment of clockwise (+) vs anti-clockwise (-) assignment is easy to change for these PDB entries with first G in syn conformation, thus the first G-tetard is ordered in Major-->WC direction. The current assignment in DSSR, by default, has considerations with regard to the calculation of rigid-body parameters (twist, rise, etc.). Following your feedback, it makes sense that the assignment of the descriptor is treated separately to follow the formalism of Mateus Webba da Silva.

How about the following for 2kqg:

Quote
List of 1 G4-stem
  Note: a G4-stem is defined as a G4-helix with backbone connectivity.
        Bulges are also allowed along each of the four strands.
  stem#1[#1] layers=3 INTRA-molecular loops=3 descriptor=3(-P-P-P) note=parallel(4+0) UUUU parallel
   1  glyco-bond=s--- sugar=.--- groove=w--n Major-->WC nts=4 GGGG A.DG2,A.DG18,A.DG14,A.DG6
   2  glyco-bond=---- sugar=---. groove=---- Major-->WC nts=4 GGGG A.DG3,A.DG19,A.DG15,A.DG7
   3  glyco-bond=---- sugar=---3 groove=---- Major-->WC nts=4 GGGG A.DG4,A.DG20,A.DG16,A.DG8
    step#1  pm(>>,forward)  area=19.15 rise=3.41 twist=21.0
    step#2  pm(>>,forward)  area=12.05 rise=3.47 twist=28.2
    strand#1  U DNA glyco-bond=s-- sugar=.-- nts=3 GGG A.DG2,A.DG3,A.DG4
    strand#2  U DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG18,A.DG19,A.DG20
    strand#3  U DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG14,A.DG15,A.DG16
    strand#4  U DNA glyco-bond=--- sugar=-.3 nts=3 GGG A.DG6,A.DG7,A.DG8
    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

While I am working on this topic, please also check (some of) the following PDB entries, and let me know your thoughts on the descriptors:

Code: [Select]
148d 186d 1bub 1c34 1c35 1c38 1hao 1hap 1hut 1i34 1qdf 1qdh 1rde 201d
230d 2e4i 2f8u 2gku 2hy9 2jpz 2jsk 2jsl 2jsm 2jsq 2kf7 2kf8 2kka 2km3
2kow 2kpr 2kqg 2kzd 2l88 2lod 2lyg 2m6v 2m6w 2m8z 2m91 2may 2mb3 2mbj
2mft 2mfu 2ms9 2mwz 2n2d 4dih 4dii 4lz1 4lz4 4ni7 4ni9 4u5m 5cmx 5ew1
5ew2 5j05 5j4p 5j4w 5j6u 5lqg 5lqh 5mjx 5mta 5mtg 5mvb 5o4d 5oph 5yey
5zev 6ac7 6ccw 6eo6 6eo7 6erl 6evv 6f4z 6fc9 6ftu 6gh0 6gn7 6gzn 6h1k
6ia4 6jkn 6jwd 6jwe 6kfj 6l8m 6l92 6r9k 6r9l 6rs3 6tc8 6tcg 6ycv 6yep
6z8v 6z8w 6z8x 6zx6 7atz 7cv3 7cv4 7ntu

Best regards,

Xiang-Jun
97
Hi Louis,

Sorry for your difficult experience in accessing the CTV website for DSSR. I've communicated with the supporting staffs, and hopefully situation would improve as a result of your feedback.

Basically, the DSSR Pro academic license charges a one-time fee of $1000 per seat. It comes with a one-year support directly from me. I do not expect another major release of DSSR in the next 4 years. As a result, the annual cost averages $250, or about a tenth of the cost of a journal publication or a two-night hotel stay. Email and video meetings are included in the one-year support. Following your suggestion, I will create a post on DSSR Pro academic license in the "Site announcements" section. [Note added on May 31, 2021: I've added a post titled "Clarification on DSSR licensing".]

Best regards,

Xiang-Jun


Below in the copied from the CTV website on DSSR Pro:

Quote
License Name

DSSR-Pro Academic ($1000, 1 seat)

Description

This academic license is for one user and includes the DSSR Pro software (macOS, linux, and windows) along with the Pro Manual. It is for people working on open academic research at, or for, an academic institution or similar non-profit. Any commercial use requires purchase of a commercial license. It is a one-time fee and does not cover future major releases of the code. Minor releases with bug-fixes and small updates are included in the fee. Thank you for purchasing DSSR. Funds help to support further development of the DSSR software product.

DSSR Pro has more functionality than DSSR Basic, including: (i) homology modeling via in silico base mutations, (ii) easy generation of regular helical models, and (iii) creation of customized structures with user-specific base sequences and rigid-body parameters. DSSR Pro supersedes 3DNA completely while DSSR basic has no modeling capabilities and less analysis/annotation features. DSSR Pro integrates disparate analysis and modeling programs of 3DNA under one umbrella, and offers an easier to use interface. DSSR Pro includes an in-depth user manual, and one year technical support directly from the developer. DSSR basic is provided AS IS, and does not include any support.

Pricing Information

Total Price $1,000.00
98
RNA structures (DSSR) / Re: Incorrect topology assignment
« Last post by kogucior on May 27, 2021, 07:10:42 am »
Quote
As long the first G is in syn conformation, you will observe the same behavior for other G4 structures in DSSR-G4DB. The results should be self-consistent.

I don't understand why the anti/syn conformation is having an effect on this. Theoretically, according to the Webba da Silva formalism [Geometric Formalism for DNA QuadruplexFolding] -P-P-P and +P+P+P topology may have a composition of fully syn or anti G-tetrad.

If the topology determination is based on the syn/anti  composition of 4 guanines in G-tetrad then I would expect +/-(LPP) topology for 2kqg. While the identical structure (2kqh) has a -P-P-P topology.

I expected that the order of the guanines in the planes is based on the order in sequence and the interaction edge (WC or H) with the other adjacent guanines.
99
RNA structures (DSSR) / Re: Incorrect topology assignment
« Last post by kogucior on May 27, 2021, 07:01:39 am »
Quote
As another concrete example, what do you think the descriptor for PDB entry 6r9k should be?

I believe it should be as it is currently described as: +L+P+P.
100
Hi,

Thank you for the quick fix !

I have an academic licence for DSSR2, but i can consider "DSSR Pro", what is the difference and how much does it cost ? (The CTV website displays a blank page)

Quote
Due to a lack of funding support, this is the only way my effort on DSSR can be justified. I will ensure that paid users always receive top-notch support.
I understand. While i entirely trust you since you have demonstrated efficiency and skills in developping DSSR and quickly replying to questions on this forum, the CTV is not very engaging, since the website regularly has issues. My first visit was in September 2020, blank page, I had to ask techventures<at>columbia.edu by email to fix it. And today i have the same issue. And i could read in the forum that other people faced problems.
I suggest you summarize the content of the page in a forum post, to provide a reliable source of information about DSSR licensing, maybe ?
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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.