[ccp4bb] DSSR-enhanced visualization of nucleic acid structures in Jmol

2017-05-07 Thread Xiang-Jun Lu
Some list members may be interested in a paper, titled ["DSSR-enhanced
visualization of nucleic acid structures in Jmol"](
https://doi.org/10.1093/nar/gkx365), recently published in *Nucleic Acids
Research* (NAR). The [DSSR-Jmol integration](http://jmol.x3dna.org)
described therein bridges the DSSR (Dissecting the Spatial Structure of
RNA) command-line analyzing tool and the Jmol molecular viewer seamlessly
together via a simple JSON interface. Now users can select DSSR-derived RNA
structural features (such as base pairs, double helices, various loops,
etc.) and visualize them in several new representations in Jmol
*interactively*. Moreover, fine-grained characteristics of these features
can be queried via the Jmol SQL for DSSR. Here are some examples:

# Jmol 14.13.1 (2017-04-09) or later
load =1ehz/dssr   # load yeast phenylalanine tRNA to Jmol with DSSR
annotation
cartoon only; set cartoonSteps
rotate best; rotate z 90
color PROPERTY DSSR stems

# Jmol selections enabled by the DSSR-Jmol integration
SELECT hairpins   # select the three hairpin loops
SELECT junctions  # select the four-way junction loop
select within(dssr, "nts WHERE is_modified")  # select modified
nucleotides (14 in total)
SELECT within(dssr, "pairs WHERE name != 'WC'")  # select
non-Watson-Crick pairs
SELECT within(dssr, "pairs WHERE name = 'WC' OR name = 'Wobble'")  #
select canonical pairs
Select within(dssr, "pairs WHERE name != 'WC' AND name != 'Wobble'")  #
select non-canonical pairs
SELECT within(dssr, "pairs WHERE LW = 'tSW'")  # select pairs of type
'tSW', per Leontis-Westhof

The DSSR-Jmol integration fills a gap in RNA structural bioinformatics,
serving a huge user base of researchers, educators, and students alike.
Give http://jmol.x3dna.org a try, and you may find it useful for exploring
RNA/DNA structures.

A summary of key links:

* [DSSR-Jmol website](http://jmol.x3dna.org)
* [DSSR-Jmol NAR paper (open access)](https://doi.org/10.1093/nar/gkx365)
* [Details for reproducing reported results](
http://forum.x3dna.org/dssr-jmol-integration/)
* [DSSR-Jmol manual](http://jmol.x3dna.org/dssr-jmol-manual.pdf)

Best regards,

Xiang-Jun

[This message is posted on ccp4bb and pdb-l. Sorry for an extra copy of it
you may receive.]

--
Xiang-Jun Lu (PhD)
Email: xiang...@x3dna.org
Web: http://x3dna.org/
Forum: http://forum.x3dna.org/


Re: [ccp4bb] convert hkl data to mtz

2017-05-07 Thread Ian Tickle
Hi Careina

POINTLESS has replaced COMBAT for converting SAINT files.

http://www.ccp4.ac.uk/html/pointless.html

Cheers

-- Ian


On 7 May 2017 at 23:10, Careina Edgooms <
02531c126adf-dmarc-requ...@jiscmail.ac.uk> wrote:

> Hi
>
> I have not been in the game of solving structures for years. In the past I
> used the program combat in ccp4 to convert my hkl output file from SAINT
> into mtz file. Now I don't see combat anymore as an option in ccp4 programs
> and none of the programs recognise my SAINT output file. Please help
>
> Careina
>


[ccp4bb] convert hkl data to mtz

2017-05-07 Thread Careina Edgooms
 Hi
I have not been in the game of solving structures for years. In the past I used 
the program combat in ccp4 to convert my hkl output file from SAINT into mtz 
file. Now I don't see combat anymore as an option in ccp4 programs and none of 
the programs recognise my SAINT output file. Please help
Careina