Re: [ccp4bb] request for help about a 2-crystal drawing tool...

[Ethan Merritt (UW)]

On Sunday, 25 August 2019 18:28:35 Laurent Maveyraud wrote:
> Dear CCP4ers,
> 
> a long time ago (something like 10 years, or even more), I used an applet 
> available on the internet for drawing small schematic 2D crystals (see 
> below). You had the possibility to draw a small motif (in my case something 
> like a  histidine side-chain) and then define the lattice you wanted to 
> generate. I used it a lots for teaching purposes… but I would now like to 
> refresh my images and generate new examples… Of course, I was not smart 
> enough to take note of the applet name or address… and google was not able to 
> help my memory

I have a copy here:

http://skuld.bmsc.washington.edu/people/merritt/bc530/local_copies/escher/

The problem is, it dates back to the good old days before everyone
got so worried about insecure java applets that java was disabled in
all the standard browsers.  So chances are you cannot run it in your
browser, you would have to download the code and run it locally.

cheers,

Ethan


> 
> 
> Does this reming something to anybody ? Any suggestions for software able to 
> generate such lattices are also welcome!
> 
> thanks a lot !
> Laurent
> 
> 
> Laurent Maveyraud
> PICT, Plateforme Intégrée de Criblage de Toulouse
> Université Paul Sabatier / CNRS / I.P.B.S. UMR 5089
> Département Biologie Structurale et Biophysique
> http://cribligand.ipbs.fr, http://www.ipbs.fr
> 205 route de Narbonne 31077 TOULOUSE Cedex FRANCE
> Tél: +33 (0)561 175 435  Mob.: +33 (0)646 042 111
> ---
> 
> 
> 1st French Congress on Integrative Structural Biology: please check 
> http://bsi-2019.ipbs.fr 
> 
> 
> 
> 
> 
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-- 
Ethan A Merritt, Dept of Biochemistry
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742



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Re: [ccp4bb] Ligand identification

[Ethan Merritt (UW)]

On Thursday, July 18, 2019 1:02:25 PM PDT Nicola Evans wrote:
> > I have an unidentfied blob of density at a crystal contact region. I
> > tried inputting a magnesium ion there, it was clearly incorrect but it
> > improved the R-factors by 3, so I would really like to identify the
> > correct molecule! Is there a tool to identify ligands in structures? I
> > have tried the Phenix ligand identification tool to no avail (although
> > it did find some nice horseshoe shaped PEG ions). I used glycerol and
> > PEG400 as a cryo protectant, and identified a few glycerol and PEG
> > molecules in other parts of the structure but not in this spot (well
> > conditions: 0.2 M Magnesium chloride hexahydrate, 0.1 M BIS-TRIS pH
> > 5.5, 25% PEG 3,350). As this is an the crystal contact region the
> > molecule isn't likely to be biologically significant. The data have
> > been solved to 1.9Å. I have attached a screenshot of the mysterious
> > density. I would appreciate any suggestions! In addition, I am adding
> > water molecules to this protein, and often there are what appear to be
> > long chains. Are these likely to be long chains of ordered waters, or
> > more PEG molecules? Thanks in advance for your help! Nicola


You might enjoy reading the recent paper by Kowiel et al (2018)
"Automatic recognition of ligands in electron density by machine learning"
https://doi.org/10.1093/bioinformatics/bty626

One of the more convincing examples they give (Fig 6D) is identification of a 
TRIS
molecule.  By coincidence the density in the this figure looks a lot like yours.

cheers,

Ethan

-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742



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