Comments (6)
Yes. Since the translation information was missing, UglyMol shows the unit cell around the structure.
Please wait for a couple of weeks. I will try to use another way to load MTZ from RCSB and assume the translation is zero. That might work for your project.
from icn3d.
I just made another release to accept MTZ from RCSB specifically. You can simply change "file mtz" to "file rcsbmtz" in the URL. One example is https://www.ncbi.nlm.nih.gov/Structure/icn3d/full.html?mmdbid=3dzu&bu=1&command=set+map+2fofc+sigma+0.2+file+rcsbmtz+%7C+https://edmaps.rcsb.org/coefficients/3dzu.mtz. It didn't cover the whole structure. But it's much better than the version with "file mtz".
The UI is in the menu "File > Open File > Electron Density > .. > Load RCSB MTZ".
from icn3d.
These two formats were implemented slightly different. The parser of DSN6 map was from RCSB. There is a final translation of the map to match the structure. The parser of MTZ map was from UglyMol, e.g., https://uglymol.github.io/view/?id=3dzu. The map around the structure was generated based on the periodicity. There is no final translation.
Do you always use MTZ file from RCSB? I noticed the final translation is always zero. We could use the same method as the DSN6 format and improve the current display. But MTZ files from other resources may require a final translation, which is not provided in the MTZ file.
Another difference between DSN6 and MTZ file is the sigma may be different. So your MTZ URL probably needs to use a sigma of ~0.2 and change "dsn6" to "mtz": https://www.ncbi.nlm.nih.gov/Structure/icn3d/full.html?mmdbid=3dzu&bu=1&command=set+map+2fofc+sigma+0.2+file+mtz+%7C+https://edmaps.rcsb.org/coefficients/3dzu.mtz
from icn3d.
My ultimate goal is to use structure and maop file from PDB_REDO, and it currently only offers MTZ files for the EDM.
Ah, my bad, I was actually using "mtz" for the type during my testing, I just got it wrong for the example here.
So is that final translation the reason why I can only see like a central box for the EDM instead of the whole structure?
from icn3d.
It seems to work well even with PDB_REDO mtz files, like:
https://pdb-redo.eu/db/3dzu/3dzu_final.mtz
However, I was unable to load the structure from PDB_REDO (I could in earlier versions), it gets stuck at "loading"
https://pdb-redo.eu/db/3dzu/3dzu_final.cif
from icn3d.
The bug was fixed: https://www.ncbi.nlm.nih.gov/Structure/icn3d/?type=mmcif&url=https://pdb-redo.eu/db/3dzu/3dzu_final.cif
from icn3d.
Related Issues (20)
- What do the colors mean for B factor? HOT 1
- Legends do not appear for hydrophobicity if Wimley-White is chosen HOT 1
- secondary structures are not being expressed in web page HOT 4
- The 3D structure information for mutations doesn't always match the info in the 2D representation HOT 1
- URL not displaying desired annotation HOT 1
- Mutation annotations HOT 6
- Bonds between atoms are appearing as thick black tubes HOT 2
- "load url" command broken in icn3d_3.29.5 HOT 1
- Ideas for improving the cartoon HOT 6
- Open AlphaFold PAE file with latest result file HOT 2
- Chemical display isn't right HOT 7
- Unable to show selected chemicals when using Chrome HOT 3
- Customize menus doesn't work as expected HOT 3
- Is there a command or function that can enable to display PAE map? HOT 2
- Inquiry drawing drawing a path from one residue to another residue HOT 9
- Legend - Coloring by Atom - show complete names HOT 2
- Please fix the spelling in Legend for Color by Charge HOT 1
- The hydrophocity legend should contain information about hydrophobicity HOT 1
- Color by Residue legend has uracil spelled wrong and is missing the X HOT 1
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from icn3d.