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@sachen1628 3 ай бұрын
Thank you! How do I get the space group and the unit cell information?
@PhenixTutorials Ай бұрын
This should be stored in your model and in your reflection file.
@hehe7617 Жыл бұрын
Hi, how can I solve the error of " Refined occupancies used in packing " during the molecular replacement?
@PhenixTutorials Жыл бұрын
Can you write an email to the phenix help? Then developers can answer. phenix-online.org/help
@chandanvishwakarma8063 Жыл бұрын
nice tutorial
@afvallejos 2 жыл бұрын
What's the "HKLviewer GUI must be run from Python 3" error while launching cctbx.HKLviewer from ubuntu terminal?
@robertoeffner9490 2 жыл бұрын
If your installation of CCTBX is based on python2 that would be the reason for this error message. The easiest way to obtain a python3 version is to install CCTBX via conda. You can find instructions on how to do this here cci.lbl.gov/docs/cctbx/installation/ Does that answer your question?
@murpholinox 2 жыл бұрын
Thanks!
@ΑΝΔΡΕΑΣΣΤΑΘΑΣ-γ2κ 2 жыл бұрын
Best
@proteinstructure2631 2 жыл бұрын
I'm a beginner. Could you please comment on these. (1) While refining, I found these options in Data labels: I-obs, SIGI-obs ; F-obs-filtered; SIGF-obs-filtered. How to choose the best one? Is there any rule for this? Thanks for help. (2) I am using Phenix.refine default parameters. How do I know all are ok for my structures (Resol: ~1.8A). I did not find any problem in molprobity or validation report. That means all are ok. Right?
@PhenixTutorials 2 жыл бұрын
(1) I-obs and SIGI-obs are the experimental data. The F-obs-filtered array comes from conversion from intensities to structure factors, including some outlier filtering. I suggest choosing I-obs and SIGI-obs for input. (2) At 1.8 Å, default parameters should be OK, but it always depends on the individual case, f.ex. if you have NCS, you might want to try NCS restraints (and if you don't, no need to apply them); if there are no problems in validation reports and if you don't see obvious issues in the maps (check in a molecular viewer, such as Coot), then your strategy is most likely fine.
@murpholinox 3 жыл бұрын
very nice!
@arleyr6364 3 жыл бұрын
Excelente video, but i have a question: how do elimination all atloc for manu proteins?
@PhenixTutorials 3 жыл бұрын
You mean many proteins? You could run the command line version of pdb tools in a script.
@ahmadfarizm3946 3 жыл бұрын
where can I get the ccp4_mtz file ?
@PhenixTutorials 3 жыл бұрын
The example data are shipped with the Phenix installation.
@philippebenas5721 3 жыл бұрын
Nice and interesting presentation. Thanks ! 👍👍
@jiangxu3895 3 жыл бұрын
Great presentation and really helpful!
@jiangxu3895 3 жыл бұрын
Thank you very much for sharing these knowledges. Very useful!!!
@王祥-k5l 4 жыл бұрын
Great talk for overview of cryo-EM tools in phenix
@PhenixTutorials 4 жыл бұрын
Thanks. We are glad it is helpful.
@AhmadMaulana-lt8oq 4 жыл бұрын
i have my own pdb structure. how can I get my reflection file??
@PhenixTutorials 4 жыл бұрын
For refinement, you would get a reflection file from a diffraction experiment.
@wenchaozhang6524 4 жыл бұрын
Thanks so much
@PhenixTutorials 4 жыл бұрын
You're welcome!
@RajeevRoy09 4 жыл бұрын
Hi, Thanks for the tutorial. I was wondering on what basis the program removes the alternate conformation of the amino acid. I mean to say, on the basis of occupancy of the conformations or on the basis of a better fit to the electron density map?
@murpholinox 4 жыл бұрын
Nice tutorial, again.... but where is the data?
@PhenixTutorials 4 жыл бұрын
Sorry, there are no tutorial data for this one.
@gp6848 4 жыл бұрын
How can I use it for the CryoEM maps that are in .mrc format? while it is working for the real space refinement under cryoEM .
@PhenixTutorials 4 жыл бұрын
You can use a map in .mrc format. Simply drag it into the "File path" box.
@jachintan3946 5 жыл бұрын
Thanks a lot
@originalAtreyu 6 жыл бұрын
How was it you were able to view the bulk solvent mask in coot? I'd love to be able to do it.
@PhenixTutorials 6 жыл бұрын
You can calculate the bulk solvent mask using (via the command line): phenix.mask model.pdb
@murpholinox 7 жыл бұрын
Need a paired-refinement tutorial! :P
@murpholinox 7 жыл бұрын
Very nice. Thanks
@PhenixTutorials 7 жыл бұрын
Thanks! Glad you like the video.
@MyllenaTofeko 7 жыл бұрын
Very useful, many thanks!
@PhenixTutorials 7 жыл бұрын
Thanks for the feedback!
@kyshark1 7 жыл бұрын
Thanks a lot for taking time out to make these videos. Its very useful. It would be great if you could make a series/playlist where you go from synchrotron image files to pdb using Phenix. That would give novice users like me a very good understanding of the program and how to solve a xtal structure from start to finish. Once again thanks for your help.
@PhenixTutorials 7 жыл бұрын
Thanks for your feedback! Such a series or playlist would be certainly helpful but I fear it goes beyond the scope of this tutorial channel about Phenix programs. If you want to learn more about a specific tool, let us know!