Re: [ccp4bb] Map grid passing from ccp4 refmac mask?

In cco4i you can select “run and view com file” then edit the appropriate command into the com file. Not sure if you can change the file name extension on the command line though - I seem to remember extensions were cast in stone to simplify. Cataloging outputs. But you can always rename any file

Re: [ccp4bb] Strange Pseudosymmetry Effects

Yes - in P1 if you have two molecules approximately related by X y z. And x+ 1/2 y z say then the spots along the axis a* will have h=2n weak. And the sections with h even will have very weak spots. If you calculate a Patterson for the data there will be a strong peak st 1/2, 0,0. But you say

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Re: [ccp4bb] Refmac and hydrogens -developers

The first thing you want to do when debugging hydrogens in refmac5 is to make sure it outputs whatever it was doing: MAKE HOUT Y This is not the default.  Normally, refmac will take a PDB file without any hydrogens in it, quietly add them before doing refinement, and then delete them before

Re: [ccp4bb] Strange Pseudosymmetry Effects

Be careful with electron diffraction and apparent absence violations. It is possible these weak spots are simply due to multiple scattering.  If so, you would see them relatively stronger with larger crystals,but much weaker relative to the strong reflections when the crystal is smaller. Do

Re: [ccp4bb] Strange Pseudosymmetry Effects

This jogged my memory of a CCP4 newsletter article many years ago covering kinematical versus dynamic scattering in protein crystals and offering a correction that could be used. I think it was Lindsay Sawyer and Igor Polikarpov in the late 90’s. I apologize if I have the authors wrong but I

[ccp4bb] visual mask editor?

Brief question: Does something like a visual density mask editor exist? Thx, BR -- Bernhard Rupp http://www.hofkristallamt.org/ b...@hofkristallamt.org +1 925 209 7429 +43

Re: [ccp4bb] visual mask editor?

You used to be able to do this in O (dating myself) From: CCP4 bulletin board On Behalf Of Bernhard Rupp Sent: Thursday, May 28, 2020 12:39 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] visual mask editor? EXTERNAL EMAIL – Use caution with any links or file attachments. Brief question: Does

Re: [ccp4bb] visual mask editor?

?You can generate maps using UCSF Chimera then convert these to binary masks. This means you can drag PDB around to generate a mask where ever you like. Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry and Biochemistry New York, NY 10031

Re: [ccp4bb] visual mask editor - why

Hi Bernhard, Did you consider trying 'polder' in the phenix package? Boaz Boaz Shaanan, Ph.D. Department of Life Sciences Ben Gurion University of the Negev Beer Sheva Israel On May 28, 2020 21:17, Bernhard Rupp wrote: Maybe I should explain an example: Say coot detects an unmodelled

Re: [ccp4bb] Strange Pseudosymmetry Effects

Dear Eddie, dear all According to ftp://ftp.ccp4.ac.uk/ccp4/newsletter/jun_95/, this article appeare in Newsletter June 95. It is mentioned in the table of contents, "Correction on perfection: primary extinction correction in protein crystallography" by Polykarpov and Sawyer. Unfortunately, the

Re: [ccp4bb] visual mask editor?

Sehr geehrter Herr Hofkristallamt, Depending on your learning style, you might want to look into blender. https://www.blender.org/download/ Together with eMPV you can do some magic from scratch. You could also use any other CAD program end export the file one

Re: [ccp4bb] visual mask editor - why

Looks like the density manipulation/carving tools might be useful. Thx, BR From: CCP4 bulletin board On Behalf Of Jurgen Bosch Sent: Thursday, May 28, 2020 11:29 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] visual mask editor - why Give this a shot: https://www.eyesopen.com/afitt

Re: [ccp4bb] visual mask editor?

Yes, there are some ways to do it, more or less cumbersome. But after being already reprimanded for using old ccp4 stuff I was looking for a 21st century solution…sort of matrix-style…put you shades on, wave your hands, and done. Cheers, BR From: CCP4 bulletin board On Behalf Of Soisson,

Re: [ccp4bb] visual mask editor - why

Yes I have already pilfered useful parts of it in the scripts. Thx, BR From: Boaz Shaanan Sent: Thursday, May 28, 2020 11:59 To: b...@hofkristallamt.org Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] visual mask editor - why Hi Bernhard, Did you consider trying 'polder' in the phenix

[ccp4bb] visual mask editor - why

Maybe I should explain an example: Say coot detects an unmodelled blob (maybe a ligand). Now, I would like to do a number of things without biasing towards a model. Like comparing these map regions, excluding intrusion of a solvent mask, etc. Now could coot for example just generate a mask

Re: [ccp4bb] visual mask editor - why

Give this a shot: https://www.eyesopen.com/afitt At least in Vida from the same suite of programs, you can select such a blob as you describe and export it in a useful way. Jürgen ___ Jürgen Bosch, Ph.D. Division of