Re: [ccp4bb] 2Fo-Fc maps in Coot vs. Pymol

I think this is part of the problem. https://pymolwiki.org/index.php/Normalize_ccp4_maps El lun., 30 de sep. de 2019 a la(s) 10:09, Chris Fage (fage...@gmail.com) escribió: > Hi Paul, > > After exporting the maps from Coot, they are directly comparable in Pymol. > That's quite a convenient featur

[ccp4bb] Job Posting: Beamline Scientist at the Swiss Light Source

Dear All, I would like draw your attention to the new position available in the Macromolecular Crystalligraphy group at the Swiss Light Source. We are looking for a Beamline Scientist Macromolecular Crystallography Your tasks You will be a part of the Macromolecular Crystallography (MX) team a

[ccp4bb] General interest

Dear Colleagues, I draw your attention to my posting at the IUCr Committee on Data Public Forum ( https://forums.iucr.org/viewtopic.php?f=39&t=423 ) about the recent USA National Academies Report on Reproducibility and Replicability in Science. Best wishes, John Emeritus Professor John R Helliwe

Re: [ccp4bb] 2Fo-Fc maps in Coot vs. Pymol

Hi Paul, After exporting the maps from Coot, they are directly comparable in Pymol. That's quite a convenient feature I was never aware of. Thanks! Yes, I was comparing the map from FFT in Coot and PyMOL. Best, Chris

Re: [ccp4bb] 2Fo-Fc maps in Coot vs. Pymol

On 30/09/2019 13:00, Chris Fage wrote: > Dear Paul, Herman, Robbie, and Santosh, > > > My version of Pymol doesn't support loading of mtz files. I think it's > only in the incentive version. > > Paul wrote: "No need to do this - just export the map (or the map > fragment)." I'm not sure how to do t

Re: [ccp4bb] 2Fo-Fc maps in Coot vs. Pymol

Hi Robbie, I guess that solves part of the problem. But when I generate a new set of maps with F1=FWT and PHI=PHWT and load them into Pymol, they are still not comparable to those in Coot. Again, the maps for ligands 1 and 2 in Pymol look about the same. Best, Chris

Re: [ccp4bb] 2Fo-Fc maps in Coot vs. Pymol

Hi Chris, You made an Fobs map not a 2Fo-Fc map. You can leave sigma empty if you want to make a map in this case. Cheers, Robbie > -Original Message- > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of > Chris Fage > Sent: Monday, September 30, 2019 14:00 > To: CCP4

Re: [ccp4bb] 2Fo-Fc maps in Coot vs. Pymol

Dear Paul, Herman, Robbie, and Santosh, Thanks for your quick replies. The FFT-generated maps and mtz maps look roughly equivalent in Coot, but there are minor differences even at the same e/A^3 level (the mtz maps actually look a bit weaker). I generated them using the default settings in FFT: s

Re: [ccp4bb] 2Fo-Fc maps in Coot vs. Pymol

Are you sure you used the right columns in FFT? AFAIK Coot uses FWT and PHWT. I thought the more recent PyMOL versions finally had MTZ support, or is this just for the incentive version? Also if it is for looking at the structure and making figures, perhaps try CCP4mg. It has proper MTZ support

[ccp4bb] AW: [EXTERNAL] [ccp4bb] 2Fo-Fc maps in Coot vs. Pymol

Dear Chris, The first thing I would do is to load the FFT map (not the mtz) in coot and see how densities of both ligands compare in that case. Also in FFT, did you calculate exactly one unit cell, or did you select a region just around the protein? If you contour the maps in terms of RMSD, the

Re: [ccp4bb] 2Fo-Fc maps in Coot vs. Pymol

On 30/09/2019 11:36, Chris Fage wrote: I recently obtained structures of a protein bound to two different small molecules. When viewing the structures in Coot with a similar contour setting, the 2Fo-Fc map around ligand 1 is clearly much weaker than that around ligand 2.However, after generat

Re: [ccp4bb] Reg: water pentagon at dimer interface

Thank you all for the overwhelming responses. To answer your questions The protein is monomer in solution. Complex formation significance score shown by PISA is "Zero" and suggested that the interface does not play any role in complex formation and seems to be a result of crystal packing only. Th

[ccp4bb] 2Fo-Fc maps in Coot vs. Pymol

Dear All, I recently obtained structures of a protein bound to two different small molecules. When viewing the structures in Coot with a similar contour setting, the 2Fo-Fc map around ligand 1 is clearly much weaker than that around ligand 2.However, after generating 2Fo-Fc maps in FFT and loading

[ccp4bb] Final reminder: MicroED Workshop 2019

Final reminder: the application deadline for the 2019 MicroED workshop is October 1, 2019. From the initial announcement: The Gonen Laboratory will hold the 5th MicroED Workshop in 2019. The workshop will be held at the MicroED Imaging Center at the UCLA David Geffen School of Medicine during