Hi all-- I'm trying to make a 2Fo-Fc map with density wrapped around my asymmetric unit to make a figure showing density for my sub-8Å structure. I am not building into this map or doing MR. My model was refined in Phenix.refine (R's in the high 30's), and so I have the output model .pdb and the output map coefficients .mtz. When I input these into cut_out_density, the only "map labels" input options it gives me are 2FOFCWT, PH2FOFCWT, which seem fine. Using either box, sphere, or model for the cutout type, I get a VERY nice looking map that looks extremely solvent flattened and tight around my model, albeit still to 8Å. Suspicious of anything that looks good, I went to try the same thing in FFT (CCP4). There I generated a simple map (using the same .mtz) to cover all atoms in a pdb file- the same model I put into cut_out_density. For the input I selected 2FOFCWT and PH2FOFCWT, leaving Sigma and Weight unassigned. The map that comes out of this looks terrible, with a lot of noise and little density corresponding to the model aside from what one might expect from a very poor resolution experimental map. I've also tried using FFT in Phenix to do the same thing, and it gives like better maps than CCP4 FFT but worse than cut_out_density. It almost appears as if there is some additional solvent flattening going on, which I know happens at the beginning of refinement, but that should be intrinsic to the map coefficients file which is common to everything I've tried. My questions are (1) what should I use for what I am trying to do (just display 2Fo-Fc density around asymmetric unit for a figure) and (2) what is the difference between what these three programs (cut_out, FFT-CCP4, FFT-Phenix) are calculating? The inputs are exactly the same -- mtz (2FOFCWT and PH2FOFCWT) and pdb output from refinement. Thanks for the help, Yunji
Hi Yunji, you can try phenix.map_box which is an alternative implementation of the idea of extracting a model and a map in a box around selected atoms. Since I wrote it I know for the matter of fact that it does what I just wrote above: extracts model and map in a box around selected atoms, and nothing else. An example of using it: phenix.map_box model.pdb map_coefficients.mtz selection="chain A and resseq 1:10" label='2FOFCWT_no_fill' and it will output 4 files: one PDB file with selected atoms in the box, one MTZ file with map coefficients and two actual map files in CCP4 and X-plor formats, so you have choices which one is more convenient for you to use. Let me know if you have questions. Pavel On 2/19/13 11:06 AM, Yunji Wu wrote:
Hi all--
I'm trying to make a 2Fo-Fc map with density wrapped around my asymmetric unit to make a figure showing density for my sub-8Å structure. I am not building into this map or doing MR. My model was refined in Phenix.refine (R's in the high 30's), and so I have the output model .pdb and the output map coefficients .mtz. When I input these into cut_out_density, the only "map labels" input options it gives me are 2FOFCWT, PH2FOFCWT, which seem fine. Using either box, sphere, or model for the cutout type, I get a VERY nice looking map that looks extremely solvent flattened and tight around my model, albeit still to 8Å.
Suspicious of anything that looks good, I went to try the same thing in FFT (CCP4). There I generated a simple map (using the same .mtz) to cover all atoms in a pdb file- the same model I put into cut_out_density. For the input I selected 2FOFCWT and PH2FOFCWT, leaving Sigma and Weight unassigned. The map that comes out of this looks terrible, with a lot of noise and little density corresponding to the model aside from what one might expect from a very poor resolution experimental map. I've also tried using FFT in Phenix to do the same thing, and it gives like better maps than CCP4 FFT but worse than cut_out_density. It almost appears as if there is some additional solvent flattening going on, which I know happens at the beginning of refinement, but that should be intrinsic to the map coefficients file which is common to everything I've tried.
My questions are (1) what should I use for what I am trying to do (just display 2Fo-Fc density around asymmetric unit for a figure) and (2) what is the difference between what these three programs (cut_out, FFT-CCP4, FFT-Phenix) are calculating? The inputs are exactly the same -- mtz (2FOFCWT and PH2FOFCWT) and pdb output from refinement.
Thanks for the help, Yunji _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
On Tue, Feb 19, 2013 at 11:06 AM, Yunji Wu
My questions are (1) what should I use for what I am trying to do (just display 2Fo-Fc density around asymmetric unit for a figure) and (2) what is the difference between what these three programs (cut_out, FFT-CCP4, FFT-Phenix) are calculating? The inputs are exactly the same -- mtz (2FOFCWT and PH2FOFCWT) and pdb output from refinement.
To answer the first question, I think it's sufficient to do one of two things: 1) carve out the mesh in PyMOL (or preferred graphics program) so it only covers the protein - you may have to experiment with the 'isomesh' command to find the perfect settings. You may not get perfectly rounded mesh where it extends beyond the protein, but at this resolution I doubt it will detract very much from the figure. 2) don't bother hiding the density outside the ASU, just show where the ASU is by displaying the cartoon model. This is what I've ended up doing in similar circumstances (for instance: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3382516/, Figure 3). It is mostly a matter of personal preference; I am very paranoid about phase bias and I've seen too many dishonest figures (e.g. 0.2 sigma density around a ligand claiming to be 1 sigma density, but without showing density for the nearby protein atoms). What you lose in aesthetic quality, you gain in realism. There are several differences between the programs themselves. I do not know what the default gridding is in CCP4; most of the time when we output a .ccp4 map it is using d_min/4. Another subtle issue is how big of a box around the protein to cut out, and how this affects the distribution of values and thus the meaning of the different sigma levels. Depending on how much bulk solvent you throw out, the density at "1 sigma" may change volume. Finally, I don't know whether cut_out_density does any kind of interpolation of values (like phenix.superpose_maps) or whether it instead preserves the original grid - if the former, this can conceivably lead to artifacts. Note that phenix.cut_out_density was really intended for preparing maps for use in MR - although I suspect many people end up using it for display purposes. All that aside, I'm a little concerned if the programs are producing that different output. Could you please send me the input files off-list so I can check whether something isn't working as intended? -Nat
participants (3)
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Nathaniel Echols -
Pavel Afonine -
Yunji Wu