Re: [ccp4bb] what to do with disordered side chains
Just create a new tag, say _atom_site.imaginary_site, which is either true or false for every atom. Then everyone would be able to either filter out the fake atoms or leave them in, without ambiguity or confusion. Aside from being a binary rather than continuous parameter, how exactly does this suggestion differ from the occupancy column of the pdb, that we already have? I guess I missed it in the flurry of replies to this thread over the last few days, but what exactly is so terrible about keeping the atoms (since you have chemical evidence from protein sequence that they are there, and even if there is X-ray damage they were originally there and are likely still there in a subset of the molecules), but changing occupancy to zero as an acknowledgment that your data does not provide evidence to support a specific atomic position for these atoms? Evette S. Radisky, Ph.D. Assistant Professor Mayo Clinic Cancer Center Griffin Cancer Research Building, Rm 310 4500 San Pablo Road Jacksonville, FL 32224 (904) 953-6372
[ccp4bb] Paper retraction
Dear young (and not so young) impressionable friends of Dark Matter, Thank you for all the kind requests for my PRL paper [1]. Unfortunately, I have to retract the paper, but buying me a beer next time we meet might help me to forget you ever asked for it. One (!) respondent got it right away, on content, timestamp, and PRL formatting. One other respondent recognized a problem, clearly smelled a rat, but did not quite tell me to take a hike. One respondent became suspicious given the date (but, there IS in fact an April 1st Vol 160(13) in PRL). These 3 fellows are herewith recognized but therefore not allowed to play anymore. The majority of respondents is still in the game: What I wrote [1], fellows, is of course composted matter of the darkest kind (well rotten garbage), albeit carefully crafted in convincing (pseudo)scientific language. That is the way con artists almost always work. Also in Science (pardon, science). So, I encourage you to turn this into an educational exercise: First, let's be Bayesian here right away. What is the prior probability -without having examined the evidence [1]- that a cantankerous curmudgeon who occasionally dabbles around on the CCP4 board all of a sudden conceives an apparently brilliant solution to a problem that has preoccupied true experts for decades? LOW, my friends. Such a strong claim should immediately trigger corresponding scrutiny of the evidence in view of known prior knowledge [2 and refs therein]. Now the question - what in fact is (totally) wrong in that one-page paper [1]? (Those who already know and wisely ignored my posting might hold off for a few days and give others a chance to exercise critical review and a little bit of freshmen physics). Responses (or practice reviewer reports, post-publication letters to the editor) perhaps to me directly, to keep clutter on the board low and to encourage more daring/scathing review. I'll confidentially summarize the best then on BB. Best regards, BR [1] http://www.ruppweb.org/select/Rupp_2011_Phys_Rev_Letters_160_13_B-factor.pdf [2] http://www.ruppweb.org/cvs/br/rupp_2010_JApplCryst_reasoning.pdf - Bernhard Hieronimus Rupp, Hofkristallrat a.D. 001 (925) 209-7429 +43 (676) 571-0536 b...@ruppweb.org hofkristall...@gmail.com http://www.ruppweb.org/ - Hey voll chillig hier in se lounge but you must sofort aufhoeren zu chillen and stattdessen aufraeuming your wohnzimmer denn it looks a little staubig and se chips on se hofkristallloungetisch are mindestens a year old -
Re: [ccp4bb] program to calculate electron density at x,y,z
On Apr 1, 2011, at 4:00 PM, Ed Pozharski wrote: I need to calculate the electron density values for a list of spatial locations (e.g. atom positions in a model) using an mtz-file that already contains map coefficients. To write my own code may be easier than I think (if one can manipulate mtz columns, isn't the only problem left how to incorporate symmetry-related reflections?), but I would need an alternative at least for troubleshooting purposes. So, Does anyone know of a software tool that can calculate point electron density for every atom in a structure? If I would have to bring a dependency into this, the best choice for me would be clipper libs. Hi Ed, You'd have to convert the map to ccp4 or XPLOR format, but once you've done that it's pretty straightforward to get the values at atom positions using Chimera, pretty much as described here: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2011-March/006202.html except skipping the part where you average them across a residue. --Eric Eric Pettersen UCSF Computer Graphics Lab
Re: [ccp4bb] what to do with disordered side chains
I guess I missed it in the flurry of replies to this thread over the last few days, but what exactly is so terrible about keeping the atoms (since you have chemical evidence from protein sequence that they are there, and even if there is X-ray damage they were originally there and are likely still there in a subset of the molecules), but changing occupancy to zero as an acknowledgment that your data does not provide evidence to support a specific atomic position for these atoms? Some users might pull up the structure, see those atoms, and think their positions were based on data, which they were not, and then draw conclusions based on them. I agree that occ=0 is tantamount to the suggestion you queried, however. A somewhat key question might be: across the various molecular visualization programs, what is the default way to handle atoms with occ=0? Perhaps those programs might be the best place to fix the problem... JPK *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program cel: 773.608.9185 email: j-kell...@northwestern.edu ***
Re: [ccp4bb] what to do with disordered side chains
Doing something sensible in the major software packages, both for graphics and for other analysis of the structure, could solve the problem for most users. But nobody knows what other software is out there being used by individuals or small groups. And the more remote the authors of that software are from protein structure solution the more likely it is that they have not/will not properly handle atoms with zero occupancy or high B values, for example. I am absolutely positive that there is software that does its voodoo on ATOM/HETATM records and pays absolutely no attention to anything beyond the x, y, z coordinates (i.e. beyond column 54). Frances Bernstein = Bernstein + Sons * * Information Systems Consultants 5 Brewster Lane, Bellport, NY 11713-2803 * * *** *Frances C. Bernstein * *** f...@bernstein-plus-sons.com *** * * *** 1-631-286-1339FAX: 1-631-286-1999 = On Sat, 2 Apr 2011, Jacob Keller wrote: I guess I missed it in the flurry of replies to this thread over the last few days, but what exactly is so terrible about keeping the atoms (since you have chemical evidence from protein sequence that they are there, and even if there is X-ray damage they were originally there and are likely still there in a subset of the molecules), but changing occupancy to zero as an acknowledgment that your data does not provide evidence to support a specific atomic position for these atoms? Some users might pull up the structure, see those atoms, and think their positions were based on data, which they were not, and then draw conclusions based on them. I agree that occ=0 is tantamount to the suggestion you queried, however. A somewhat key question might be: across the various molecular visualization programs, what is the default way to handle atoms with occ=0? Perhaps those programs might be the best place to fix the problem... JPK *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program cel: 773.608.9185 email: j-kell...@northwestern.edu ***
Re: [ccp4bb] what to do with disordered side chains
I think Frances is right, i.e. most non crystallographers ignore anything beyond the x, y, z coordinates (i.e. beyond column 54) [as Frances wrote]. Thus if a crystallographer put in coords that he/she does NOT see, even with OCC=0, or an enormously large Bfactor, these coords are usually treated in just the same way that experimentally observed coords are treated. Thus my feeling is that if one does NOT see the coords in the electron density, they should NOT be included, and let someone else try to model them in, but they should be aware that they are modeling them. Joel L. Sussman On 3 Apr 2011, at 06:15, Frances C. Bernstein wrote: Doing something sensible in the major software packages, both for graphics and for other analysis of the structure, could solve the problem for most users. But nobody knows what other software is out there being used by individuals or small groups. And the more remote the authors of that software are from protein structure solution the more likely it is that they have not/will not properly handle atoms with zero occupancy or high B values, for example. I am absolutely positive that there is software that does its voodoo on ATOM/HETATM records and pays absolutely no attention to anything beyond the x, y, z coordinates (i.e. beyond column 54). Frances Bernstein = Bernstein + Sons * * Information Systems Consultants 5 Brewster Lane, Bellport, NY 11713-2803 * * *** *Frances C. Bernstein * *** f...@bernstein-plus-sons.com *** * * *** 1-631-286-1339FAX: 1-631-286-1999 = On Sat, 2 Apr 2011, Jacob Keller wrote: I guess I missed it in the flurry of replies to this thread over the last few days, but what exactly is so terrible about keeping the atoms (since you have chemical evidence from protein sequence that they are there, and even if there is X-ray damage they were originally there and are likely still there in a subset of the molecules), but changing occupancy to zero as an acknowledgment that your data does not provide evidence to support a specific atomic position for these atoms? Some users might pull up the structure, see those atoms, and think their positions were based on data, which they were not, and then draw conclusions based on them. I agree that occ=0 is tantamount to the suggestion you queried, however. A somewhat key question might be: across the various molecular visualization programs, what is the default way to handle atoms with occ=0? Perhaps those programs might be the best place to fix the problem... JPK *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program cel: 773.608.9185 email: j-kell...@northwestern.edu ***
