Hi Markus, Just to make sure that things are clear: PDB-REDO adds missing side chains (that is a design choice) and it also adds missing loops if, and only if, there is a homologous template, there is sufficient density (although the criteria are rather forgiving), and the geometry of the loop stays okay upon real-space refinement. We do not build termini.
Your water example is a very nice one, this also happens for main chain atoms unfortunately. So unlike building parts of the protein that are chemically attached, please be careful with building waters. Only build ones that you are sure are waters. If you know that it is something else, but you don’t know what, please don’t build anything. I actually encourage students to build waters by hand. It is really simple and fast in Coot and it takes though a tour of you structure model enabling you to spot other issues. HTH, Robbie From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> On Behalf Of Rudolph, Markus Sent: Tuesday, March 14, 2023 15:58 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] [Sender Not Verified] Re: [ccp4bb] To Trim or Not to To Trim Hello Adrian, Provided a crystal contains the intact protein, as measured by mass spectrometry of a washed and dissolved crystal, leaving out side-chains makes little sense, even if some of them are destroyed by X-rays during data collection. I realize that most of the time, no such analysis is done on crystals, but if you assume all residues are there, then they must fit into the asymmetric unit. This includes N- and C-terminal residues, loops, and any side-chains without density. If side-chains won't fit, e.g. by crashing into symmetry neighbors, then the main-chain trace is very likely wrong. Thus, placing side-chains in a model is a good test for a correct main-chain trace. I understand many protein architects out there omit the terminal extensions and longer loops, and so do I. pdb_redo will automatically complete a model, so one could say - don't bother, as a user I'll retrieve the re-refined model from there. This is not my personal choice of model building, but a practical option from the viewpoint of downstream users. Sometimes, however, I see models where side-chains are truncated but the little density still present for the side-chain is interpreted by water (see image attached, in which case the water comes from a symmetry-related position). If one says "don't build what you don't see but build what the data tell you", a well-intended but mis-interpreted water molecule may occupy the density belonging to a truncated side-chain. I as a user would be confused by this, especially when using such models for ligand binding studies where water is important. In our SBDD projects, we always take B-values into account, and we welcome complete models or we complete and re-refine them ourselves. So yes, my 12 points go to the "let the B-factors take care of it” song. But really, I'm thankful for _any_ published structure, even with sup-optimal parameterization, experienced structural biologists can deal with that and communicate the information to their collaborators. <open_can_of_worms> ...which brings up the other evergreen, whether the PDB should be more strict about ... </open_can_of_worms> Best wishes, Markus On Fri, Mar 10, 2023 at 5:33 PM Goldman, Adrian <adrian.gold...@helsinki.fi<mailto:adrian.gold...@helsinki.fi>> wrote: Maybe simplest just to trim it back. I do worry that the presence of a wrong conformation will lead to inaccurate vdw clashes that could negatively affect other atoms. Sent from my iPhone > On 10 Mar 2023, at 18:25, Phil Jeffrey > <pjeff...@princeton.edu<mailto:pjeff...@princeton.edu>> wrote: > > On 3/10/23 4:05 AM, Julia Griese wrote: >> Hi all, >> My impression has been that the most common approach these days is to “let >> the B-factors take care of it”, but I might be wrong. Maybe it’s time to run >> another poll? >> Personally, I call any other approach R-factor cosmetics. The goal in model >> building is not to achieve the lowest possible R-factors, it’s to build the >> most physically meaningful, most likely to be correct, model. > > And I could call your approach "model cosmetics". > > If you can't see the side-chain, you don't know where it is and you probably > don't even know where the centroid of the distribution is. Only in the case > of very short side-chains with few rotamers can you make a reasonable volume > approximation to where the side-chain is and "let the B-factors" smear out > the density to cover a range of the projected conformations. > > For longer side-chains, if you put it in a single conformation, you are very > likely NOT coming close to correctly modeling the actual distribution of the > conformations. So let's circle back on "most likely to be correct model" and > ask what we *actually* know about where the atoms are. > > Put your disordered Arg in with 10 alternate conformations, each with a > refined relative occupancy, and then let the B-factors smear that lot out, > and that's your better model. > > Phil Jeffrey > Princeton > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > This message was issued to members of > www.jiscmail.ac.uk/CCP4BB<http://www.jiscmail.ac.uk/CCP4BB>, a mailing list > hosted by www.jiscmail.ac.uk<http://www.jiscmail.ac.uk>, terms & conditions > are available at https://www.jiscmail.ac.uk/policyandsecurity/ ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB<http://www.jiscmail.ac.uk/CCP4BB>, a mailing list hosted by www.jiscmail.ac.uk<http://www.jiscmail.ac.uk>, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
