Re: [ccp4bb] model bias

And given that all these maps (Fo, Fc, and their differences) are made without the F000 term and so have average value zero, it is highly likely that Fc will be negative in the region of the deleted subunit (solvent is the lowest density in the model except for the chinks of vacuum between the

Re: [ccp4bb] model bias

This is hard to understand/impossible, at least in terms of simple 2fo-fc and fo-fc maps. We can think of a difference map as the difference between two maps, like fo-fc map = fo map - fc map. There is no model in the region, since you deleted it, so Fc=0, and Fo-Fc negative => Fo<0, so 2fo-fc

Re: [ccp4bb] model bias

A round of refinement with simulated annealing followed by minimization should address your concern. Pavel On Wed, Oct 11, 2017 at 4:48 PM, Karsten Dreifus wrote: > Dear all, > I have a 120 aa protein. Matthews coefficient indicates 3 mol in asu. > Molrep (template with

[ccp4bb] model bias

Dear all, I have a 120 aa protein. Matthews coefficient indicates 3 mol in asu. Molrep (template with 70 % seq identity) finds three NCS molecules (the template model has only 1 chain as it is in different space group). Now, REFMAC refines it to 25/30 % R/RFREE. I was just worried about model

[ccp4bb] model bias

Dear CCP4 users, I am currently solving a structure (2.8-2.9 A resolution) of a protein complexed with a ligand using MR with the apo-form of this protein as model (resolution of the model is 2.4). After MR-phasing I performed a regular autobuild run giving me good outputs and thus I refined

Re: [ccp4bb] model bias

If you know what residues are likely to be involved, then set their occupancies to 0.0 (In coot go to Measures - Residue info - edit occ) then do a few cycles of refinement with that model, and then see if there is difference density for those residues... Quicker than an omit map procedure.

Re: [ccp4bb] model bias

Hello, I would certainly try the usual approaches (map coefficients that are less sensitive to model-bias, i.e. Sigmaa; OMIT maps - there are several of these which can be calculated). In addition, you may have a look at the approach of Liu and Xiong (2014, J. Mol. Biol. 426, 980-993). It is

Re: [ccp4bb] model bias

Dear Aleksandar, I did use SA-OMIT map feature in Phenix, implemented by Tom Terwilliger. I would strongly recommend you to use this feature. Remove the suspicious residues from the pdb and run first SA-omit map in phenix with default settings, and later with different starting temperatures. Make

Re: [ccp4bb] model bias

Hi Aleks: Maybe you can try CNS ( Initial refinement by simulated annealing) also. It may help to get rid of the model bias and takes short time to run. Xiaodi Date: Wed, 29 Apr 2015 13:52:53 +0200 From: frederic.velli...@ibs.fr Subject: Re: [ccp4bb] model bias To: CCP4BB@JISCMAIL.AC.UK

Re: [ccp4bb] model bias

Dear All, thank you all for your suggestions and support. The quick look (by removing interacting AA and subsequent refinement with and without little SA) revealed that some AAs are mislocated and indeed seem to be more directed to the density belonging to the ligand. So, I will try some of

Re: [ccp4bb] model bias

You dont give the resolution of your data. There are always things to check 1) space group - could it be P222 or P21 2 2 or P 21 21 2 or P2 21 2 etc etc - there are 8 possibilities. You can use absences along the axial lines to help decide on the screw axes, but these can be misleading if

Re: [ccp4bb] model bias

Hi Manoj, Following on from Poul's reply, and maybe whilst you are waiting to get derivatives ;) you could try something like the following for getting around the model-bias-after-borderline-MR-issue. 1) generate a prime--switch'd map from resolve. 2) use this map to prune your model (be quite

[ccp4bb] model bias

Hi all, I am working with a protein that have 28% similar to my MR template. I have processed data in HKL2000 for one of my crystal and I got unique sol in space group P212121. with LLG 131 and TFZ score 13.5 I have used buccaneer and coot for model building and my Rfee came to 45%. I

Re: [ccp4bb] model bias

Great that you have MR phases - it will help you identify heavy-atom sites for phasing and perhaps even the sulphur sites will be enough. Poul On 11/08/2009, at 20.33, ManojSaxena wrote: Hi all, I am working with a protein that have 28% similar to my MR template. I have processed data in

[ccp4bb] model bias: phaser + prime-and-switch VS simulated annealing in phenix VS simulated annealing in cns + prime and switch

First off sorry for the cross post across bbs I have a molecular replacement solution for a single site mutant for data that goes out to 2.8 A. After molecular replacement in phaser I run the following and examine the maps for bias from the model. Option1: simluated annealing refinement in