Re: [ccp4bb] high B factor

I also should backtrack a little. I assumed that Anandhi has good data reduction with good statistics, no data problems (such as twinning), a good molecular replacement solution, and refinement stuck, but he didn't give any of those details. What are the R and Rfree values, the RMS bonds &

Re: [ccp4bb] high B factor

Okay, I'm an idiot. The letter did say molecular replacement. I have no excuse for being so blind. I do stand by my statement: I don't see that an average B factor of 82 A^2, by itself, indicates any serious problem with a model at 2.65 A resolution. I have generally found that the

Re: [ccp4bb] high B factor

Did I miss a follow-up letter with more information? All I've seen is that Dr. Anandan said that there was a model based on 2.65 A resolution data with an average B factor of 82 A^2. Does this fact alone call for weeks of work attempting to remove model bias? Dr. Anandan didn't even say this

Re: [ccp4bb] high B factor

Hard to comment on PHEIX refne but check these things: such results must either mean your molecular replacement solution is wrong or there is something wrong with the data. Refinement packages will always try to match the Mean B factor to the Wilson plot B so I think the problem must be before

Re: [ccp4bb] high B factor

By the way, I would recommend running simulated annealing with each composite omit map you generate to help in overcoming model bias. -Daniel On Sat, Nov 10, 2018 at 9:31 PM Daniel M. Himmel, Ph. D. < danielmhim...@gmail.com> wrote: > Anandhi, > > Assuming the data reduction went well, and

Re: [ccp4bb] high B factor

Anandhi, Assuming the data reduction went well, and you're in the right space goup, there could be a lot of model bias in your structure stemming from the starting model. There are a lot of things to try. I would set all the B-factors to an artificially low B-factor to help de-mask errors.

Re: [ccp4bb] high B factor

Dear Anandhi, you might be interested in PMID: 29752562. BW, Oliviero On 09.11.2018 01:30, Anandhi Anandan wrote: Hello everyone, I am trying to solve the structure of a protein with a bound ligand at 2.65 A resolution. XDS was used for data reduction, phaser-MR for molecular replacement

[ccp4bb] Antw: Re: [ccp4bb] Antw: Re: [ccp4bb] High B factor

CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of > > Matthias Barone [bar...@fmp-berlin.de] > > *Sent:* Friday, October 14, 2016 8:00 AM > > *To:* CCP4BB@JISCMAIL.AC.UK > > *Subject:* [ccp4bb] Antw: Re: [ccp4bb] High B factor > > > > Picking up the mail of Pav

Re: [ccp4bb] Antw: Re: [ccp4bb] High B factor

- > > *From:* CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of > > Matthias Barone [bar...@fmp-berlin.de] > > *Sent:* Friday, October 14, 2016 8:00 AM > > *To:* CCP4BB@JISCMAIL.AC.UK > > *Subject:* [ccp4bb] Antw: Re: [ccp4bb]

Re: [ccp4bb] Antw: Re: [ccp4bb] High B factor

*From:* CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Matthias Barone [bar...@fmp-berlin.de] *Sent:* Friday, October 14, 2016 8:00 AM *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* [ccp4bb] Antw: Re: [ccp4bb] High B factor Picking up

Re: [ccp4bb] Antw: Re: [ccp4bb] High B factor

think to color it by occupancy. > > -- > *From:* CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Matthias > Barone [bar...@fmp-berlin.de] > *Sent:* Friday, October 14, 2016 8:00 AM > *To:* CCP4BB@JISCMAIL.AC.UK > *Subject:* [ccp4bb] Antw

Re: [ccp4bb] Antw: Re: [ccp4bb] High B factor

] High B factor Picking up the mail of Pavel, Phenix refines occupancies.. If you expect the loops to be disordered, did you try to lower the occupancy of these residues, following Ethan Merritt statement that "general uncertainty [...] is represented better by occupancy <1 rather than an a

Re: [ccp4bb] High B factor

I agree that it would certainly be bad if your model was inconsistent with the Wilson B. When I first ran into people who were worried about this I recommended that they calculate the Wilson B of their model, not look at the average B as a proxy. You can calculate structure factors from your

[ccp4bb] Antw: Re: [ccp4bb] High B factor

Picking up the mail of Pavel, Phenix refines occupancies.. If you expect the loops to be disordered, did you try to lower the occupancy of these residues, following Ethan Merritt statement that "general uncertainty [...] is represented better by occupancy <1 rather than an arbitrary large B

Re: [ccp4bb] High B factor

> If you are still worry about your Bfactor, you could try TLS, > Or NCS, but SA with MLHL might be better. (A joke).

Re: [ccp4bb] High B factor

Sunanda, As "common people", ... "agreement" don't means for me "equals" ... So I hope I'm not so "incorrect" if I keep one mind the Wilson B as the model refinement goes and the average B factor changes with different strategies. If you are still worry about your Bfactor, you could try

Re: [ccp4bb] High B factor

It seems to be common for people to make the incorrect assumption that the average of the atomic B factors in the PDB file should equal the Wilson B. The Wilson B is actually a weighted average of the individual B factors where the weighting is rather mysterious, but the small B factors have

Re: [ccp4bb] High B factor

Sorry for not making the problem clear! The overall B factor for the 3.0 A structure is around 98.00 A*2. Most of the deposited structures in the PDB site around this resolution has an av B around 70 A*2 All other statistics looks fine. I got a warning message while trying to upload the

Re: [ccp4bb] High B factor

Hi Sunanda They don't need to be "better" ... they need to be in agreement with you experimental B factor ... Wilson plot? Best Carlos On 10/13/16 04:59, sunanda williams wrote: Hi all, I have a structure at 3.0 A and R/Rfree of 24/28. The mean B value is around 98. The B value is

Re: [ccp4bb] High B factor

I fully agree with Dale in not understanding what the problem is. Perhaps I have a better chance if you clearly explain what exactly you mean by "is there any way to better the B factors". Pavel On Thu, Oct 13, 2016 at 12:57 PM, Dale Tronrud wrote: >I'm sorry but I

Re: [ccp4bb] High B factor

Hi Sunanda, If you model is good, high average B-factors are just caused by the quality of your data. You can sometimes improve this a bit by careful reprocessing (e.g. by not using the last frames where radiation damage really kicked in). Sometimes you can have a better crystal and your data

Re: [ccp4bb] High B factor

I'm sorry but I don't understand what your problem is. Do you think the B factors are too small for a 3A data set? A range of 70 to 75 is a little smaller than usual but probably not out of bounds. Dale Tronrud On 10/12/2016 7:59 PM, sunanda williams wrote: > Hi all, > I have a structure at

Re: [ccp4bb] High B-factor for metal

Dear Kavyashree, I expect that you have a low-occupancy cadmium ion bound. If your resolution is not too low, say better than 2.5 Å, I would try to refine the occupancies of all cadmium ions. They are so big that it should work. If this does not work, you can make a rough estimate of the

Re: [ccp4bb] High B-factor for metal

On 05/11/2011 10:30 AM, ka...@ssl.serc.iisc.ernet.in wrote: Dear users, I have refined a structure in R3 with cadmium bound to it, which was present in the crystallization condition. There are 2 chains in the asu. The structure is twinned. R and Rfree is around 22% and 28%. One of the

Re: [ccp4bb] High B-factor for metal

: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of ka...@ssl.serc.iisc.ernet.in Sent: Wednesday, May 11, 2011 12:00 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] High B-factor for metal Dear Sir, The resolution is 2.35Ang. I was trying to refine Cadmium occupancy using

Re: [ccp4bb] High B-factor for metal

Wouldn't it be possible to estimate the occupancy of the Cd-ions from the peak heights of a DANO-map. Especially useful if there is doubt about the presence of Cd at this low occupied site. Cheers, Georg Am 11.05.11 11:33, schrieb herman.schreu...@sanofi-aventis.com: Dear Kavyashree, I

Re: [ccp4bb] High B-factor for metal

@JISCMAIL.AC.UK] On Behalf Of ka...@ssl.serc.iisc.ernet.in Sent: Wednesday, May 11, 2011 12:00 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] High B-factor for metal Dear Sir, The resolution is 2.35Ang. I was trying to refine Cadmium occupancy using the option of SAD data directly in refmac