Re: [ccp4bb] low resolution data refinement

2023-11-21 Thread Albert Castellvi Toledo
Also forget to observe side chains at 4A! At this resolution is crucial to critically assess the position of each amino acid in your model, taking into account factors such as hinges in your structure, hydrophobic and hydrophilic regions, and the types of contacts between secondary structure el

Re: [ccp4bb] low resolution data refinement

2023-11-21 Thread Albert Castellvi Toledo
Hello, At low resolutions, model bias becomes a significant issue, capable of yielding inaccurate MR solutions even with favorable figures of merit. In my experience, it is always necessary to validate MR solutions at low resolution. One effective approach involves systematically omitting sma

[ccp4bb] CryoEM Current Practices Roundtable 12/14/2023

2023-11-21 Thread Christina Zimanyi
Dear all, The NIH Transformative High Resolution CryoEM Program service centers will be hosting a special roundtable discussion in December as part of our CryoEM Current Practices webinar series. Time: Thursday, December 14, 2023 at 9 AM pacific / 12 PM eastern time Topic: Do you see what I see?

Re: [ccp4bb] low resolution data refinement

2023-11-21 Thread Eleanor Dodson
Q0. Echoing Randy - how accurate is your starting model - Xray structure at resolution 1.5A or high quality EM or NMR?? Q1. Are the solutions the same? There is a CCP4 tool in ccp4i2 - Match my model which will check this taking into account symmetry and origin shifts. On Tue, 21 Nov 2023 at 14

Re: [ccp4bb] low resolution data refinement

2023-11-21 Thread Randy John Read
Hi, Whether or not you’ll get anything useful from a 4.3 A MR solution depends on your question — maybe you’re interested in something large-scale like complex formation or domain movement, in which case it could tell you something. In any case, it’s important to have a good starting model. Unl

[ccp4bb] RES: [ccp4bb] low resolution data refinement

2023-11-21 Thread Rafael Marques
Hi, As the others have already mentioned, it is hard to get any decent MR solution at this resolution. The best thing to do would be to set up more crystal plates and harvest crystals growing at different conditions. You also have not mentioned where you diffracted your crystals. If you did it

Re: [ccp4bb] low resolution data refinement

2023-11-21 Thread Paul Emsley
On 21/11/2023 12:02, Yahui Liu wrote: Dear all, I got a protein crystal dataset of 4.3 A and would like to some the structure with MR. Now I am suffering with the refinement. Just for the record, then intention of refinement is not to make you suffer. Paul. ##

Re: [ccp4bb] low resolution data refinement

2023-11-21 Thread Eleanor Dodson
Sorry - the simplest answer - is get higher resolution data! But there are some improvements possible. How clear is your MR solution. What is the similarity between model and your sequence? Etc. On Tue, 21 Nov 2023 at 12:03, Yahui Liu wrote: > Dear all, > I got a protein crystal dataset of 4.3

[ccp4bb] low resolution data refinement

2023-11-21 Thread Yahui Liu
Dear all, I got a protein crystal dataset of 4.3 A and would like to some the structure with MR. Now I am suffering with the refinement. I used both Refmac and Phenix. Someone could give me a hand or any suggestions? All the best #

Re: [ccp4bb] CCP4 Study Weekend 2024 - Early bird registration including standard student bursary deadline EXTENDED TO FRIDAY 24TH NOVEMBER!

2023-11-21 Thread Karen McIntyre - STFC UKRI
The early bird deadline for in-person registration for the CCP4 Study Weekend 2024 has been extended until Friday 24th November. Regards Karen McIntyre CCP4 Project Administrator CCP4 Equality, Diversity and Inclusion Champion Member of SCD ED&I Working Group Science and Technology Facilities