[ccp4bb] Treating Missing Reflections as Zero or Fcalc

My fault for not changing the thread subject! I'm sorry! Greetings to ccp4bb readers! This is a long-delayed reply to requests that I received after I posted an observation on the ccp4bb almost three years ago. (I think it was early 2012). The paper had not yet been published (pending final

Re: [ccp4bb] Free Reflections as Percent and not a Number

Greetings to ccp4bb readers! This is a long-delayed reply to requests that I received after I posted an observation on the ccp4bb almost three years ago. (I think it was early 2012). The paper had not yet been published (pending finalization of experiments unrelated to structural biology) a

Re: [ccp4bb] Free Reflections as Percent and not a Number

>We just had a chance to read this most interesting discussion. We would agree with Ian that jiggling or SA refinement may not be needed if refinement can in fact be run to convergence. However, this will be difficult to achieve for large structures, especially when only moderate to low resolution

Re: [ccp4bb] Balbes

Hi Jon, Thanks, got the answer. regards Atul On Thu, Nov 27, 2014 at 8:58 PM, Jon Agirre wrote: > Hi, > > the Balbes database is now nearly 3 years old, so obviously it won't use > that structure as template... and as Mark has correctly pointed out, Balbes > is a bit of an overkill for this pr

[ccp4bb] Free Reflections as Percent and not a Number

We just had a chance to read this most interesting discussion. We would agree with Ian that jiggling or SA refinement may not be needed if refinement can in fact be run to convergence. However, this will be difficult to achieve for large structures, especially when only moderate to low resoluti

Re: [ccp4bb] Balbes

Hi Mark, Thanks for your suggestion. I have already got the solution from Phaser. Just wanted to know the problem with Balbes, why it is taking random structures as template? regards Atul On Thu, Nov 27, 2014 at 8:34 PM, Mark J van Raaij wrote: > Just use Amore, Molrep or Phaser and give them

Re: [ccp4bb] Balbes

Hi, the Balbes database is now nearly 3 years old, so obviously it won't use that structure as template... and as Mark has correctly pointed out, Balbes is a bit of an overkill for this problem. Just follow his advice and you'll solve it in no time. MR tools are very automated and easy to use nowa

Re: [ccp4bb] Balbes

Just use Amore, Molrep or Phaser and give them the apo structure as model. I especially recommend Amore for first-time MRers, as it forces you to understand some basics of MR. And it runs very fast. Molrep and especially Phaser can probably solve more difficult problems with lower homology model

[ccp4bb] Balbes

Hi all, I am trying to solve complex structure of my proteins. Apo protein structure is already known. Balbes should take this structure as template for MR, whereas, it is taking some random proteins as template. I was wondering, whether it is synchronized with pdb or uses its own databank. Since

Re: [ccp4bb] large empty spaces in solved crystal structure

Hi, I'm inclined to say that you may have indexed your data with the wrong space group -your description violates the definition of a crystal. What happens if you index in P1 and resolve the x-tal using the structure from your current phases as an MR search model? This is assuming that you ha

[ccp4bb] large empty spaces in solved crystal structure

Dear all, I ran into a problem when I was solving a structure using SAD. After determining phase and building an initial model using AutoSol, I suddenly found that every two well ordered protein molecule layers were separated by a large empty space that extended across the entire crystal. Th

Re: [ccp4bb] omit map

Dear Rohit Kumar Singh, the ccp4 gui offers 'Calculate Omit Map' and 'Calculate Composite Omit Map' from the 'Map & Mask Utilities' menu. Neither GUI askes for much input and should be run with much further ado. Regards, Tim On Thu, Nov 27, 2014 at 07:05:09PM +0530, rohit kumar wrote: > dear a

[ccp4bb] omit map

dear all, can any one tell me how to calculate omit map in ccp4?. -- WITH REGARDS Rohit Kumar Singh Lab. no. 430, P.I. Dr. S. Gourinath, School of Life Sciences, Jawaharlal Nehru University New Delhi -110067

[ccp4bb] OT: Feedback on AutoITC200 system

Dear BB, I realise this isn’t a CCP4 (or even crystallography) related topic, however such is the vast and widely experienced nature of the community I thought this might be a good place to start. We have had our AutoITC200 system in place for around one year now (upgraded from the manual syst