Re: [ccp4bb] AW: Re: AW: [ccp4bb] tNCS problem

[Green, Todd Jason]

On a side note, I assume that you have searched with both P2 as well as P21 for 
your space group. If not, I will point out that there are 265 submissions in 
the rcsb for the P2 space group, compared to 20,698 for P21. That makes P2 
fairly rare. Good Luck! - Todd






Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von ???
Gesendet: Dienstag, 8. Mai 2018 16:41
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [EXTERNAL] [ccp4bb] tNCS problem



Dear all, Recently, I collected a data set of a crystal of a big protein, which 
contains 1000 amino acids. I processed the data to P2. But the data set has 
tNCS problem. I want to do molecular replacement. Is there anyone know how to 
deal with this problem? Thanks, JiYG

[ccp4bb] AW: Re: AW: [ccp4bb] tNCS problem

[Herman . Schreuder]

Dear JiYG,

With an unknown number of 1000 aa monomers, you definitively have a challenging 
project!
In that case, you will have to do some homework before running phaser:

1)  The Matthews program should give you an indication how many monomers to 
expect.

2)  P2 is a very low symmetry space group, so it might indeed be a good 
idea to process in P1 and run MR in P1.

3)   With a lot of crashes (clashes?) you may have to truncate exposed 
loops from your model. If a number of homologous structures are available in 
the pdb, you could superimpose them, truncate the loops that are different and 
use the ensemble as a search model.

4)  How good is your search model, e.g. what is the %identity or homology? 
If the model is quite remote, MR might be difficult.

In the CCP4, there is now a whole collection of automatic MR packages: Molrep, 
MrBUMP, Balbes, AMPLE, MoRDA, SIMBAD etc. you could try these as well. It will 
mainly take CPU time, not your time.

Good luck!
Herman

Von: 苏纪勇 [mailto:sujy...@nenu.edu.cn]
Gesendet: Dienstag, 8. Mai 2018 17:03
An: Schreuder, Herman /DE
Cc: CCP4BB@JISCMAIL.AC.UK
Betreff: [EXTERNAL] Re: AW: [ccp4bb] tNCS problem

Dear Herman, I tried phaser. It worked. But there are a lot of crashes in the 
structure. Meanwhile, R factors could not be lowered. I tried to use P1 to 
process the data, but I do not know how many monomers in the asymetric unit. 
Bests, JiYG
On 05/08/2018 22:50, 
herman.schreu...@sanofi.com wrote:
Dear JiYG,

Unless the tNCS has caused processing problems, Phaser should automatically 
deal with tNCS and I would recommend to just give it a try. If it fails, you 
could try more sophisticated approaches.

Best,
Herman

Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von ???
Gesendet: Dienstag, 8. Mai 2018 16:41
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [EXTERNAL] [ccp4bb] tNCS problem

Dear all, Recently, I collected a data set of a crystal of a big protein, which 
contains 1000 amino acids. I processed the data to P2. But the data set has 
tNCS problem. I want to do molecular replacement. Is there anyone know how to 
deal with this problem? Thanks, JiYG