[ccp4bb] Refmac flag to keep intensities, DANO and other columns in mtz output

[hari jayaram]

Hi ,
A trivial procedural question.

When running refmac from ccp4i , is there someway that I can have it only
add or substitute columns in the output mtz . I am currently running cad
after refmac to add back in my DAno column and the anomalous intensities ,
but was wondering if there is someway I can have refmac not drop the DAnos
and other columns from my input mtz in the output Mtz.

I seem to remember that older versions ( I am running the lates 6.1.3
provided refmac) did not drop these columns.

Thanks for your help
Hari

[ccp4bb] Grouped B-factors in Refmac5

[Jason Porta]

Hi everyone,

I am currently doing a rigid-body refinement with a 3 A dataset using Refmac5. 
I would like to calculate a grouped B-factor for each rigid body (instead of an 
overall B-factor). Is there a way I can do this in Refmac? Perhaps a command 
line trick? I would also like to simultaneously refine TLS groups. 

Any help and/or insight is appreciated.

Best regards,

Jason Porta
Graduate Student
Dept. Biochemistry  Molecular Biology
University of Nebraska Medical Center
Omaha, NE 68198
402-559-5533

[ccp4bb] how to refine RNA with two phosphate at 5' by phenix

[Lisa Wang]

hi all,
I have one structure contains dsRNA with two phosphate group at 5'.. I named
the first residue GDP and got a cif file by running phenix.elbow. Then I
refine my structure by running phenix.refine my.pdb my.cif. But the fist and
the second residue do not link with each other, that is no bond between O3*
of the fist residue and P of the second residue.
Please give me some idea. Thanks

Re: [ccp4bb] how to refine RNA with two phosphate at 5' by phenix

[Ralf W. Grosse-Kunstleve]

In the most recent phenix.refine version, the links should be automatic if the
backbone atom names are consistent with the naming for standard RNA residues.
Let me know if you're having problems with phenix 1.6 or 1.6.1.
Ralf



- Original Message 
From: William G. Scott wgsc...@chemistry.ucsc.edu
To: CCP4BB@JISCMAIL.AC.UK
Sent: Fri, April 2, 2010 5:07:09 PM
Subject: Re: [ccp4bb] how to refine RNA with two phosphate at 5' by phenix

Lisa Wang wrote:
 hi all,
 I have one structure contains dsRNA with two phosphate group at 5'.. I
 named
 the first residue GDP and got a cif file by running phenix.elbow. Then I
 refine my structure by running phenix.refine my.pdb my.cif. But the fist
 and
 the second residue do not link with each other, that is no bond between
 O3*
 of the fist residue and P of the second residue.
 Please give me some idea. Thanks


You have to explicitly link them.  Something like the following:

  geometry_restraints.edits {
bond {
  action = *add delete change
  atom_selection_1 = chain A and resid 1 and name O3\\*
  atom_selection_2 = chain A and resid 2 and name P
  symmetry_operation = None
  distance_ideal = 1.59
  sigma = 0.01
}
angle {
  action = *add delete change
  atom_selection_1 = chain A and resid 1 and name C3\\*
  atom_selection_2 = chain A and resid 1 and name O3\\*
  atom_selection_3 = chain A and resid 2 and name P
  angle_ideal = 120
  sigma = 1
}
  }

Re: [ccp4bb] CAQ

[Garib Murshudov]

It is part of the new dictionary we are preparing. Please find  
attached dictionary. It was not in the distributed dictionary.


Garib



CAQ.cif
Description: Binary data


On 2 Apr 2010, at 22:53, Vin Purp wrote:

Does anyone know what happened to the monomer CAQ? There are several  
structures in the RCSB with this ligand, and it is not in the  
sketcher/ccp4 monomer library (anymore?).  I also found it on the  
HIC-UP page as CAQso it seems at one time it used to be in the  
monomer library, and now is not (why not?).