Re: [ccp4bb] help with Buccaneer

[Christian Roth]

Depending on the actual thing you want to do. The options vary a lot.
If you have a MR model I strongly recommend gui2 and the MR mode. In that
case you supply the model and Buccaneer runs Refmac in advance to generate
the necessary phase information it needs.
If you have run CRANK2 in gui2  use the experimental phasing option in i2.
If you have external phases import and convert them with the HL converison
task
In i1 use f.e. phi and FOM (form ShelXE as input)
you might wnat tor tun density modification in the cas of NCS or
experimental phasing when this didn't happen already Difficult to say
without so less information.

Cheers

Christian



On Mon, Jan 23, 2017 at 7:52 AM, Vikram Dalal 
wrote:

> Thanks to all for suggestions.
>
>
>

Re: [ccp4bb] help with Buccaneer

[Vikram Dalal]

Thanks to all for suggestions.

Re: [ccp4bb] help with Buccaneer

[Bellini, Dom]

If you look carefully in the GUI of Buccaneer there has been for quite sometime 
now an option to use Phi and FOM instead of HL coefficients (quickest solution).


Although Buccaneer is optimized to use HL coefficients, getting your ABCD from 
MR solutions will results in CD equal to zero anyway.


D




From: CCP4 bulletin board <CCP4BB@jiscmail.ac.uk> on behalf of Carlos 
CONTRERAS-MARTEL <carlos.contreras-mar...@ibs.fr>
Sent: 20 January 2017 07:33:28
To: CCP4BB@jiscmail.ac.uk
Subject: Re: [ccp4bb] help with Buccaneer

You need go first for some density improvement, see

http://ccp4wiki.org/~ccp4wiki/wiki/index.php?title=Automated_phase_improvement_with_Parrot
Automated phase improvement with Parrot - Media 
Wiki<http://ccp4wiki.org/~ccp4wiki/wiki/index.php?title=Automated_phase_improvement_with_Parrot>
ccp4wiki.org
Main Page - Using the CCP4 software - Phase improvement with CCP4 - Automated 
phase improvement with Parrot. Parrot is a program which takes an initial set 
of phase ...




All the best

Carlos


On 01/20/17 05:10, Vikram Dalal wrote:
Hi Everyone,

I want to run the Buccaneer. I need Hendrickson-Lattman coefficients for it. 
How I can find Hendrickson-Lattman coefficients?




Thanks & Regards,











--
 Carlos CONTRERAS MARTEL, Ph.D.
 (CR1 CNRS)

 carlos.contreras-mar...@ibs.fr<mailto:carlos.contreras-mar...@ibs.fr>

 "Bacterial Pathogenesis Group"
Institut de Biologie Structurale
 UMR5075 CEA-CNRS-UGA

  IBS
  Campus EPN
  71, avenue des Martyrs
  CS 10090
  38044 Grenoble CEDEX 9
  FRANCE


 tel : (+33) (0)4 57 42 86 41

http://www.ibs.fr/groupes/groupe-pathogenie-bacterienne/?lang=fr
http://www.ibs.fr/groups/bacterial-pathogenesis-group/?lang=en

Re: [ccp4bb] help with Buccaneer

[Carlos CONTRERAS-MARTEL]

You need go first for some density improvement, see

http://ccp4wiki.org/~ccp4wiki/wiki/index.php?title=Automated_phase_improvement_with_Parrot

All the best

Carlos


On 01/20/17 05:10, Vikram Dalal wrote:

Hi Everyone,

I want to run the Buccaneer. I need Hendrickson-Lattman 
coefficients for it. How I can find Hendrickson-Lattman coefficients?



*
*

Thanks & Regards,











--
 Carlos CONTRERAS MARTEL, Ph.D.
 (CR1 CNRS)

 carlos.contreras-mar...@ibs.fr

 "Bacterial Pathogenesis Group"
Institut de Biologie Structurale
 UMR5075 CEA-CNRS-UGA

  IBS
  Campus EPN
  71, avenue des Martyrs
  CS 10090
  38044 Grenoble CEDEX 9
  FRANCE


 tel : (+33) (0)4 57 42 86 41

http://www.ibs.fr/groupes/groupe-pathogenie-bacterienne/?lang=fr
http://www.ibs.fr/groups/bacterial-pathogenesis-group/?lang=en

Re: [ccp4bb] help with Buccaneer

[Edward A. Berry]

When faced with a program requiring HL coefficients, and having
phases from a (partial) model, I used to run a ccp4 program called
sigmaa to generate the HL coefficients. I'm not sure if this is
theoretically a good idea, but at least it allows the program to run.

On 01/19/2017 11:10 PM, Vikram Dalal wrote:

Hi Everyone,

I want to run the Buccaneer. I need Hendrickson-Lattman coefficients for it. 
How I can find Hendrickson-Lattman coefficients?


*
*

Thanks & Regards,

[ccp4bb] help with Buccaneer

[Vikram Dalal]

Hi Everyone,

I want to run the Buccaneer. I need Hendrickson-Lattman coefficients for
it. How I can find Hendrickson-Lattman coefficients?




Thanks & Regards,