[sharp-discuss] Questions about sharp 2.8.1

[Clemens Vonrhein]

Dear Nian,

sorry to hear that you have problems installing SHARP/autoSHARP. We
have a few questions though:

On Fri, Mar 01, 2013 at 02:48:37AM -0500, Nick Huang wrote:
> To add a little progress from my own investigation,
> 1. I was able to customize the path after unzip the tar file and run install.sh.

What do yo mean with 'customize the path' in relation to the httpd?
Do you want to use a different httpd binary after installation? Or
change some other paths?

We would highly recommend _not_ to untar the *.tar file we provide and
then run various install scripts by hand (where did you find a
install.sh script anyway?): this will result in a broken installation
most of the time.

If you want to fine-tune/change the installation afterwards, you
should always do

  1. install the software according to the default instructions at

       http://www.globalphasing.com/sharp/installation/start.html

     This will work in 99% of cases if

       a) you have the requisites setup (CCP4, shelxc/d, ARP/wARP)

       b) you have 'gcc' installed on your OS (to compile the Apache
          httpd on-the-fly, ensuring the binary works on that
          particular machine)

  2. make use of various administrative tools, e.g.

       cd /where/ever/sharp-2.8

       . ./setup.sh                      # bash/ksh/sh/zsh
         - or -
       source ./setup.csh                # tcsh/csh

     and then

       adm/bin/httpd-setup
       adm/bin/ccp4-setup
       adm/bin/host-setup
       ... etc ...

  3. if you feel confident: edit various *.setup files by hand (at
     your own risk)

If you can clarify a bit what you mean with 'customise path', maybe we
can point you to the exact procedure to achieve whatever it is you
need here?

> 2. I can't find Fdm column in the final output. I can see Density
> modification stopped at Solvent Flattening step from the log file.
> Same dataset could proceed to the final density modification in sharp
> 2.6 (32 bit). Currently I am running sharp 2.8 64 bit.

Yes, older versions of SHARP/autoSHARP (together with older versions
of CCP4) did run a final DM run after SOLOMON for one reason only: the
SIGMAA program of older CCP4 versions didn't output
Hendrickson-Lattmann coefficients for the density modified phases. In
order to use such HL coefficients (to feed back into SHARP for
stabilisation of poor parameter refinements and/or improved LLG
residual maps) we needed to run DM to get those.

However, newer versions of CCP4/SIGMAA will now write out those HL
coeffcients and we don't need to run DM. In our experience, the maps
from SOLOMON are of at least the same quality as those from an
additional, final DM run ... unless you are working at about 6A or
worse. So please use the default map coefficients FBshasol/PHIBshasol
(or Fcentshasol/PHIcentshasol) for calculaiton of density-modified
maps from SHARP/autoSHARP - as you would get when using the interface
for plotting maps with Coot.

If you want to run DM yourself (e.g. to do NCS averaging): make sure
to use the correct columns from the eden_flat_XY.Zpc.mtz file. If in
doubt: please let us know.

> A question related to it is where to find the new model building
> module "Buccaneer".

Buccaneer isn't a program by us, but by Kevin Cowtan and distributed
with CCP4. Our new(ish) model-building tool (called "Long John Silver"
- because it is using K. Cowtan's parrot and buccaneeer programs) makes
use of this. You should already have this as part of your CCP4
installation ... unless you use a broken or VERY old version of CCP4?

Does that help?

Kind regards

Clemens (for sharp-develop)

-- 

***************************************************************
* Clemens Vonrhein, Ph.D.     vonrhein AT GlobalPhasing DOT com
*
*  Global Phasing Ltd.
*  Sheraton House, Castle Park 
*  Cambridge CB3 0AX, UK
*--------------------------------------------------------------
* BUSTER Development Group      (http://www.globalphasing.com)
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