Re: [ccp4bb] mystery disappearance of CCP4 website(s)

[Andrew Sharff]

You are not alone. They are unreachable from here too!


Andrew


On 25/05/17 14:09, R. Michael Garavito wrote:
I have been trying to reach some of the CCP4 websites (www.ccp4.ac.uk/ 
) from the US and they all seem to be 
unreachable, even from the http://www.ccp.ac.uk/ site.  Any ideas? Or 
did I miss some announcement.  Most of the other CCPs seem to be up.


Michael

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*Dr. Andrew J. Sharff D.Phil**
*Research Scientist / Software Developer
Global Phasing Ltd
Sheraton House
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Tel: +(0)1223 353033
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[ccp4bb] atom names for beta-D-xylopyranose

[Andrew Sharff]

Does anyone out there have some insight into, or a credible explanation 
for, why PDB ligand id XYP (beta-D-xylopyranose) has what seems like  
non-standard atom notation, at least compared to other sugars!


The standard atom naming convention for nearly all monosaccharides, 
including XYS (alpha-D-xylopyranose), is to name the ring carbons C1, C2 
etc and their attached oxygens O1, O2 etc - perfectly logical and 
understandable.


However, XYP has a totally different naming scheme. This makes 
automatically defining sugar linkages (based on atom naming) very difficult.


Quite apart from not understanding the logic of the naming convention 
for XYP, even more confusingly, XYP replaced the now deprecated 3-letter 
code for beta-D-xylopyranose (HSZ), and this older version has the more 
standard notation.


Thanks

Andrew

--
--
*Dr. Andrew J. Sharff D.Phil**
*Research Scientist / Software Developer
Global Phasing Ltd
Sheraton House
Castle Park
Cambridge CB3 0AX
UK
Tel: +(0)1223 353033
Fax: +(0)1223 366889

Re: [ccp4bb] CCP4 update 6.3.0 006

[Andrew Sharff]

On 09/10/12 15:09, William G. Scott wrote:

Dear Ronan et al:

I apologize if I have missed it, but is there a simple way to obtain the 
corresponding changes in the source code for those of us who compile ccp4 
ourselves?

I looked on the web site and the ftp site but can't seem to find it.


Can I second that as well.

Thanks

Andrew


Many thanks in advance.

Bill



On Oct 8, 2012, at 11:20 AM, ronan.kee...@stfc.ac.uk wrote:


Dear CCP4 Users,

A CCP4 update has just been released, consisting of the following changes:

*   MrBUMP: model building options added
*   PISA: new QT interface
*   AMPLE: bug fixes and expanded interface (Linux and MAC only)
*   tlsextract: correction of output format which broke parsing of output
*   DiffractionImage: corrections to reading of pilatus mini-cbf
*   ccp4i: New AMPLE (Linux and Mac) and MrBUMP interfaces, QT-PISA 
launcher and bug fixes
*   crank: bug fix (Windows only)

The easiest way to obtain the update is to install the CCP4 update client, if 
you have not done so already. Note that auto-updates will work correctly only 
with CCP4 release 6.3.0, therefore upgrade if necessary. Report bugs to 
c...@stfc.ac.uk.

Many thanks for using CCP4,

-- Ronan Keegan



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--
--
*Dr. Andrew J. Sharff D.Phil**
*Research Scientist / Software Developer
Global Phasing Ltd
Sheraton House
Castle Park
Cambridge CB3 0AX
UK
Tel: +(0)1223 353033
Fax: +(0)1223 366889