Re: [ccp4bb] finding NCS in water
Simplest is to submit your current structure to PDBe - they have software which moves all waters to lie close to protein. However the waters IDs don't help you know if A OH 123 matches B OH 123 for example. The very old utility water tidy tries to give meaningful names to your waters, but those names are inconsistent with deposition.Maybe you could run water tidy for information about which waters obey NCS although the output is not standard nomenclature.. Alternately just use the coot facility to fit chain A over chain B and see which waters overlap each other in the Copy and original.. (Remember to turn symmetry ON) Eleanor On 22 April 2012 16:33, Rajesh Kumar ccp4...@hotmail.com wrote: Dear All, I would like to learn how to relate water molecules by NCS and refine them. When I googled, CCP4 utilities sortwater and watncs showed up. I also found Applying NCS to a high resolution structure http://www.globalphasing.com/buster/wiki/index.cgi?AutoBusterExample4chawaterNCS, including water molecules in NCS restraints on autobuster examples. Some how I got error Interpreting card: NOTE BUSTER_SIM_DEFINE ncsUV Chain_U V Number of atoms in template set= 109 Number of related chains (other than template) in SIM set=1 List of chains to be restrained (excluding template)= V *** ERROR a chain specified has less than 3 matching atoms to the template *** ERROR the chain in question is 'V' *** ERROR number of matching atoms is=0 *** ERROR found in finding matching atoms for NCS set up (END) Could you please point me to place where I could find one or two good examples or extended information to learn how this works? Also would like to know if this helps the refinement in general. Thanks Rajesh
Re: [ccp4bb] finding NCS in water
Thank you Professor. Its very helpful. Regards,Rajesh Date: Mon, 23 Apr 2012 12:19:09 +0100 Subject: Re: [ccp4bb] finding NCS in water From: eleanor.dod...@york.ac.uk To: ccp4...@hotmail.com CC: CCP4BB@jiscmail.ac.uk Simplest is to submit your current structure to PDBe - they have software which moves all waters to lie close to protein. However the waters IDs don't help you know if A OH 123 matches B OH 123 for example. The very old utility water tidy tries to give meaningful names to your waters, but those names are inconsistent with deposition.Maybe you could run water tidy for information about which waters obey NCS although the output is not standard nomenclature.. Alternately just use the coot facility to fit chain A over chain B and see which waters overlap each other in the Copy and original..(Remember to turn symmetry ON) Eleanor On 22 April 2012 16:33, Rajesh Kumar ccp4...@hotmail.com wrote: Dear All, I would like to learn how to relate water molecules by NCS and refine them. When I googled, CCP4 utilities sortwater and watncs showed up. I also found Applying NCS to a high resolution structure , including water molecules in NCS restraints on autobuster examples. Some how I got error Interpreting card: NOTE BUSTER_SIM_DEFINE ncsUV Chain_U V Number of atoms in template set= 109 Number of related chains (other than template) in SIM set=1 List of chains to be restrained (excluding template)= V*** ERROR a chain specified has less than 3 matching atoms to the template *** ERROR the chain in question is 'V' *** ERROR number of matching atoms is=0 *** ERROR found in finding matching atoms for NCS set up(END) Could you please point me to place where I could find one or two good examples or extended information to learn how this works? Also would like to know if this helps the refinement in general. ThanksRajesh
[ccp4bb] finding NCS in water
Dear All, I would like to learn how to relate water molecules by NCS and refine them. When I googled, CCP4 utilities sortwater and watncs showed up. I also found Applying NCS to a high resolution structure , including water molecules in NCS restraints on autobuster examples. Some how I got error Interpreting card: NOTE BUSTER_SIM_DEFINE ncsUV Chain_U V Number of atoms in template set= 109 Number of related chains (other than template) in SIM set=1 List of chains to be restrained (excluding template)= V *** ERROR a chain specified has less than 3 matching atoms to the template *** ERROR the chain in question is 'V' *** ERROR number of matching atoms is= 0 *** ERROR found in finding matching atoms for NCS set up(END) Could you please point me to place where I could find one or two good examples or extended information to learn how this works? Also would like to know if this helps the refinement in general. ThanksRajesh
