Re: [ccp4bb] Enforcing ncs on water molecules
Well - I usually use the COOT ncs map generation first. You place waters into good peaks in the 3 fold averaged map -say it is A B C - check that there are reasonable peaks in the other rotated maps - then once the waters are generated for A, fit those coordinates A to B and save them, then A to C and save. Youneed to change the water chain ID for the B set and C set .. Eleanor from the On 11/15/2010 08:46 PM, Dale Tronrud wrote: Hi I'm refining my first structure with a significant amount of ncs and am not looking forward to my usual, manual, editing of the water model. Could someone point me in the direction of a program that will encourage my water to obey the ncs? What I have in mind is to, first, find each cluster of water molecules related by the ncs. Then if some threshold is not reached, say only 1/3rd of the sites are occupied for a particular cluster, kill that cluster. If more than some threshold are occupied but less than 100%, fill in the missing water molecules. I would also like to reset the waters in each cluster to the average location. Has someone already written something along these lines? If so, I would rather not duplicate their effort. Thanks in advance, Dale Tronrud
Re: [ccp4bb] Enforcing ncs on water molecules
Dear Dale, concerning the first part of your request you can use BUSTER and include your water molecules in ncs restraints. Here is the link for the wiki explaining that http://www.globalphasing.com/buster/wiki/index.cgi?AutoBusterExample4chawaterNCS HTH All the best David Le 15 nov. 10 à 21:46, Dale Tronrud a écrit : Hi I'm refining my first structure with a significant amount of ncs and am not looking forward to my usual, manual, editing of the water model. Could someone point me in the direction of a program that will encourage my water to obey the ncs? What I have in mind is to, first, find each cluster of water molecules related by the ncs. Then if some threshold is not reached, say only 1/3rd of the sites are occupied for a particular cluster, kill that cluster. If more than some threshold are occupied but less than 100%, fill in the missing water molecules. I would also like to reset the waters in each cluster to the average location. Has someone already written something along these lines? If so, I would rather not duplicate their effort. Thanks in advance, Dale Tronrud -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.
[ccp4bb] Enforcing ncs on water molecules
Hi I'm refining my first structure with a significant amount of ncs and am not looking forward to my usual, manual, editing of the water model. Could someone point me in the direction of a program that will encourage my water to obey the ncs? What I have in mind is to, first, find each cluster of water molecules related by the ncs. Then if some threshold is not reached, say only 1/3rd of the sites are occupied for a particular cluster, kill that cluster. If more than some threshold are occupied but less than 100%, fill in the missing water molecules. I would also like to reset the waters in each cluster to the average location. Has someone already written something along these lines? If so, I would rather not duplicate their effort. Thanks in advance, Dale Tronrud
