Hi Mousheng,
The first step to solve your problem is easy. You make your mask for NCS smaller so it only includes your bigger domain. This will still improve the density for the big domain. Your smaller domain probably got hurt by using an operator that is not correct. So the first part of the solution for the smaller domain is "don't touch it". Hopefully you can see it clearly enough that you could build a new mask for the smaller domain only and determine the new operator that relates the two smaller domains - this is the hard part. I guess that there is no guarantee for this to work so if you do not get favorable results, I'd try to solve the smaller domain without averaging. Two-fold averaging does not contribute all that much to your phases anyway but it is always worth trying.
Hope this helps.
Mark
-----Original Message-----
From: Wu Mousheng <[EMAIL PROTECTED]>
To: [email protected]
Sent: Mon, 31 Jul 2006 19:26:49 +0800
Subject: [ccp4bb]: DM problem
Dear all,
Recently, I have a problem with domain averaging using DM.
I solved my protein structure at 3.2 Å by molecular replacement using PHASER. The model contains two domains (one bigger and one smaller) and there are a homodimer in the asymmetric unit. I used two domains separately to search the model.
Then I tried to use domain averaging with DM to improve the electron density map. I used LSQKAB to calculate the matrixes and used MAMA to get the masks. The map from DM showed that the electron density of bigger domain is pretty well. I even can see the side chain clearly. However, the density of smaller domain is lost. The DM also showed that the CC for bigger domains is high (~0.88). However, the CC for the smaller domains is only 0.2.
I then checked the matrix for the smaller domain. I am very surprised to find that the CHI of Polar angle is 162 degree but not around 180 degree. It may suggest these two domains are not 2-fold NCS-related. I am quite confused about this point.
Does any expert know how to solve this DM problem? How can I improve the map of smaller domain using DM?
Thanks in advance.
Sincerely,
Mousheng Wu
Institute of Molecular and Cell Biology, Singapore
| DISCLAIMER: |
| This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its contents to any other person as it may be an offence under the Official Secrets Act. Thank you. |
