[ccp4bb] Tips on fitting poorly defined loop regions

Hello all, I'm just finishing up my first structure, a membrane protein with 5 fold NCS. The native dataset is good to about 2.1A. The R factors are good, around .22/.26 without waters. The only problem is that I'm having a difficult time fitting what looks to be a very important (potential

[ccp4bb] low resolution scaling + merging... negative scales!

Hello all I've got a situation where I have a P321 space group to about 8.0A, it was able to scale and merge fine in hkl2000 but now I'm getting negative scales for Scala. Any suggestions on low resolution scaling and merging? Thanks FR -

[ccp4bb] issues with TLS refinement

Hi All, We recently upgraded to ccp4suite 6.1.1 version and have been experiencing some issues while running refmac_5.5.0088 (for tls refinement) through this ccp4 interface. We use these softwares through sbgrid. I would really appreciate any help to troubleshoot this issue. The issue

[ccp4bb] Post-doc positions at the Netherlands Cancer Institute (NKI)

Post-doctoral positions are available in the Netherlands Cancer Institute in the groups of Tassos Perrakis and Titia Sixma respectively (http://xtal.nki.nl). The Netherlands Cancer Institute (http://www.nki.nl) is a center of excellence with a high standard of biological research and an

Re: [ccp4bb] Tips on fitting poorly defined loop regions

Hi Drew, Have you tried arp/wARP (the LOOPY option) or the AutoBuild option in Phenix ? If you haven't tried this you can try a complete rebuilding using you model as it stands and providing the complete sequence of your protein. At this resolution (2.1A) , they may be able to rescue your loops at

Re: [ccp4bb] Tips on fitting poorly defined loop regions

Dear Drew, Your loop region might or might not obey the ncs of the rest of the molecule, so you should be sure to examine both the ncs averaged map and each individual, nonaveraged, map. You should be willing to accept, however, that this region may not structured and it may not be

Re: [ccp4bb] how to optimize crystal without sharp boundary

Hi Jerry, did you check out the CCP4 wiki - there's a lot of information at http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Crystals HTH, Kay Jerry McCully schrieb: Dear All: Recently we got some crystals from ammonium sulfate and PEG400. They look like hexagonal single

Re: [ccp4bb] Tips on fitting poorly defined loop regions

Thanks for these suggestions. The protein is purified and crystallized in the presence of substrate at all times. A reason that I'd like to assign all the polypeptide density is that the remaining density in the active site could be my substrate. I am fairly certain that the loops do not obey the

[ccp4bb] how to optimize crystal without sharp boundary

Dear All: Recently we got some crystals from ammonium sulfate and PEG400. They look like hexagonal single crystals but without sharp boundary. They did not diffract well. This protein can also be crystallized from PEG6000 in star shape. We tried hampton additive screen but can

Re: [ccp4bb] How to improve crystal which is twinning?

Hello Annie, How effective have you found using sparse matrix screens as additives vs. traditional additive screens? I've tried this only a few times without success and would like to hear from someone with more experience. Thanks! Ho UC Berkeley

Re: [ccp4bb] How to improve crystal which is twinning?

Hi Ho-- We have had lots of success using the Hampton Research Crystal Screens 1 2 as additives. Sometimes these improve the crystal quality whereas the 96 Additive Screen does not. Whenever I screen for additives, I include Crystal Screen 1 2. What I have NOT had a great deal of success

Re: [ccp4bb] issues with TLS refinement

The issue is: While running tls and restrained refinement, the program doesn't perform the given no. of tls refinements. For e.g., if you ask it to perform 10 TLS and 5 restrained refinement rounds, it'll run may be 2 or 3 rounds of TLS and then jump to restrained refinement rounds and finish