Re: [ccp4bb] Question about modeling SAM into a protein structure

Yuan Cheng wrote: Hi everyone, I am trying to model a S-adenosylmethionine (SAM) molecule into the active site of a protein using the SAH (exists in the crystal structure) as the template. What I have already tried but failed so far are 1)Pymol: I loaded the pdbs of SAM and protein-SAH

[ccp4bb] Question about modeling SAM into a protein structure

Hi everyone, I am trying to model a S-adenosylmethionine (SAM) molecule into the active site of a protein using the SAH (exists in the crystal structure) as the template. What I have already tried but failed so far are 1)Pymol: I loaded the pdbs of SAM and protein-SAH into pymol and copy S

[ccp4bb] Question about merging of data from different crystals

Hi everyone, I have some question about the merging of diffraction data from different crystals. I have two (room-temperature) datasets in my hand and each of them can be scaled in P21 space group and the screw axis is along k. However,each dataset only have below 55% completeness. To get

[ccp4bb] Questions about cryoprotectants

Hi, Thank you for all your suggestions! I will test them and let you know what happens! Yuan

Re: [ccp4bb] Rfactor got stuck with a data having alternate strong and weak reflections.

an be best detected by an analysis of the data statistics. Eleanor Yuan Cheng wrote: Eleanor Dodson wrote: You must have a pseudo translation vector of ~ 0.02 0.5 0.0 That relates solution 1 and 2, and 3 and 4. That makes it hard to determine space group - there will be absences along 0k0

Re: [ccp4bb] Rfactor got stuck with a data having alternate strong and weak reflections.

Eleanor Dodson wrote: You must have a pseudo translation vector of ~ 0.02 0.5 0.0 That relates solution 1 and 2, and 3 and 4. That makes it hard to determine space group - there will be absences along 0k0 because of the translation so the space group could be P 2i 2 2i or P2i 21 2i But which

Re: [ccp4bb] Questions about Phaser

Peter Zwart wrote: Hi, This can might well be due to wrong space group. I suggest fixing the space groups by hand and running it in each possible space group that is possible. (P 31 2 1, P 32 2 1, P 3 2 1 are your options) Did you run xtriage already? P 2009/8/17 Yuan Cheng : Hey, I am

[ccp4bb] Questions about Phaser

Hey, I am trying to use phaser to solve a protein structure. There is predicted to be 8 mol/asu based on Matthew coefficient analysis.I am using a protein that shares about 35% identity with my protein as a search model. Phaser found the first five solutions and then failed to find the 6th.