Hi,

I can try to help if you send me the Fobs data and current model. Plus, tell me the coordinates of two anchor points marking the start and the end of the segment that you want to build, and the sequence that is supposed to be in-between these anchor point. The I can try using my tool (that I'm still developping) to build that segment from scratch into whatever map you have. This tool is not picky about map quality and builds things in seconds.

Pavel

On 2/8/12 11:15 PM, intekhab alam wrote:

Hi all

I have a 3A dataset for a protein-protein complex. I have successfully build the first protein and refined it to R/Rfree 24/28. I can see some density for my second protein but the density is a bit noisy. I have attached the coot image of the density. I want to model the aminoacid having sequence as given

peptide:

MGKKGKNKKGRGRPGVFRTRGLTDEEYDEFKKRRESRGGKYSIDDYLADREREEELLERDEEEAIFGDGFGLE

1.Based on map features which segemnt should i start with.

2. Is there anyway that i can build the best fit segment of my second protein.

I tried autobuild but it failed to build any peptide for my second protein.

Your help is highly appreciated.

regards

--

INTEKHAB ALAM
LABORATORY OF STRUCTURAL BIOINFORMATICS
KOREA UNIVERSITY, SEOUL
_______________________________________________
phenixbb mailing list
[email protected]
http://phenix-online.org/mailman/listinfo/phenixbb