[ccp4bb] Calculation of electron density map for a twinned dataset

Hi All, I have a dataset that shows about 50 % twinning. I was curious what will be the best way for the refinement and calculation of electron density maps, including the composite omit map. Thanks a lot. Mariah -- Mariah Jones Department of Biochemistry University of Florida

[ccp4bb] Mark Houwink Parameter of a Protein

Hi All, I was looking for Mark Houwink Parameter of a Protein. Is there any software that I can use to measure that? Thanks for your help. Mariah -- Mariah Jones Department of Biochemistry University of Florida

[ccp4bb] Sigma Cutoff in HKL2000 Data Processing

What is the Sigma Cutoff that one should use for Data Processing using HKL2000. Is there a minimum or maximum value. Also if there is a variation then what all does it depend on. Thanks in Advance for your help. Mariah -- Mariah Jones Department of Biochemistry University of Florida

[ccp4bb] Stacked Plate Like Crystals

Hello All, I have some plate crystals that are stacked to each other. They are about 60X50 micron. What are some methods that I can use to optimize them. Thank you all for the suggestions. Mariah -- Mariah Jones Department of Biochemistry University of Florida

[ccp4bb] Protein Protein interactions

Hello All, Can anyone tell me what are the programs used to find out the different interactions in a protein. I am talking about both intra and intermolecular interactions. Thanks in advance. Mariah -- Mariah Jones Department of Biochemistry University of Florida

[ccp4bb] Ligand PDB

Dear All, What is the best way to find the coordinates of a ligand. I do not find teh ligand in Pdb.org. I am trying to draw it in prodrug but the server is showing error. Also if I draw it how do I make sure that the geometry is correct. Thanks, Mariah -- Mariah Jones Department of Biochemistr

[ccp4bb] Pymol

Dear All, I have a question about PYMOL. I am trying to make a cartoon diagram of my protein showing the secondary structural elements. However for some reasons it is not showing the N terminal strand and showing that as a loop. Is there any command for selecting a range of residues and showing

[ccp4bb] P21 and C2

Hello All, I am having a problem in processing a dataset. I have other datasets of the same protein and they are processed in P21. However this one only can be processed in C2. I do not know where I am going wrong. Please let me know if you have any suggestion. Thanks, Mariah -- Mariah Jones

[ccp4bb] Purification with ligand

Hello, I wanted to know if there is a standard procedure for purification of protein with ligand. I have never done this before so it will be nice to get some help. Thanks, Mariah -- Mariah Jones Department of Biochemistry University of Florida

[ccp4bb] Occupancy Refinement

Dear All, I have a question about the occupancy refinement of a ligand. I have a dataset of 2.3 angstrom and the ligand binds in multiple conformations in the active site. My question is if it is possible to tell which orientation(s) has/have the highest occupancy based on occupancy refinement. W

[ccp4bb] Ligand binding in multiple conformation

Hi, I had a question about flexibility in ligand binding in an enzyme active site. Is it possible for a substrate/product analogue to bind in more than one conformation in the active site. Since the ligand/enzyme interactions are very specific I am a little confused about this. Also which progra