[ccp4bb] about .ins file for SHELXD

2011-11-07 Thread Lu Yu
Hi, I was trying to use SHELXD to solve peptide structure. But I got stuck in the input .ins file, and I need some advice. In the .ins file, TITLE CELL ZERR LATT SYMM SFAC C H N O *UNIT* *FIND* *PLOP* NTRY HKLF END A rough estimate, there will be 62 C, 122 H, 14 N, 32 O in one unit cell. 1 for *

[ccp4bb] about .ins file for SHELXD

2011-11-07 Thread Lu Yu
Hi, I was trying to use SHELXD to solve peptide structure. But I got stuck in the input .ins file, and I need some advice. In the .ins file, TITLE CELL ZERR LATT SYMM SFAC C H N O *UNIT* *FIND* *PLOP* NTRY HKLF END A rough estimate, there will be 62 C, 122 H, 14 N, 32 O in one unit cell. 1 for *

[ccp4bb] how to add Cadmium ion to structure and do the refinement

2011-11-28 Thread Lu Yu
Hi ALL, This is the first structure I am working with. As the title said, I was stuck in the middle of model building using coot, and I found a big positive peak for Cadmium ion. The coot program doesn't *know* the cadmium ion when I add a Cd atom there (under the "place atom at pointer" menu--> "

Re: [ccp4bb] how to add Cadmium ion to structure and do the refinement

2011-11-30 Thread Lu Yu
) to be CD > ATOM471 CD CD A 81 23.896 6.780 5.956 1.00 60.81.. > > The residue number must be different from any existing residue.. > > The REFMAC log will trell you what it disliked, but not very well marked.. > > > > > On 11/28/2011 08:16 PM, Lu Yu wro

[ccp4bb] [ccp4]questions about SHELXD

2012-02-18 Thread Lu Yu
Hi all, I was trying to use SHELXD program for protein peptides (6-7 residues) for the very first time, and I got the .pdb file which should be the correct solution. However, in the .pdb file, the atoms are labeled as ABC and they are not recognized as amino acids. My question is normally what pr

[ccp4bb] question about input .hkl file for SHELXD

2012-02-18 Thread Lu Yu
Hi, I was confused with the input .hkl file for SHELXD. I was using ccp4 to prepare these files, and I am not sure whether I was doing it correctly. 1st I did scale2mtz to generate .mtz file 2nd I used mtz2various to convert .mtz to .hkl format. I also found a program prephadata which can convert

[ccp4bb] unstable refinement error in SHELXL

2012-03-19 Thread Lu Yu
Hi all, I was using SHELXL for the refinement of a small peptide molecule (6-7 residues), and it was working for the first round. But then it gave me an error message. I don't know what's going on and have you had the same problems? Can you give me some suggestions? *For more information*: I was