Re: [COOT] Flying hydrogen issue in coot 0.5

2008-10-21 Thread Mark Collins
Hi Jonathan Did you find/get a fix for this? I just switched to pdb v3 file, from the happy and well behaved v2 file. It seems that all H_3 position Hydrogens are the problem (ie HB3, HG3 etc.) and as descirbed fly off when using RSR. Thanks Mark (os 10.4 G4, coot 0.5) On Sun, 5 Oct

Re: [COOT] Flying hydrogen issue in coot 0.5

2008-10-21 Thread Paul Emsley
In message [EMAIL PROTECTED] Paul Emsley [EMAIL PROTECTED] writes: Hi Mark, The issue here is that the dictionary does not define those atoms for e.g. ARG and GLN. For ARG and GLN, the atoms bound to the CG are HG1 and HG2 - not Hx3. i.e. Coot doesn't know about bonds to those

[COOT] SSM problem

2008-10-21 Thread Engin Ozkan
Hi everyone, I have a peculiar problem. Whenever I copy fragment a domain, the copied fragment fails in SSM. I am not talking about a small fragment, but more like a 250-residue domain. If I save the fragment as a molecule, go back and Open Coordinates that saved fragment, SSM works just fine