Re: [Jmol-users] Jsmol mutate behaviour

2017-01-31 Thread Jaime Prilusky
Angel suggested yesterday the minimizing solution which works. Thank you both! Jaim Here’s Angel complete solution: mutate 148 SER; select [SER]148:A; color CPK; wireframe 0.2; color opaque; minimize (selected and sidechain); // alternative: minimize fix (not (selected and sidechain));

Re: [Jmol-users] Jsmol mutate behaviour

2017-01-31 Thread Robert Hanson
(sorry for the delay -- the images were over the byte limit for the list) I just meant that I think the flexible fit algorithm in Jmol just uses the carbon atoms, not the rest of the atoms, so it is quite possible that a C-O bond will be rotated. Did you try minimizing? ​

Re: [Jmol-users] Jsmol mutate behaviour

2017-01-31 Thread Jaime Prilusky
On 29 Jan 2017, at 2:39 PM, Robert Hanson > wrote: Might be just the carbon atoms. Can you please be more explicit? What I’m doing wrong? Is there a way to apply the mutate command and get the correct rendering?

Re: [Jmol-users] Jsmol mutate behaviour

2017-01-29 Thread Robert Hanson
Might be just the carbon atoms. On Sun, Jan 29, 2017 at 3:31 AM, Jaime Prilusky < jaime.prilu...@weizmann.ac.il> wrote: > > Something funny on the results I get from the mutate command. > > By mutating a residue into the same residue, I was expecting no > conformational change. > > What I’m