Bugs item #916600, was opened at 2004-03-15 13:50 Message generated for change (Comment added) made by michaelthoward You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=916600&group_id=23629
Category: Graphics Group: None >Status: Closed >Resolution: Fixed Priority: 5 Submitted By: Michael T Howard (michaelthoward) Assigned to: Michael T Howard (michaelthoward) Summary: trace temperature Initial Comment: We are now showing mean positional displacement in trace temperature. Perhaps we should have scaling as an option. >I added 'trace displacement' as a temporary way to implement this and for >us to look at it. It calculates the mean positional displacement using the >formula cited by Bernhard Rupp above. > >I think my questions are: > >Q: Is it useful to see temperature values, displacement values, or both? > > Yes, may be, we should allow to add a factor for scaling? trace displacement 0.5 >Q: In either case, should the values correspond to absolute diameters? Or >should they be scaled relative to the values that are present in that >file? Or, do you want both? > > if I can get both, both, but I would prefer trace displacement (and an optional factor) -------- Original Message -------- Subject: trace temperature and mean positional displacement From: "Miguel Howard" <[EMAIL PROTECTED]> Date: Mon, March 15, 2004 13:46 To: <[EMAIL PROTECTED]> Jan wrote: > about trace temperature > >>However, after implementing it I was not very happy with the results. >> There seems to be a variety of temperature values stored in .pdb >> files. But the resulting range of displacement values is relatively >> small. >> >> > that my be a good structure :-) > >>The range for the alpha carbon temp values in 1crn goes from 3.38 to >> 10.80, corresponding to mean positional displacement values of 0.21 >> to 0.37 Angstroms (If my calculations are correct). >> >> > I think you have to use a factor of 2 for the diameter, because it is > anisotropic displacement from mean value. That is correct, I was using the mean positional displacement as a diameter instead of a radius. I just checked in code to correct this. So 'trace temperature' now displays the mean positional displacement of each atom. Miguel ---------------------------------------------------------------------- >Comment By: Michael T Howard (michaelthoward) Date: 2004-03-31 16:43 Message: Logged In: YES user_id=608250 I am closing this. Trace temperature is done. If someone does not like the way that it works then they can raise it as an issue. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=916600&group_id=23629 ------------------------------------------------------- This SF.Net email is sponsored by: IBM Linux Tutorials Free Linux tutorial presented by Daniel Robbins, President and CEO of GenToo technologies. Learn everything from fundamentals to system administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click _______________________________________________ Jmol-developers mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-developers
