On Sat, 2004-12-18 at 21:47 -0500, Miguel wrote: > > Clearly, the two structures are far apart and hence only one is > > 'visible' at a time - unless I translate them > > Adjust so that one is off by 10,0,0 instead of 1000,1000,1000. Then you > will be able to see what the behavior is like in PyMOL.
Right. I took a modified version of 1CRN.pdb (see below) and made a copy with 10 added to the X coordinate. Loaded the first version in Pymol. OK. Then I load the second version and the first one 'disappears' However if I zoom out, then both are visible. > You said: > > > And if I center the > > second one, the first one disappears. > > Q: In PyMOL do you pick which molecule is the center of rotation? When multiple molecules are loaded can indicate that a specific molecule is centered. Now what this appears to mean is that the molecule is centered in the *current view*. So say I load the first one - it is automatically centered in the screen. Then I load the second one and this one is automatically centered in the screen - as a result the first one is not visible. Zooming out brings them both into view. >From this state if I choose to 'center the second molecule', then the first molecule disappears. > Q: What happens to the 'center of the universe' ? I'm not sure I understand what the center of the universe is. If its 0,0,0 then when the second molecule is loaded the center of the universe shifts to the new coordinates. OR the center of the univserse stays at 0,0,0 and the screen coordinate shift to the new set of coordinates 10,0,0 > Take a PDB file that MOE likes. > Go in with a text editor. > delete all the atoms except those in the first group. > Confirm that MOE still likes your file. > Then, make a copy and add 10 to the x coordinate of each of the atoms. Thanks for the pointer. I used a modified version of 1CRN.pdb and you can get these modified versions as well as screenshots of what MOE looks like with the molecules loaded at http://blue.chem.psu.edu/~rajarshi/misc/jmol - the png's are big :( Basically, when loading a molecule MOE allows asks if you want the molecule to be centered. So when loading the molecule the first molecules (xxx.pdb) I choose this option. When loading the second molecule (xx1.pdb) I tried choosing center as well as not choosing center. You can see the resultant display of the two molecules in the screenshots at the above link After both molecules have been loaded a rotation about the Y axis appears to occur around a point somewhere near the first molecule that was loaded - which makes sense since the first molecule was 'centered' ------------------------------------------------------------------- Rajarshi Guha <[EMAIL PROTECTED]> <http://jijo.cjb.net> GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE ------------------------------------------------------------------- Q: What's purple and commutes? A: An abelian grape. ------------------------------------------------------- SF email is sponsored by - The IT Product Guide Read honest & candid reviews on hundreds of IT Products from real users. Discover which products truly live up to the hype. Start reading now. http://productguide.itmanagersjournal.com/ _______________________________________________ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
