Re: [Jmol-users] multiple molecular models

Bob Hanson Sun, 19 Dec 2004 11:22:02 -0800

Not precisely appropriate to this discussion, perhaps, but see

http://www.stolaf.edu/people/hansonr/jmol/merge/merge.htm

Note that this bit of code merges two model files (of the same type) and then displays them at some desired offset. Jmol will think they are one molecule, but of course with proper selection scripting, one could display them independently, highlight them, etc. It also reads an "sdf" file and manipulates the data before displaying them side by side.

Obviously this isn't a great solution. But it interesting that it can be done already, now that we have "show file" and ".loadInline()" functions. Thanks, Miguel, for these very useful functions.


I do think it would be great to have something like:

select atomno >=1 and atomno <=30
displace 2. 2. 2.

Bob

Rajarshi Guha wrote:

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


--
--

Robert M. Hanson, [EMAIL PROTECTED], 507-646-3107
Professor of Chemistry, St. Olaf College
1520 St. Olaf Ave., Northfield, MN 55057
mailto:[EMAIL PROTECTED]
http://www.stolaf.edu/people/hansonr

"Imagination is more important than knowledge." - Albert Einstein

Re: [Jmol-users] multiple molecular models

Reply via email to