Rolf, what you describe IS the intended behavior of the
conformation
command. Sorry, I think I didn't make that clear.
conformation
by itself is supposed to do precisely what you wish, I think. (I see
that I have a bug there -- will be fixed momentarily.)
For example, say you have five models loaded. You want to define, in
general, for all models the "conformation" to involve alternate
location C. Then you might script:
select *%,*%C
conformation
This is what you were thinking, right? Now all models are set to
display the third set of alternate locations.
Or, if you wanted this only model 3, just use:
select (*%,*%C) and */3
conformation
However, by placing a number with the word "conformation" you are
necessarily selecting a predefined set of atoms. It is a convenience
measure only. No need to use it if you prefer to do the selection
ahead of time.
So if you prefer to define your conformation yourself, simply do not
use conformation followed by a number.
I note that right this instant JmolAppletProto also screens for the
currently displayed model with just "conformation", but I think you
are right, and I will make that change so that it operates on the
entire selection set and does no filtering.
Thanks for that feedback.
Bob
Rolf Huehne wrote:
Bob Hanson wrote:
Rolf Huehne wrote:
Bob Hanson wrote:
load "1vwh" "alt/1VWH.cif" "alt/1VWH.cif";color altloc;restrict
none;select *;cartoon on
model 1001;conformation 1
model 2001;conformation 2
model 0
Do you see what that is doing?
It first loads "1VWH.cif" twice as separate models, setting "1vwh" as
the name displayed.
Then it colors by altloc and displays only cartoon.
With "conformation 1/2" the cartoon is calculated for both
conformations.
And finally both models are displayed simultaneously.
Very nice!
But I don't understand how the conformation commands are restricted to a
specific model.
because they are. They are designed to be restricted to the "current"
model. Otherwise, say you had 5 models loaded, the conformation
command would drive you crazy.
Q: Doesn't that break with the general rule that the current selection
is the basis for any manipulation command?
At first sight I don't think that I like this behaviour. And I don't
think the usual behaviour would drive anyone crazy. It would just
provide full control by setting the selection as desired prior to the
"conformation" command.
After loading the command "select *" selects all 4494 atoms from both
models.
correct
"model 1001" doesn't change the selection.
correct
After "conformation 1" no atoms are selected any more.
all of model 1001, conformation 1, are selected. Check this with
color green
or
select selected
This is exactly what I did, a "select selected" after each command in
the Jmol console.
And Jmol reported "0 atoms selected" after "conformation 1".
"model 2001" doesn't change the selection.
After "conformation 2" still no atoms are selected.
oh yes, all of conformation 2 are selected.
Same as above.
Another question is how the conformation numbers "1","2" correspond to
the altLoc indicators?
1 refers to the first found in the file, 2 to the next, ....
At least in the PDB format file they are "A","B" for 1VWH. Since I am
not used to read mmCIF files I couldn't figure out yet if they were
changed to "1","2" there. Since the following characters
'*1234ABCDEFGHIJKLMNOPQRSTUVXYZ
are currently used as altLoc indicators throughout the PDB database it
would not be obvious how these are mapped to numbers.
whatever order they are in the file, that maps to the 1 2 3 of the
conformations. Almost certainly this is ABCDE or 12345, so it should
be a pretty natural mapping.
Hmm, you can have altloc "*", eh? Then we will have to take out
%*
and change that to
%?
But, really, this "*" and "'" business appears to have been abandoned
or maybe just never implemented. Jaime Prilusky has gathered
information for the ENTIRE PDB database at
http://bip.weizmann.ac.il/oca-bin/altloc and
http://bip.weizmann.ac.il/oca-docs/altLocations.txt, and they always
start with ABC or 123 or sometimes an odd alphabetic character. So the
statement, "are currently used as altLoc indicators throughout the PDB
database" is not quite correct. Do you know of cases where this is *
or '? (maybe outside the context of mmCIF?)
My pivot table tells me there are 7174 models in the database with
altlocs. Of these, 78 are of the type "123", 7092 are of the type
"ABCDE", and 4 have a mix. Eric has looked, and many of these
numerical or odd ones are mistakes. Of the ABC type, the vast majority
are just "AB", a few more are "ABC", and then we have some others.
1mx5 uses Y and Z only, for instance. So those would be "conformation
1 (Y) and conformation 2 (Z).
None use * or ', even though those might be officially allowed. My
guess is that they are NOT actually being allowed.
We could write Jmol to allow * or ' when the bug report comes in. :)
Bob
We have just started to include "altLoc" in our parsing of the entire
PDB database, so I havn't looked yet into this in detail. My list above
was just a distinct list of all altLoc indicators thast were reported by
our parser. We use the PDB format files for parsing. Maybe Jaime used
the mmCIF files instead and that could explain differences.
After taking a look at some of those entries with "'" (1luh) and "*"
(1d6d, 1esy, 1gt2, 1gy8, 1h86, 1vyr, 484d) I would agree that they look
like mistakes.
Regards,
Rolf
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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
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