I think MODELs are the right thing to use for animations, MODELs could be thought, in best case, as states of the molecule at different time (space) points (as are alternative locations *;B)... It seems to me that these multiple frames in a .xyz file are closely related to the MODELs in a .pdb file.
Q: Is there any reason why we can't support multiple frames in a .xyz file in exactly the same way that we support multiple MODELs in a .pdb file?
On
http://molmovdb.mbb.yale.edu/molmovdb/
such animations as interpolations between two PDB structures could be downloaded as "NMR formated PDB files", which means using MODEL records.
we already had discussed that it should be possible to alter this, to get a defined fixed relation between size (pixel) and scaling, e.g.The topic of the day is ... How do you define the 'center' of a group of atoms?
Maybe it isn't that interesting, and it probably isn't that critical, but the subject has come up in passing several times and we need to get it resolved.
This is the default center that is used when the molecule is first
displayed. It is also important because it has a direct impact on the
scaling that is used to map from Angstroms to screen coordinates. (Once
the center is chosen, the distance to the outermost point determines the
scale ... we want that point to fit on the screen.)
zoom 50.0
(zoom 50.0/100) which should be 100% (width) is 50.0 A
I'm fine with this, but there is a very useful command in RasMol2.7.2.1 which is
We are going to talk about different ways to define it. And I am interested in knowing which of these should be used and under what circumstances.
I can think of 4 ways to do it ... maybe there are others.
1. Minimal Enclosing Sphere
2. Center of the bounding box (aligned with euclidean axes)
center selected
e.g. in 1hag you would like to focus on chain *:I and rotate around this chain
http://www.imb-jena.de/cgi-bin/SCOPlnk.exe?CHIME=1&JMOL=1hag
in RasMol you could do
center *:I
or
select *:I
center selected
and now the center is moved to the (I guess) unweighted center of gravity of the selected chain :I
other RasMol2.7.2.1 center commands are center [250 250 250] rasmol vector from "center of gravity" center (<expression>) (translate|center)
3. Center of Mass/GravityI think this is the only one which makes sense by itself
4. Average location (Unweighted center of gravity)and this was the easiest and therefore most implemented.
Without the aspect of RasMol/Chime compatibility there was no need to alter Jmol starting centering, but there should be the possibility to recenter the scene, and my first thought would be that this is done by using UCoG
2> center boundbox selected 3> center mass selected ? error if an atom type could not be determined? 4> center [centers] selected
On Saturday 21 February 2004 18:53, Miguel Howard wrote:only under user command.
...
>> >> Q: Should this 'moving to the unitcell box' be automatic at load
>> >> time, or under user command? >>
even after translation of the unitcell to contain 3cro it is not packed. May be it was better to start with the PDB file definition and move the unit cell cage only after the first
>> > It is mathematically correct to take the atoms of the asymmetric
>> >> unit (those that comprise the structure model) and apply all the >> symmetry elements of the space group. This generates a unit cell. >> >> OK, that makes sense.
> > Ok, but that part is not covered yet...
We got a little confusion here.
These terms are getting too overloaded, so I am going to adopt a new term. The 'unitcell cage' is the wireframe rendering that I draw around the unitcell.
What I was trying to ask was: Is it always the case that we want to move the asymmetric unit to inside the unitcell cage? And if there are multiple copies of the asymmetric unit (molecules) then do we always want to pack them into the unitcell cage?
Yes, if only one unit cell is in the file and non P1 symmetry. Possibly, if only one unit cell and P1 symmetry. No, if more than one unit cell is in the file.
Let's look at two examples:
3CRO.pdb has the asymmetric unit outside the unitcell cage. Does anyone
ever want to see it that way?
No, one unit cell, P1, while possibly, this is a clear situation where it should be translated... especially, because it is just one unit cell, and it clearly cannot display (without unit cell duplication by Jmol itself) any interactions with molecules from surrounding unit cell.
"pack unitcell"
command, when the unitcell gets packed?
Though you may be right, this is not what I'm expecting on load at least in "RasMol/Chime compatible" mode
They way that it is in the file ... the way that *I* am most comfortable displaying it (most comfortable because I am faithfully reproducing the junk that is in the file)
Egon, your f1.cephalo file has 4 copies of the asymmetric unit. Do you *never* want to be able to display your crystal in its unpacked form.
Well never... in principle this again is one unit cell, but P1... so possibly the file does intend to display some packing information, but the file doesn't in any way, so I would say (and this is what I would prefer) it again to place all asymmetric parts into the unit cell cage...
In writing this, I think I have answered my own question. I don't think that I should move anything into the unitcell cage. By default, I render what is in the file.
Right... my point too. And I believe that when symmetry operations are given *and* only one unit cell is given in the file, then 'packed' is meant...
I prefer this to be an command that has to be explicitly called by the script.To pack things into the unitcell cage the user is going to have to send a script command which will do the packing.
Yes, that's perfect as a backup option.
in e.g. 1gu8 they mentioned an SYMOP which may be useful to address specific symmetry operations e.g.
That is my position. If you disagree then you will have to convince me
Just tried to do so.
>> > The problem is >> > that to the person *viewing* this collection of atoms it may not be
>> >> the view which best expresses the nature of the >> packing/interactions. At that point molecules associated with other >> unitcells are added to form the nicest picture.
I think that Rich was saying that people like to see the packed form, but he is talking about achieving it in a different way.
>> Yes, I understand how that would work.
> > In my vision, Jmol scripts will take care of this in the end (in > pseudo script commands) >
>> show unitbox 3 3 3 >> hide atoms 56 - 99 >> show h bonds between atoms 5-9 >> show h bonds between atoms 11-20 >> set vanderwaals on >> color atoms 77-5 # steric hindering
Egon says that we can do this with scripting. And he is right.
But there is a slight difference in what Egon and Rich are talking about. Rich is talking about about doing this to *form* a (over)packed unitcell. I think that Egon is assuming that we are starting with a packed unitcell, because we packed it as soon as the file got read.
Well, given the above guidelines, which should be fine as a default, maybe this adjustment: the possible for the second option, can be a no, if we would
add the first command to the above script (still pseudo script ;):
pack unitcell show unitbox 3 3 3 hide atoms 56 - 99 show h bonds between atoms 5-9 show h bonds between atoms 11-20 set vanderwaals on color atoms 77-5 # steric hindering
>> > The way this was often done for molecular entities was to generate
>> >> all the molecules in the unit cell plus all those 1 unit cell to each >> side and then keep only those molecules with atoms inside the cell >> boundaries of the origin cell. At the expense of having more that the >> exact number of symmetry copies you got the complete view of the >> packing.
> > I think this will be covered by the scripting commands... we will > probably need some syntax for atom naming 76[0,0,0] to de note the > 76th atom in a unit cell 0,0,0... > > BTW, Miguel, does the scripting language allow selecting of molecules, > by first partioning into connectes sets, add (by Jmol) labels to > those sets and then select them with a script command? Something > > like:
>> load samples/f1.cephalo >> partition >> select m1 >> color red
Effectively, yes.
I am going to post another question regarding the interactions of models and unitcells in pdb files.
>> OK. I can see that you would end up with 'extra' copies hanging off >> of all of the edges. >> You know that we hope to implement a 'multicell', so that would also >> help a a bit.
> > Indeed. Combine the multicell with scripting already available makes > very much possible in making custom views...
OK.
>> > Some programs give you a finer level of control by allowing you to
>> >> specify which symmetry operator plus translation is to be applied to >> the asymmetric unit. But this is usually only done to generate >> specific figures to illustrate particluar packing aspects. >> >> Not sure I understood all that ... but doesn't sound like a viable >> option.
> > Right, again, I think scripting will take care of this... > > Once we have symmetry operations available too, we can apply these by > scripting too... combine this with selecting one molecule from the > unit cell ...
pack unitcell 1555 2555
or out of the unitcell
pack unitcell 1555 2456
http://www.rcsb.org/pdb/docs/format/pdbguide2.2/part_74.html
not in the moment, but>
>> > For Jmol I'd probably pick the default action to be to display all
>> >> molecules which have their (unweighted) centre of gravity within the >> unit cell. >> >> OK, that code works today (although it is *not* unweighted cg -- >> another discussion topic)
> > I think the unweighted) centre of gravity is simply the geometric > center of the molecule, right?
I don't think so. I will post a separate question about this.
Yes, please do... we is curious about the difference...
Egon
I implemented %x %y %z in the labels.
Q: Do you want/need to be able to control the number of digits of display
to the right of the decimal point?
I think this would be in general a nice formating feature but I would use %7.2x for 2 digits right, e.g.Q: If so, what do you think about '%2x' => 2 digits to the right of the decimal point?
label "%5i [%n]%r^%I:%c.%a;%A/%M\n%2e%C %8.3x %8.3y %8.3z %b"
Yes, onClick?I have also been thinking of implementing a new type of label command. What do people think of this ...
A 'hover' popup is a little message that pops up when your mouse sits in one spot for a while. You have all seen them.
What do you think about doing the same thing for atoms? When you hover over an atom for a while the 'hover' window would appear.
Q: In general, would this be useful functionality?
To give the script writer control over what appears in the hover, I was thinking of using the same formatting syntax as the label command.
hover "My element symbol is %e"
Q: Is the 'label' syntax sufficient, or is there some other type of
information that people would want in a hover?
If you would like to parse the HETNAM FORMUL records, maybe people want to use hover " %h" label "[%n]%r %f"
Regards, Jan
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