Re: [Jmol-users] electrostatic potential surface coloring
Reichsman Frieda wrote:
>Thanks Bob. If I understand correctly, this means that Jmol is
>calculating the surface MEP based on the values in the file, which do
>not represent absolute MEP but rather, are partial charges. And that
>means that when Jmol calculates the surface MEP for only part of the
>amino acid (the side chain), the absence of the 'backbone' atoms
>greatly influences the calculation of the potential over the side
>chain, yes? And so the absence of those atoms is creating the effect
>I'm seeing of diminishing the potential on the charged side chain, and
>magnifying it a bit on the uncharged side chain?
>
>
That could be.
>This leads to another question, would it be possible to show a partial
>surface? That is, 'build' the surface for the entire amino acid, but
>only display only the surface over the side chain. I imagine this
>would be a feature request, would it be feasible to do this?
>
>
>
I think you want
isosurface select {} molecular map select {*} mep
That is, when you run the mep, you want to indicate that for THAT part
of the calculation, you want all atoms selected. I hadn't realized
myself that two selects work here -- I suppose it could be useful. Or not.
Bob
>Frieda
>
>
>On Aug 5, 2008, at 12:11 PM, Bob Hanson wrote:
>
>
>
>> if you are mapping MEP data, remember that a MEP calculation is
>>being done that converts charge on atoms to potential at some distance
>>(on the surface) from a bunch of atoms, collectively. This value falls
>>off with distance. So that's probably why your numbers are low. They
>>aren't just charges, and really they are just approximations of
>>electron
>>potential, as well. If you want to map the charges themselves, you
>>will
>>need to use "map property partialcharge". But that will look somewhat
>>blotchy, I suspsect.
>>
>>I'm sure you have the color range/absolute business correct.
>>
>>
>
>
>
>
>>Bob
>>
>>
>>
>>>Am I misunderstanding what "color range/absolute x.xxx y.yyy" should
>>>be doing? Is there a way to get the coloring for "color range all"
>>>but
>>>only show the surface for the side chains?
>>>
>>>Frieda
>>>
>>>
>>>//
>>>
>>>Frieda Reichsman, PhD
>>>Molecules in Motion
>>>Interactive Molecular Structures
>>>http://www.moleculesinmotion.com
>>>413-253-2405
>>>
>>>//
>>>
>>>
>>>
>>>
>>>
>>>-
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>>>
>>>
>>>
>>--
>>Robert M. Hanson
>>Professor of Chemistry
>>St. Olaf College
>>Northfield, MN
>>http://www.stolaf.edu/people/hansonr
>>
>>
>>If nature does not answer first what we want,
>>it is better to take what answer we get.
>>
>>-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>>
>>
>>
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>>
>
>
>-
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--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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Re: [Jmol-users] electrostatic potential surface coloring
Thanks Bob. If I understand correctly, this means that Jmol is calculating the surface MEP based on the values in the file, which do not represent absolute MEP but rather, are partial charges. And that means that when Jmol calculates the surface MEP for only part of the amino acid (the side chain), the absence of the 'backbone' atoms greatly influences the calculation of the potential over the side chain, yes? And so the absence of those atoms is creating the effect I'm seeing of diminishing the potential on the charged side chain, and magnifying it a bit on the uncharged side chain? This leads to another question, would it be possible to show a partial surface? That is, 'build' the surface for the entire amino acid, but only display only the surface over the side chain. I imagine this would be a feature request, would it be feasible to do this? Frieda On Aug 5, 2008, at 12:11 PM, Bob Hanson wrote: > if you are mapping MEP data, remember that a MEP calculation is > being done that converts charge on atoms to potential at some distance > (on the surface) from a bunch of atoms, collectively. This value falls > off with distance. So that's probably why your numbers are low. They > aren't just charges, and really they are just approximations of > electron > potential, as well. If you want to map the charges themselves, you > will > need to use "map property partialcharge". But that will look somewhat > blotchy, I suspsect. > > I'm sure you have the color range/absolute business correct. > > > Bob > >> Am I misunderstanding what "color range/absolute x.xxx y.yyy" should >> be doing? Is there a way to get the coloring for "color range all" >> but >> only show the surface for the side chains? >> >> Frieda >> >> >> // >> >> Frieda Reichsman, PhD >> Molecules in Motion >> Interactive Molecular Structures >> http://www.moleculesinmotion.com >> 413-253-2405 >> >> // >> >> >> >> >> >> - >> This SF.Net email is sponsored by the Moblin Your Move Developer's >> challenge >> Build the coolest Linux based applications with Moblin SDK & win >> great prizes >> Grand prize is a trip for two to an Open Source event anywhere in >> the world >> http://moblin-contest.org/redirect.php?banner_id=100&url=/ >> ___ >> Jmol-users mailing list >> Jmol-users@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/jmol-users >> >> > > > -- > Robert M. Hanson > Professor of Chemistry > St. Olaf College > Northfield, MN > http://www.stolaf.edu/people/hansonr > > > If nature does not answer first what we want, > it is better to take what answer we get. > > -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 > > > > - > This SF.Net email is sponsored by the Moblin Your Move Developer's > challenge > Build the coolest Linux based applications with Moblin SDK & win > great prizes > Grand prize is a trip for two to an Open Source event anywhere in > the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] selections with more than one variable?
Thanks very much Rolf and Bob -- Your suggestions have done the trick!
Bob: Yes, I agree: the first thing I looked for was a construct such as "and
chain='A'", but found that it is not an option. Obviously, I have a
tendency to overcomplicate things & your concise suggestions are very
educational for me
I think I don't entirely understand the use of parentheses "()" and brackets
"{}" .(when needed, when not)
Many, many thanks for your continued willingness to help!
-Tom
On Tue, Aug 5, 2008 at 9:20 AM, Rolf Huehne <[EMAIL PROTECTED]> wrote:
> Thomas Stout wrote:
> > Has anyone ever made selections using more than one variable
> > simultaneously? I'm referring to something like:
> >
> >
> > select {((resno=xres) and :{x[i]} )};// this is meant to make a
> > selection based on separate algorithmic
> > // identifications
> of
> > desired residue number and chain
> >
> > I've tried several different implementations of this:
> >
> > //within for loop
> > ChX = x[i];
> > select {(resno=xres) and :[EMAIL PROTECTED];
> >
> > and
> >
> > //within for loop
> > selection_expression = "*:"+x[i];
> > select {(resno=xres) and [EMAIL PROTECTED];
> >
>
> This last version works for me with Jmol 11.5.35. Although I havn't used
> a loop but replaced 'x[i]' by ChX (the outer braces made no difference
> so I removed them):
>
> ChX="R"
> sel="*:"+ChX
> select (resno=xres) and (@sel)
>
> When I observe freezing of the display while for example the console
> still responds, there usually was thrown some exception. Have you looked
> at the Java console for error messages?
>
> Regards,
> Rolf
>
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Re: [Jmol-users] draw pointgroup disables isosurface commands
Bill, a few issues there. First, the point group business is still in development (after just a few days!) -- there are known bugs in 11.5.52 that are being fixed for 11.5.53. So please be patient. One issue was that "draw pointgroup" was messing with the set of selected atoms. So when you went to do the isosurface, it was probably creating an isosurface for "select none" or something like that. I think I have that fixed now. Also, I've fixed the way the pointgroup calculation selects its atoms. Now it is more like the MO command -- when you switch to a new model using the FRAME command, if no atoms of that model are selected, all atoms in the current model are assumed to be part of the calculation. In the version you have, you have to explicitly say "select visible" to select the atoms in the frame currently viewed. -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] selections with more than one variable?
Thomas Stout wrote:
> Has anyone ever made selections using more than one variable
> simultaneously? I'm referring to something like:
>
>
> select {((resno=xres) and :{x[i]} )};// this is meant to make a
> selection based on separate algorithmic
> // identifications of
> desired residue number and chain
>
> I've tried several different implementations of this:
>
> //within for loop
> ChX = x[i];
> select {(resno=xres) and :[EMAIL PROTECTED];
>
> and
>
> //within for loop
> selection_expression = "*:"+x[i];
> select {(resno=xres) and [EMAIL PROTECTED];
>
This last version works for me with Jmol 11.5.35. Although I havn't used
a loop but replaced 'x[i]' by ChX (the outer braces made no difference
so I removed them):
ChX="R"
sel="*:"+ChX
select (resno=xres) and (@sel)
When I observe freezing of the display while for example the console
still responds, there usually was thrown some exception. Have you looked
at the Java console for error messages?
Regards,
Rolf
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Re: [Jmol-users] selections with more than one variable?
Thomas Stout wrote:
>
> Has anyone ever made selections using more than one variable
> simultaneously? I'm referring to something like:
>
>
> select {((resno=xres) and :{x[i]} )};// this is meant to make a
> selection based on separate algorithmic
> //
> identifications of desired residue number and chain
>
The ":" designation for a chain is very specific. It needs a chain
descriptor. Right now there is no way to test for chain descriptors (one
could imagine, perhaps, "and chain='A'" for example, but that is not
available.
However, there is a simple way to do ANY complex selection. Simply
create the full select command as a string and then execute it using
script inline. So:
var x = "select resno=xres and :" + x[i]
script inline @x
Also, I don't think that @{x[i]} notation will work. There are a couple
of ways you could do this, though. I would recommend:
select {((resno=xres) and {x[i]} )};
> I've tried several different implementations of this:
>
> //within for loop
> ChX = x[i];
> select {(resno=xres) and :[EMAIL PROTECTED];
>
> and
>
> //within for loop
> selection_expression = "*:"+x[i];
> select {(resno=xres) and [EMAIL PROTECTED];
>
> I've actually lost track of all of the different permutations I've
> tried, but everything seems to result in a null selection, with no
> error. Most recently now, too, the Jmol graphics have been freezing
> as a result of issuing this, so I'm wondering if it is even possible?
>
> Thanks for any suggestions,
> Tom
>
>
>
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>
>
>
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>
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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Re: [Jmol-users] bug in "select"
Sérgio Ceroni da Silva wrote: > Just noticed that 11.4.6 has the old bug where H1, H2 and H3 from DNA > bases are selected as backbone. > Did it resurface or the fix was applied only to 11.5.x ? I think the fix was only applied to 11.5.x. We need to move to 11.6 soon and abandon 11.4. Bob > >-- >Dr. Sérgio Ceroni da Silva >Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul >Av. Bento Gonçalves, 9500 - Prédio 43421 - Campus do Vale - Caixa Postal 15005 >Porto Alegre, RS - Brasil - 91501-970 >== >Tel.: +55 (51) 3316-6091 | Fax: +55 (51) 3316-7309 >http://www6.ufrgs.br/bioquimica > > > > >- >This SF.Net email is sponsored by the Moblin Your Move Developer's challenge >Build the coolest Linux based applications with Moblin SDK & win great prizes >Grand prize is a trip for two to an Open Source event anywhere in the world >http://moblin-contest.org/redirect.php?banner_id=100&url=/ > > > >___ >Jmol-users mailing list >Jmol-users@lists.sourceforge.net >https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] electrostatic potential surface coloring
Reichsman Frieda wrote: >Hi All, >In response to the command above, Jmol comes back with this for Asp: >color range -0.6478 0.2751; mapped data range -0.26758346 to 0.03863874 > > > Frieda, if you are mapping MEP data, remember that a MEP calculation is being done that converts charge on atoms to potential at some distance (on the surface) from a bunch of atoms, collectively. This value falls off with distance. So that's probably why your numbers are low. They aren't just charges, and really they are just approximations of electron potential, as well. If you want to map the charges themselves, you will need to use "map property partialcharge". But that will look somewhat blotchy, I suspsect. I'm sure you have the color range/absolute business correct. Bob >Am I misunderstanding what "color range/absolute x.xxx y.yyy" should >be doing? Is there a way to get the coloring for "color range all" but >only show the surface for the side chains? > >Frieda > > >// > >Frieda Reichsman, PhD >Molecules in Motion >Interactive Molecular Structures >http://www.moleculesinmotion.com >413-253-2405 > >// > > > > > >- >This SF.Net email is sponsored by the Moblin Your Move Developer's challenge >Build the coolest Linux based applications with Moblin SDK & win great prizes >Grand prize is a trip for two to an Open Source event anywhere in the world >http://moblin-contest.org/redirect.php?banner_id=100&url=/ >___ >Jmol-users mailing list >Jmol-users@lists.sourceforge.net >https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] extracting chain ID's into an array?
Thomas Stout wrote:
>
> My sincere thanks to you Rolf! I apologize for taking so long to
> respond, but I had some unexpected travel to do over the weekend. I
> was "not seeing" the concept of "x=script("show chains");" -- it is
> not intuitively obvious (to me) that that will create an array rather
> than just a string (although it is rather flexible and handy that it
> does).
>
> Thanks again!
> -Tom
>
> PS -- I've been busily working at implementing your suggestion and it
> does appear to be working as expected, but I have currently gotten
> hung up with something in this portion of my script causing the Jmol
> graphics to freeze and stop responding. It's quite odd: the console
> still works.
I think that's a bug in mixing ":" with @{...}.
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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