Re: [Jmol-users] mol2 files
- Ursprüngliche Nachricht - Von: Bob Hanson <[EMAIL PROTECTED]> Gesendet: Donnerstag, 14. August 2008 20:19 An: jmol-users@lists.sourceforge.net Betreff: Re: [Jmol-users] mol2 files Where do these files come from? The mol2 format does not allow for anything between the number and the element symbol on that atom line. http://www.tripos.com/tripos_resources/fileroot/mol2_format_Dec07.pdf Bob Reichsman Frieda wrote: > Hi Bob, > > I have some mol2 files wherein Jmol cannot read the embedded EPS (or > are they more correctly called partial charge) values, and also Jmol > fails to render one atom in the file. An example file is attached, > along with one that Jmol reads fine: ala-problem.mol2 (Jmol won't > read EPS) and ala.mol2 (Jmol does read EPS), > > Comparing the two mol2 files, the format is slightly different. I am > not sure if the file is formatted incorrectly (generated by the > program AtomSmith), or if Jmol is too strict. The differences are as > follows. > > In the ala-problem.mol2 file, > 1. The eps values from are offset by one additional space from the > coordinates, and > 2. the three-letter abbreviation for the amino acid is missing in > each row from inbetween the number "1" and the EPS values. > > When I change both these aspects to mimic the file ala.mol2, Jmol can > read the eps values. > > 3. In the ala-problem.mol2 file I also had to remove the ALA that > appears as characters 4, 5 and 6 in the line for atom #1, in order > for Jmol to be able to render that particular atom. > > > Frieda > > > // > > Frieda Reichsman, PhD > Molecules in Motion > Interactive Molecular Structures > http://www.moleculesinmotion.com > 413-253-2405 > > // > > > > > // > > Frieda Reichsman, PhD > Molecules in Motion > Interactive Molecular Structures > http://www.moleculesinmotion.com > 413-253-2405 > > // > > > > > > >- [Die ursprüngliche Nachricht wird nicht vollständig eingefügt.] - 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] mol2 files
Just send them that documentation. Pretty clear that they have that wrong and will want to correct it. Reichsman Frieda wrote: >They come from AtomSmith, which is from Bitwixt software. The file >that works in Jmol is included with the program; the file that does >not work in Jmol is AtomSmith's output when it starts with a pdb file, >puts an EP surface around it, and exports it as mol2. If it's their >formatting needs changing, then I can urge them to deal with it - I >have already emailed them about it twice. > >Frieda > > > >On Aug 14, 2008, at 2:19 PM, Bob Hanson wrote: > > > >>Where do these files come from? The mol2 format does not allow for >>anything between the number and the element symbol on that atom line. >> >>http://www.tripos.com/tripos_resources/fileroot/mol2_format_Dec07.pdf >> >>Bob >> >> >>Reichsman Frieda wrote: >> >> >> >>>Hi Bob, >>> >>>I have some mol2 files wherein Jmol cannot read the embedded EPS (or >>>are they more correctly called partial charge) values, and also Jmol >>>fails to render one atom in the file. An example file is attached, >>>along with one that Jmol reads fine: ala-problem.mol2 (Jmol won't >>>read EPS) and ala.mol2 (Jmol does read EPS), >>> >>>Comparing the two mol2 files, the format is slightly different. I am >>>not sure if the file is formatted incorrectly (generated by the >>>program AtomSmith), or if Jmol is too strict. The differences are as >>>follows. >>> >>>In the ala-problem.mol2 file, >>>1. The eps values from are offset by one additional space from the >>>coordinates, and >>>2. the three-letter abbreviation for the amino acid is missing in >>>each row from inbetween the number "1" and the EPS values. >>> >>>When I change both these aspects to mimic the file ala.mol2, Jmol can >>>read the eps values. >>> >>>3. In the ala-problem.mol2 file I also had to remove the ALA that >>>appears as characters 4, 5 and 6 in the line for atom #1, in order >>>for Jmol to be able to render that particular atom. >>> >>> >>>Frieda >>> >>> >>>// >>> >>>Frieda Reichsman, PhD >>>Molecules in Motion >>>Interactive Molecular Structures >>>http://www.moleculesinmotion.com >>>413-253-2405 >>> >>>// >>> >>> >>> >>> >>>// >>> >>>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 > > -- 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 -
Re: [Jmol-users] mol2 files
They come from AtomSmith, which is from Bitwixt software. The file that works in Jmol is included with the program; the file that does not work in Jmol is AtomSmith's output when it starts with a pdb file, puts an EP surface around it, and exports it as mol2. If it's their formatting needs changing, then I can urge them to deal with it - I have already emailed them about it twice. Frieda On Aug 14, 2008, at 2:19 PM, Bob Hanson wrote: > Where do these files come from? The mol2 format does not allow for > anything between the number and the element symbol on that atom line. > > http://www.tripos.com/tripos_resources/fileroot/mol2_format_Dec07.pdf > > Bob > > > Reichsman Frieda wrote: > >> Hi Bob, >> >> I have some mol2 files wherein Jmol cannot read the embedded EPS (or >> are they more correctly called partial charge) values, and also Jmol >> fails to render one atom in the file. An example file is attached, >> along with one that Jmol reads fine: ala-problem.mol2 (Jmol won't >> read EPS) and ala.mol2 (Jmol does read EPS), >> >> Comparing the two mol2 files, the format is slightly different. I am >> not sure if the file is formatted incorrectly (generated by the >> program AtomSmith), or if Jmol is too strict. The differences are as >> follows. >> >> In the ala-problem.mol2 file, >> 1. The eps values from are offset by one additional space from the >> coordinates, and >> 2. the three-letter abbreviation for the amino acid is missing in >> each row from inbetween the number "1" and the EPS values. >> >> When I change both these aspects to mimic the file ala.mol2, Jmol can >> read the eps values. >> >> 3. In the ala-problem.mol2 file I also had to remove the ALA that >> appears as characters 4, 5 and 6 in the line for atom #1, in order >> for Jmol to be able to render that particular atom. >> >> >> Frieda >> >> >> // >> >> Frieda Reichsman, PhD >> Molecules in Motion >> Interactive Molecular Structures >> http://www.moleculesinmotion.com >> 413-253-2405 >> >> // >> >> >> >> >> // >> >> 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] mol2 files
Where do these files come from? The mol2 format does not allow for anything between the number and the element symbol on that atom line. http://www.tripos.com/tripos_resources/fileroot/mol2_format_Dec07.pdf Bob Reichsman Frieda wrote: > Hi Bob, > > I have some mol2 files wherein Jmol cannot read the embedded EPS (or > are they more correctly called partial charge) values, and also Jmol > fails to render one atom in the file. An example file is attached, > along with one that Jmol reads fine: ala-problem.mol2 (Jmol won't > read EPS) and ala.mol2 (Jmol does read EPS), > > Comparing the two mol2 files, the format is slightly different. I am > not sure if the file is formatted incorrectly (generated by the > program AtomSmith), or if Jmol is too strict. The differences are as > follows. > > In the ala-problem.mol2 file, > 1. The eps values from are offset by one additional space from the > coordinates, and > 2. the three-letter abbreviation for the amino acid is missing in > each row from inbetween the number "1" and the EPS values. > > When I change both these aspects to mimic the file ala.mol2, Jmol can > read the eps values. > > 3. In the ala-problem.mol2 file I also had to remove the ALA that > appears as characters 4, 5 and 6 in the line for atom #1, in order > for Jmol to be able to render that particular atom. > > > Frieda > > > // > > Frieda Reichsman, PhD > Molecules in Motion > Interactive Molecular Structures > http://www.moleculesinmotion.com > 413-253-2405 > > // > > > > > // > > 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
[Jmol-users] mol2 files
I wrote: > and also Jmol fails to render one atom in the file. this only occurs after I fix problems 1 and 2 (as listed in previous post). // 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
[Jmol-users] mol2 files
Hi Bob, I have some mol2 files wherein Jmol cannot read the embedded EPS (or are they more correctly called partial charge) values, and also Jmol fails to render one atom in the file. An example file is attached, along with one that Jmol reads fine: ala-problem.mol2 (Jmol won't read EPS) and ala.mol2 (Jmol does read EPS), Comparing the two mol2 files, the format is slightly different. I am not sure if the file is formatted incorrectly (generated by the program AtomSmith), or if Jmol is too strict. The differences are as follows. In the ala-problem.mol2 file, 1. The eps values from are offset by one additional space from the coordinates, and 2. the three-letter abbreviation for the amino acid is missing in each row from inbetween the number "1" and the EPS values. When I change both these aspects to mimic the file ala.mol2, Jmol can read the eps values. 3. In the ala-problem.mol2 file I also had to remove the ALA that appears as characters 4, 5 and 6 in the line for atom #1, in order for Jmol to be able to render that particular atom. Frieda ala-problem.mol2 Description: Binary data ala.mol2 Description: Binary data // Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com 413-253-2405 // // 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
Re: [Jmol-users] Mol2 files (again!)
> # applySymmetryToBonds
> #
> # When set TRUE, this flag instructs Jmol when applying symmetry
> # to atoms, as in "load xxx.cif {1 1 1}", to also apply symmetry
> # to the bonds indicated in the file. The flag is useful when
> # normal Jmol autobonding would not properly connect atoms, but
> # the model is "molecular" -- the base atom coordinates are correct
> # for whole molecules. The flag should NOT be used in cases where
> # the application of symmetry operations creates new bonds that
> # were not present in the original set, as for quartz.cif, where
> # there is only one bond initially, and after applying symmetry
> # new bonds are created that are between atoms that were created
> # using two different symmetry operations.
>
> This appears to work perfectly for the example file Aiden provided.
> It does connect the atoms properly in quartz.cif, but some bonds
> are missing, as
> noted above. It also fails to connect bonds properly in a test sample
> I have that involves a cif file with alternative locations but bonding
> only shown for one alternative. So there are definitely limitations,
> and I have set the default to be FALSE -- no change from previous
> behavior. You must explicitly include:
>
> applySymmetryToBonds = true
>
> prior to loading a file to instruct Jmol to carry out this bonding
> algorithm.
Bob, you are a pearl. Thanks heaps. I look forward to testing this out.
Cheers
Aidan
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Re: [Jmol-users] Mol2 files (again!)
OK, this code is checked in as part of 11.1.29. I have bit more
testing to do on that today, and then that should be available. The
flag looks like this:
version=11.1.29
# adds applySymmetryToBonds (default: FALSE)
# applySymmetryToBonds
#
# When set TRUE, this flag instructs Jmol when applying symmetry
# to atoms, as in "load xxx.cif {1 1 1}", to also apply symmetry
# to the bonds indicated in the file. The flag is useful when
# normal Jmol autobonding would not properly connect atoms, but
# the model is "molecular" -- the base atom coordinates are correct
# for whole molecules. The flag should NOT be used in cases where
# the application of symmetry operations creates new bonds that
# were not present in the original set, as for quartz.cif, where
# there is only one bond initially, and after applying symmetry
# new bonds are created that are between atoms that were created
# using two different symmetry operations.
This appears to work perfectly for the example file Aiden provided.
It does connect the atoms properly in quartz.cif, but some bonds are missing, as
noted above. It also fails to connect bonds properly in a test sample
I have that involves a cif file with alternative locations but bonding
only shown for one alternative. So there are definitely limitations,
and I have set the default to be FALSE -- no change from previous
behavior. You must explicitly include:
applySymmetryToBonds = true
prior to loading a file to instruct Jmol to carry out this bonding algorithm.
Bob Hanson
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Re: [Jmol-users] Mol2 files (again!)
I've added this flag, but I don't know what to call it.
On 4/23/07, Bob Hanson <[EMAIL PROTECTED]> wrote:
> OK I see how to do this right now, and I'll see if I can set up a user
> flag for bonding the symmetry atoms. Actually, maybe in the case of
> mol2 files this should be automatic -- as I recall they are always
> packed or, to put it another way, we can't deal with the symmetry
> operators anyway, so we just call it "P1*".
>
> It is a nice application of the new "load append" capability.
> You can do it with the following:
>
> appendnew = false
> load t.mol2
> select *;translateselected {1/1 0 0}
> load append ""
>
> select *;translateselected {0 1/1 0}
> load append ""
>
> ...etc...
>
>
>
> On 4/23/07, Bob Hanson <[EMAIL PROTECTED]> wrote:
> > Well, let's see.
> >
> > I can display the molecules one at a time using:
> >
> > display molecule=1
> > display molecule=2
> >
> > etc.
> >
> > So that takes care of the no-symmetry issue.
> >
> > But you want to take this file and apply symmetry operators and
> > multiple unit cells, is that right?
> >
> > OK, the problem comes down to the fact that in general when you apply
> > symmetry operators it is quite common to have redundant operators.
> > BUT, am I correct that this kind of data is "prepacked" - that is,
> > only the translational operators are necessary? All the rotations and
> > reflections and such are already represented? No duplicate atom
> > positions if we just added translations?
> >
> > Bob
> >
>
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Re: [Jmol-users] Mol2 files (again!)
OK I see how to do this right now, and I'll see if I can set up a user
flag for bonding the symmetry atoms. Actually, maybe in the case of
mol2 files this should be automatic -- as I recall they are always
packed or, to put it another way, we can't deal with the symmetry
operators anyway, so we just call it "P1*".
It is a nice application of the new "load append" capability.
You can do it with the following:
appendnew = false
load t.mol2
select *;translateselected {1/1 0 0}
load append ""
select *;translateselected {0 1/1 0}
load append ""
...etc...
On 4/23/07, Bob Hanson <[EMAIL PROTECTED]> wrote:
> Well, let's see.
>
> I can display the molecules one at a time using:
>
> display molecule=1
> display molecule=2
>
> etc.
>
> So that takes care of the no-symmetry issue.
>
> But you want to take this file and apply symmetry operators and
> multiple unit cells, is that right?
>
> OK, the problem comes down to the fact that in general when you apply
> symmetry operators it is quite common to have redundant operators.
> BUT, am I correct that this kind of data is "prepacked" - that is,
> only the translational operators are necessary? All the rotations and
> reflections and such are already represented? No duplicate atom
> positions if we just added translations?
>
> Bob
>
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Re: [Jmol-users] Mol2 files (again!)
Well, let's see. I can display the molecules one at a time using: display molecule=1 display molecule=2 etc. So that takes care of the no-symmetry issue. But you want to take this file and apply symmetry operators and multiple unit cells, is that right? OK, the problem comes down to the fact that in general when you apply symmetry operators it is quite common to have redundant operators. BUT, am I correct that this kind of data is "prepacked" - that is, only the translational operators are necessary? All the rotations and reflections and such are already represented? No duplicate atom positions if we just added translations? Bob - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Mol2 files (again!)
Bob Hansen said: > Aidan asked: > >> In a previous email you said >> >> "Bonds are not projected into symmetry-generated atoms when there is >> bonding indicated already in the file." >> >> Is there a reason why this is so? > Yes, because some of the atoms in a bond may be in special > positions and > others may not be, so when symmetry is applied, the number of bonds > may > not be a multiple of the number of new atoms. I think > > But you can still do this, I think. Show me the file. And also: > Actually, it's just: > > set minbonddistance 0.9 > load x.xxx Thanks for the suggestions, but this does not work for this example: http://rsc.anu.edu.au/~aidan/PCNB_lowsymm_packed.mol2 which is an extreme example of the sort of substitutional disorder we commonly encounter. Could there be a user settable flag to attempt to use as much bonding information from the "base atoms" as possible? If this is not possible, could you point out to me where in the code I would implement this change and I could have a go at making my own patched version of Jmol. I tried to find where the symmetry expansion is done, but to be honest I couldn't find it. This is a real show- stopper for me and I am in the middle of making a javascript application using Jmol to define intermolecular contact vectors. Cheers Aidan - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Mol2 files (again!)
Actually, it's just:
set minbonddistance 0.9
load x.xxx
Aidan Heerdegen wrote:
>Bob,
>
>Sorry to be a pain, but I'm back to trying to get jmol to read in my
>disordered mol2 files.
>
>My problem boils down to this, when I do this:
>
> > load disordered.mol2 {444 666 1}
>
>My disordered molecules (which lie on similar sites in the unit cell)
>are autobonded together. Not good.
>
>If I do this:
>
> > set autobond false; load disordered.mol2 {444 666 1}
>
>the bonding is correct in the molecules read from the file, but the
>ones generated by translations are not bonded at all.
>
>In a previous email you said
>
>"Bonds are not projected into symmetry-generated atoms when there is
>bonding indicated already in the file."
>
>Is there a reason why this is so?
>
>Thanks
>
>Aidan
>
>
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Re: [Jmol-users] Mol2 files (again!)
Aidan Heerdegen wrote:
>Bob,
>
>Sorry to be a pain, but I'm back to trying to get jmol to read in my
>disordered mol2 files.
>
>My problem boils down to this, when I do this:
>
> > load disordered.mol2 {444 666 1}
>
>My disordered molecules (which lie on similar sites in the unit cell)
>are autobonded together. Not good.
>
>If I do this:
>
> > set autobond false; load disordered.mol2 {444 666 1}
>
>the bonding is correct in the molecules read from the file, but the
>ones generated by translations are not bonded at all.
>
>In a previous email you said
>
>"Bonds are not projected into symmetry-generated atoms when there is
>bonding indicated already in the file."
>
>Is there a reason why this is so?
>
>
>
Yes, because some of the atoms in a bond may be in special positions and
others may not be, so when symmetry is applied, the number of bonds may
not be a multiple of the number of new atoms. I think
But you can still do this, I think. Show me the file.
>Thanks
>
>Aidan
>
>
>-
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>
>
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[Jmol-users] Mol2 files (again!)
Bob,
Sorry to be a pain, but I'm back to trying to get jmol to read in my
disordered mol2 files.
My problem boils down to this, when I do this:
> load disordered.mol2 {444 666 1}
My disordered molecules (which lie on similar sites in the unit cell)
are autobonded together. Not good.
If I do this:
> set autobond false; load disordered.mol2 {444 666 1}
the bonding is correct in the molecules read from the file, but the
ones generated by translations are not bonded at all.
In a previous email you said
"Bonds are not projected into symmetry-generated atoms when there is
bonding indicated already in the file."
Is there a reason why this is so?
Thanks
Aidan
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