Re: [Jmol-users] Need definitions of protein, nucleic

[Miguel]

> For a revision I am making to firstglance.jmol.org, I need definitions of
> the predefined atom sets "protein", "dna", "rna", and "nucleic".

OK

> By that I
> mean I need the lists of group names for amino acids and nucleotides that
> are selected when you "select (protein,nucleic)". Can someone please give
> me those lists from the Jmol source code?

Given the way that you phrased the question ... this does not have a
direct answer. That is, 'protein' and 'nucleic' are defined by structure,
not by group name. Therefore, there is no list of group names.

I'll make an attempt to define the sets ... ask me if you have additional
questions.

amino
=
Group name of one of the following. This is based only upon group name and
has nothing to do with the actual atoms that make up the group.

"ALA", // 1
"ARG",
"ASN",
"ASP",
"CYS",
"GLN",
"GLU",
"GLY",
"HIS",
"ILE",
"LEU",
"LYS",
"MET",
"PHE",
"PRO", // 15 Proline
"SER",
"THR",
"TRP",
"TYR",
"VAL",
"ASX", // 21 ASP/ASN ambiguous
"GLX", // 22 GLU/GLN ambiguous
"UNK", // 23 unknown -- 23


water
=
based only on group name ... one of the following:

"HOH", // 70
"DOD", // 71
"WAT", // 72

ions

based only on group name

"PO4", // 73 phosphate ions
"SO4", // 74 sulphate ions

protein
===
The 'protein' set is based solely on the atoms that make up the group. It
is independent of the group name and independent of whether the atoms are
defined in ATOM records or HETATM records.

This has the advantage that modified groups and interesting things that
are not amino acids can still be identified as part of the protein.

The atoms that make up the set are recognized by the names of the atoms.

Case 1:
If the group has 4 atoms named 'N', 'CA', 'C' and ('O' or 'O1') and they
are bonded in the correct order, then the group is considered protein.

Case 2:
If the group has exactly 1 atom whose name is 'CA' then it is considered
protein. The purpose of this is to pick up alpha-carbon-only models


nucleic
===
A group is considered 'nucleic' iff it contains (sugar?) atoms with all of
the following names:

JmolConstants.ATOMID_C5,   //  3 C5
JmolConstants.ATOMID_C6,   //  4 C6
JmolConstants.ATOMID_N1,   //  5 N1
JmolConstants.ATOMID_C2,   //  6 C2
JmolConstants.ATOMID_N3,   //  7 N3
JmolConstants.ATOMID_C4,   //  8 C4

JmolConstants.ATOMID_O5_PRIME,  // 22 O5' terminus

JmolConstants.ATOMID_O3_PRIME,  // 24 O3' terminus

JmolConstants.ATOMID_C3_PRIME,  // 26 C3'


rna
===
a group is in the rna group if it is 'nucleic' and it also contains at
atom named O2'

dna
===
a group is in the dna group if it is 'nucleic' and it does *not* contain
an atom named O2'


other nucleic-related groups

// nucleic acid base ring functional groups
//
"N4",  // 74 - base ring N4, unique to C
"N2",  // 75 - base amino N2, unique to G
"N6",  // 76 - base amino N6, unique to A
"C5M", // 77 - base methyl carbon, unique to T

"O6",  // 78 - base carbonyl O6, only in G and I
"O4",  // 79 - base carbonyl O4, only in T and U
"S4",  // 80 - base thiol sulfur, unique to thio-U

[SNIP]

"@c nucleic & within(group,_a=74)", // ATOMID_N4
"@g nucleic & within(group,_a=75)", // ATOMID_N2
"@cg c,g",
"@a nucleic & within(group,_a=76)", // ATOMID_N6
"@t nucleic & within(group,_a=77)", // ATOMID_C5M
"@at a,t",
"@i nucleic & within(group,_a=78) & !g", // ATOMID_O6
"@u nucleic & within(group,_a=79) & !t", // ATOMID_O4
"@tu nucleic & within(group,_a=80)", // ATOMID_S4


Finally, here are the definitions of a lot of other predefined sets ...
most of which are consistent with RasMol.

  
  // predefined sets
  

  public static String[] predefinedSets = {
//
// protein related
//
// protein is hardwired
"@amino _g>0 & _g<=23",
"@acidic asp,glu",
"@basic arg,his,lys",
"@charged acidic,basic",
"@negative acidic",
"@positive basic",
"@neutral amino&!(acidic,basic)",
"@polar amino&!hydrophobic",

"@cyclic his,phe,pro,trp,tyr",
"@acyclic amino&!cyclic",
"@aliphatic ala,gly,ile,leu,val",
"@aromatic his,phe,trp,tyr",
//"@cystine",

"@buried ala,cys,ile,leu,met,phe,trp,val",
"@surface !buried", // this looks wrong to me -- mth

// doc on hydrophobic is inconsistent
// text description of hydrophobic says this
//"@hydrophobic ala,leu,val,ile,pro,phe,met,trp",
// table says this
"@hydrophobic ala,gly,ile,leu,met,phe,pro,trp,tyr,val",
"@ligand hetero & !solvent",
"@mainchain backbone",
"@small ala,gly,ser",
"@medium asn,asp,cys,pro,thr,val",
"@large arg,glu,gln,his,ile,leu,lys,met,phe,trp,tyr",

//
  

Re: [Jmol-users] "Define" a bond

[Timothy Driscoll]

On Jan 5, 2006, at 9:36 a, Eyal, Eran wrote:
Is there an option to artificially create and show a bond between  
two atoms, even if the distance between them is smaller or larger  
than the range which is considered by default for a covalent bond?

hi Eran,

for example, if you want a yellow, 0.3 Angstrom diameter cylinder  
between atoms 1 and 2:


monitor 1 2
set monitors off
set monitors 0.3
color monitors yellow

the command 'set monitors off' turns off the measurement label, which  
is visible by default.  the command 'set monitors 0.3' subsequently  
sets the diameter of the cylinder.


you could also edit the pdb file by hand and add CONECT records, but  
this is more complicated.


hth,

tim
--
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im: molvisions
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Re: [Jmol-users] Need definitions of protein, nucleic

[Timothy Driscoll]

On Jan 5, 2006, at 1:46 p, Eric Martz wrote:

For a revision I am making to firstglance.jmol.org, I need  
definitions of the predefined atom sets "protein", "dna", "rna",  
and "nucleic". By that I mean I need the lists of group names for  
amino acids and nucleotides that are selected when you "select  
(protein,nucleic)". Can someone please give me those lists from the  
Jmol source code?



hi Eric,

see the file src/org/jmol/viewer/JmolConstants.java, especially  
starting around line 1675, for details.


protein and nucleic are determined by atomic composition, not by  
group names.  if I remember the rules correctly, any group with N,  
CA, and C is part of the protein set.  (amino is still determined by  
group names, though - ala, arg, asn, etc.).  the carbonyl O can be  
either O or O1, and I can't recall if that is required for inclusion  
in the protein set.  I don't think so.


for nucleic acids, any group that has the backbone sugar atoms (O5',  
C5', C4', C3', O3', C2', C1') is part of the nucleic set.  the  
presence of an O2' distinguishes RNA from DNA.


hope that helps,

tim
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[Jmol-users] Need definitions of protein, nucleic

[Eric Martz]

For a revision I am making to firstglance.jmol.org, I need definitions of 
the predefined atom sets "protein", "dna", "rna", and "nucleic". By that I 
mean I need the lists of group names for amino acids and nucleotides that 
are selected when you "select (protein,nucleic)". Can someone please give 
me those lists from the Jmol source code?


Should we start a wiki page PredefinedAtomSets ?

Thanks, -Eric

/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor Emeritus, Dept Microbiology
U Mass, Amherst -- http://www.umass.edu/molvis/martz

Protein Explorer - 3D Visualization: http://proteinexplorer.org
See 3D Molecules, Install Nothing! - http://firstglance.jmol.org
Workshops: http://workshops.proteinexplorer.org
Biochem 3D Education Resources http://MolviZ.org
World Index of Molecular Visualization Resources: http://molvisindex.org
ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il
Atlas of Macromolecules: http://atlas.proteinexplorer.org
PDB Lite Macromolecule Finder: http://pdblite.org
Molecular Visualization EMail List (molvis-list):
  http://bioinformatics.org/mailman/listinfo/molvis-list
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Re: [Jmol-users] "Define" a bond

[Timothy Driscoll]

On Jan 5, 2006, at 9:36 a, Eyal, Eran wrote:
Is there an option to artificially create and show a bond between  
two atoms, even if the distance between them is smaller or larger  
than the range which is considered by default for a covalent bond?

hi Eran,

for example, if you want a yellow, 0.3 Angstrom diameter cylinder  
between atoms 1 and 2:


monitor 1 2
set monitors off
set monitors 0.3
color monitors yellow

the command 'set monitors off' turns off the measurement label, which  
is visible by default.  the command 'set monitors 0.3' subsequently  
sets the diameter of the cylinder.


you could also edit the pdb file by hand and add CONECT records, but  
this is more complicated.


hth,

tim
--
Timothy Driscollem: [EMAIL PROTECTED]
molvisions - see. grasp. learn. ph: 919-368-2667
im: molvisions
usa:virginia:blacksburg tx: [EMAIL PROTECTED]







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Re: [Jmol-users] "Define" a bond

[Miguel]

>> Is there an option to artificially create and show a bond between two
>> atoms, even if the distance between them is smaller or larger than the
>> range which is considered by default for a covalent bond?
>>
> There is no script command to create a bond, but there is a workaround
> to create the same effect.
> In CML files you can define bonds between any two atoms, and in that
> case the default Jmol definitions are overruled.

Just to clarify ...

the ability to define bonds in molecular model files works for many file
types, not just CML files. Some of the file types that support
connectivity tables:

  .mol
  .cif
  .pdb (see explanatory note below)

The file types that do *not* support connectivity include:

  .xyz
  gaussian and other molecular modelling types


If connectivity information is present in a file, then Jmol will always
use that information. (see below for extended explanation for .pdb files)


Miguel


PDB files and CONECT records


The PDB specification includes CONECT records which are used to define
bond connectivity between atoms. However, CONECT records are not specified
for "standard residue connectivity".

CONECT records are used for HETATMs, salt bridges, and hydrogen bonding.
These CONECT records supplement the "standard residue connectivity".

Jmol supports an extended definition of CONECT records to give more
flexibility for supporting .pdb files.

The PDB specification says that CONECT records must specify bonding in
both directions. That is, CONECT A->B and CONECT B->A must both be
specified. Jmol does not require this.

If the number of CONECT records is more than 1/2 of the number of
ATOM/HETATM records, then Jmol assumes that all of the connectivity
information is contained in the CONECT records and the 'autobond'
mechanism is not used.

Otherwise, the number of CONECT records is <= 1/2 the number of
ATOM/HETATM records and Jmol runs the 'autobond' calculations to
supplement the connectivity specified by the CONECT records.

CONECT records can also be used to specify double and triple bonds.
Multiple connections that are repeated immediately after the preceding
connection are interpreted as as double or triple bonds. They may be
specified as multiple CONECT records or as multiple destination entries in
the same CONECT record.

So, the following specify double bonds

 CONECT A -> B B
or
 CONECT A -> B
 CONECT A -> B


Finally, note that Jmol strictly interprets the column numbers for
hydrogen bonds. That is, if the destination is in a column for hydrogen
bonds then Jmol will interpret it as a hydrogen bond and will render it as
a dotted line/broken cylinder. I have received complaints about this
because there is at least one software package out there that exports
"PDB" files with full connectivity information where the covalent bonds
are mistakenly put into fields that are designated for hydrogen bonds.


Miguel



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Re: [Jmol-users] "Define" a bond

[Hens Borkent]

Hi Eran,


Hi,

 

Is there an option to artificially create and show a bond between two 
atoms, even if the distance between them is smaller or larger than the 
range which is considered by default for a covalent bond?


 


Eran

 

There is no script command to create a bond, but there is a workaround 
to create the same effect.
In CML files you can define bonds between any two atoms, and in that 
case the default Jmol definitions are overruled.
You can even make a CML file consisting of two identical structures, 
only differing in the definition of one (or more) extra bonds. Now make 
a button that animates the structure, and the effect is that the bond is 
switched on and off.

Send me a structure file if you want me to try it.

Regards,

Hens Borkent
CMBI, Nijmegen


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[Jmol-users] "Define" a bond

[Eyal, Eran]

Hi,

 

Is there an option to artificially create and show a bond
between two atoms, even if the distance between them is smaller or larger than
the range which is considered by default for a covalent bond?

 

Eran