Re: [Jmol-developers] current work
On Wed, Sep 15, 2010 at 7:38 PM, Jonathan Gutow gu...@uwosh.edu wrote: On Sep 15, 2010, at 10:41 AM, Robert Hanson wrote: -- proposing a NEW DEFAULT for Jmol for 12.1 and 12.0: double bonds in the plane of the atoms, not twisty with orientation. This is the default I always expected, but the current default makes sure that you can tell which are double bonds. I'm not sure if I really want it changed to what I expected I believe that the original argument for doing it the current way is to ensure that the double bond always has full visibility... if in the atoms plane (which atoms), and that plane happens to be perpendicular to the eyes, then one will not see the double bond, but a single bond instead... Egon -- Dr E.L. Willighagen Post-doc @ Uppsala University (only until 2010-09-30) Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg Homepage: http://egonw.github.com/ LinkedIn: http://se.linkedin.com/in/egonw Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers -- Start uncovering the many advantages of virtual appliances and start using them to simplify application deployment and accelerate your shift to cloud computing. http://p.sf.net/sfu/novell-sfdev2dev ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
[Jmol-developers] supercell option
Dear all,
could be possible to add an option to re-set the dimensions of the cell once
you the original cell is manipulated?
For instance load { 2 2 2} ; the command could be setSupercell ?
So then when the structure is esported both the coordinate and the cell
parameters are correctely exported.
Thanks, Piero
--
Please consider the environment before printing this e-mail.
Pieremanuele Canepa
Room 104
Functional Material Group
School of Physical Sciences, Ingram Building,
University of Kent, Canterbury, Kent,
CT2 7NH
United Kingdom
e-mail: pc...@kent.ac.uk
mobile: +44 (0) 7772-9756456
---
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Re: [Jmol-developers] current work/double bond view...
I've played with Bob's example and here is my opinion. Before I used Jmol I thought the default should be double bonds all in one plane, but now feel that Jmol's present default where you see the double bonds no matter what the viewing angle is better. I do think the scale of the double bond should be set smaller than the current default and like the idea of an option to make the double bond plane fixed relative to the molecule axes. The double bonds in a fixed plane should be an option not the default. Should we do a poll and maybe on the user's list? Joanthan Dr. Jonathan H. Gutow Chemistry Department gu...@uwosh.edu UW-Oshkosh Office:920-424-1326 800 Algoma Boulevard FAX:920-424-2042 Oshkosh, WI 54901 http://www.uwosh.edu/facstaff/gutow -- Start uncovering the many advantages of virtual appliances and start using them to simplify application deployment and accelerate your shift to cloud computing. http://p.sf.net/sfu/novell-sfdev2dev ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
[Jmol-developers] [ jmol-Bugs-3066682 ] Bug in secondary prediction
Bugs item #3066682, was opened at 2010-09-15 10:48
Message generated for change (Comment added) made by lili35
You can respond by visiting:
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Category: Applet
Group: v11
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: lili35 (lili35)
Assigned to: Miguel (migueljmol)
Summary: Bug in secondary prediction
Initial Comment:
Jmol seems to have a problem with some secondary structure prediction.
Some amino acids represented in turn in some molecular graphic software (Pymol,
Chimera, Rasmol, VMD...) are represented in beta sheet in Jmol.
You can see it in attachment.
I think it is a bug. How can I fix it ?
--
Comment By: lili35 (lili35)
Date: 2010-09-17 16:42
Message:
Thanks for your help.
On my website, I will use Jmol to visualize hundred of models like this.
So manually disable structure is not easier.
I prefer reduce phi / psi angle allowed in the function 'isSheet' and
create my own JmolApplet. I do this, it works but I can't build the Applet
with build.xml. I work on a Mac OS 10.6.4 and Eclipse Helios (3.6).
I have this error message :
Buildfile: ~/Documents/workspace/Jmol/build.xml
[taskdef] Could not load definitions from resource
net/sf/antcontrib/antlib.xml. It could not be found.
BUILD FAILED
~/Documents/workspace/Jmol/build.xml:54: Cannot find tools/build-i18n.xml
imported from ~/Documents/workspace/Jmol/build.xml
Can you help me again ? ;-)
--
Comment By: Nobody/Anonymous (nobody)
Date: 2010-09-16 17:02
Message:
It may not be a bug - as you point out, the torsions are 'strand like' -
but isolated segments like this are definitely not sheets. A sheet has at
least two strands, hbonded to each other. In fact, this stretch of chain is
something like a poly-proline helix conformation, I think.
--
Comment By: Bob Hanson (hansonr)
Date: 2010-09-16 16:58
Message:
This is not a bug. Usually Jmol uses the HELIX and SHEET designations in
the PDB file, but this file has no header, so Jmol is doing the calculation
itself. That calculation is simply:
private static boolean isSheet(float psi, float phi) {
return
( (phi = -180) (phi = -10) (psi = 70) (psi = 180) ) ||
( (phi = -180) (phi = -45) (psi = -180) (psi = -130) )
||
( (phi = 140) (phi = 180) (psi = 90) (psi = 180) );
}
In this case we have for phi/psi:
GLU29 -75.46 -41.95
ASN30 -111.74 70.29 *
ILE31 -94.93 109.93 *
PRO32 -52.12 166.21 *
so 30-32 are being tagged as sheet. I'm sure the other programs are using
hydrogen bonding.
If you don't like it, use in this case
structure none {30-32}
cartoons on
Bob
--
Comment By: lili35 (lili35)
Date: 2010-09-15 22:15
Message:
It's done !
--
Comment By: Bob Hanson (hansonr)
Date: 2010-09-15 17:28
Message:
please upload the PDB file.
--
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Re: [Jmol-developers] supercell option
load {2 2 2}
works just fine, right?
Bob
On Fri, Sep 17, 2010 at 2:04 AM, P.Canepa pc...@kent.ac.uk wrote:
Dear all,
could be possible to add an option to re-set the dimensions of the cell
once you the original cell is manipulated?
For instance load { 2 2 2} ; the command could be setSupercell ?
So then when the structure is esported both the coordinate and the cell
parameters are correctely exported.
Thanks, Piero
--
*Please consider the environment before printing this e-mail.*
**
Pieremanuele Canepa
Room 104
Functional Material Group
School of Physical Sciences, Ingram Building,
University of Kent, Canterbury, Kent,
CT2 7NH
United Kingdom
e-mail: pc...@kent.ac.uk
mobile: +44 (0) 7772-9756456
---
--
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and start using them to simplify application deployment and
accelerate your shift to cloud computing.
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--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
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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[Jmol-developers] [ jmol-Bugs-3066682 ] Bug in secondary prediction
Bugs item #3066682, was opened at 2010-09-15 03:48
Message generated for change (Comment added) made by hansonr
You can respond by visiting:
https://sourceforge.net/tracker/?func=detailatid=379133aid=3066682group_id=23629
Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: Applet
Group: v11
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: lili35 (lili35)
Assigned to: Miguel (migueljmol)
Summary: Bug in secondary prediction
Initial Comment:
Jmol seems to have a problem with some secondary structure prediction.
Some amino acids represented in turn in some molecular graphic software (Pymol,
Chimera, Rasmol, VMD...) are represented in beta sheet in Jmol.
You can see it in attachment.
I think it is a bug. How can I fix it ?
--
Comment By: Bob Hanson (hansonr)
Date: 2010-09-17 11:02
Message:
I do hate to see you create an all new applet just for this. Why don't we
make it adjustable?
--
Comment By: lili35 (lili35)
Date: 2010-09-17 09:42
Message:
Thanks for your help.
On my website, I will use Jmol to visualize hundred of models like this.
So manually disable structure is not easier.
I prefer reduce phi / psi angle allowed in the function 'isSheet' and
create my own JmolApplet. I do this, it works but I can't build the Applet
with build.xml. I work on a Mac OS 10.6.4 and Eclipse Helios (3.6).
I have this error message :
Buildfile: ~/Documents/workspace/Jmol/build.xml
[taskdef] Could not load definitions from resource
net/sf/antcontrib/antlib.xml. It could not be found.
BUILD FAILED
~/Documents/workspace/Jmol/build.xml:54: Cannot find tools/build-i18n.xml
imported from ~/Documents/workspace/Jmol/build.xml
Can you help me again ? ;-)
--
Comment By: Nobody/Anonymous (nobody)
Date: 2010-09-16 10:02
Message:
It may not be a bug - as you point out, the torsions are 'strand like' -
but isolated segments like this are definitely not sheets. A sheet has at
least two strands, hbonded to each other. In fact, this stretch of chain is
something like a poly-proline helix conformation, I think.
--
Comment By: Bob Hanson (hansonr)
Date: 2010-09-16 09:58
Message:
This is not a bug. Usually Jmol uses the HELIX and SHEET designations in
the PDB file, but this file has no header, so Jmol is doing the calculation
itself. That calculation is simply:
private static boolean isSheet(float psi, float phi) {
return
( (phi = -180) (phi = -10) (psi = 70) (psi = 180) ) ||
( (phi = -180) (phi = -45) (psi = -180) (psi = -130) )
||
( (phi = 140) (phi = 180) (psi = 90) (psi = 180) );
}
In this case we have for phi/psi:
GLU29 -75.46 -41.95
ASN30 -111.74 70.29 *
ILE31 -94.93 109.93 *
PRO32 -52.12 166.21 *
so 30-32 are being tagged as sheet. I'm sure the other programs are using
hydrogen bonding.
If you don't like it, use in this case
structure none {30-32}
cartoons on
Bob
--
Comment By: lili35 (lili35)
Date: 2010-09-15 15:15
Message:
It's done !
--
Comment By: Bob Hanson (hansonr)
Date: 2010-09-15 10:28
Message:
please upload the PDB file.
--
You can respond by visiting:
https://sourceforge.net/tracker/?func=detailatid=379133aid=3066682group_id=23629
--
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and start using them to simplify application deployment and
accelerate your shift to cloud computing.
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[Jmol-developers] [ jmol-Bugs-3066682 ] Bug in secondary prediction
Bugs item #3066682, was opened at 2010-09-15 03:48
Message generated for change (Comment added) made by hansonr
You can respond by visiting:
https://sourceforge.net/tracker/?func=detailatid=379133aid=3066682group_id=23629
Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: Applet
Group: v11
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: lili35 (lili35)
Assigned to: Miguel (migueljmol)
Summary: Bug in secondary prediction
Initial Comment:
Jmol seems to have a problem with some secondary structure prediction.
Some amino acids represented in turn in some molecular graphic software (Pymol,
Chimera, Rasmol, VMD...) are represented in beta sheet in Jmol.
You can see it in attachment.
I think it is a bug. How can I fix it ?
--
Comment By: Bob Hanson (hansonr)
Date: 2010-09-17 12:57
Message:
12.1.15 -- I've added
structure SHEET set [-180,-40, 50, 80, -160, -30, 60, 90] # nonsense
numbers here.
meaning define SHEET to be phi=-180 and phi =-40 and psi = 50 and psi
80 OR phi =-160 and phi =-30 and psi =60 and psi = 90
similar --- structure HELIX... structure TURN
I realize this does not solve the issue that strands are not sheets, but
it is what I propose for now. Ages ago Jmol did attempt to use hydrogen
bonding to identify sheets, but this was only for intra-strand sheets,
which was not very satisfactory. We could still do something along those
lines, but really it is so rarely the issue -- mostly we use PDB files that
have all this defined already -- and the calculation is fairly involved to
get all the hydrogen bonds.
Bob
Bob
--
Comment By: Bob Hanson (hansonr)
Date: 2010-09-17 11:02
Message:
I do hate to see you create an all new applet just for this. Why don't we
make it adjustable?
--
Comment By: lili35 (lili35)
Date: 2010-09-17 09:42
Message:
Thanks for your help.
On my website, I will use Jmol to visualize hundred of models like this.
So manually disable structure is not easier.
I prefer reduce phi / psi angle allowed in the function 'isSheet' and
create my own JmolApplet. I do this, it works but I can't build the Applet
with build.xml. I work on a Mac OS 10.6.4 and Eclipse Helios (3.6).
I have this error message :
Buildfile: ~/Documents/workspace/Jmol/build.xml
[taskdef] Could not load definitions from resource
net/sf/antcontrib/antlib.xml. It could not be found.
BUILD FAILED
~/Documents/workspace/Jmol/build.xml:54: Cannot find tools/build-i18n.xml
imported from ~/Documents/workspace/Jmol/build.xml
Can you help me again ? ;-)
--
Comment By: Nobody/Anonymous (nobody)
Date: 2010-09-16 10:02
Message:
It may not be a bug - as you point out, the torsions are 'strand like' -
but isolated segments like this are definitely not sheets. A sheet has at
least two strands, hbonded to each other. In fact, this stretch of chain is
something like a poly-proline helix conformation, I think.
--
Comment By: Bob Hanson (hansonr)
Date: 2010-09-16 09:58
Message:
This is not a bug. Usually Jmol uses the HELIX and SHEET designations in
the PDB file, but this file has no header, so Jmol is doing the calculation
itself. That calculation is simply:
private static boolean isSheet(float psi, float phi) {
return
( (phi = -180) (phi = -10) (psi = 70) (psi = 180) ) ||
( (phi = -180) (phi = -45) (psi = -180) (psi = -130) )
||
( (phi = 140) (phi = 180) (psi = 90) (psi = 180) );
}
In this case we have for phi/psi:
GLU29 -75.46 -41.95
ASN30 -111.74 70.29 *
ILE31 -94.93 109.93 *
PRO32 -52.12 166.21 *
so 30-32 are being tagged as sheet. I'm sure the other programs are using
hydrogen bonding.
If you don't like it, use in this case
structure none {30-32}
cartoons on
Bob
--
Comment By: lili35 (lili35)
Date: 2010-09-15 15:15
Message:
It's done !
--
Comment By: Bob Hanson (hansonr)
Date: 2010-09-15 10:28
Message:
please upload the PDB file.
--
You can respond by visiting:
https://sourceforge.net/tracker/?func=detailatid=379133aid=3066682group_id=23629
--
Start uncovering the many advantages of virtual appliances
and start using them to simplify application deployment and
accelerate your shift to cloud computing.
http://p.sf.net/sfu/novell-sfdev2dev
[Jmol-developers] [ jmol-Bugs-3066682 ] Bug in secondary prediction
Bugs item #3066682, was opened at 2010-09-15 03:48
Message generated for change (Comment added) made by hansonr
You can respond by visiting:
https://sourceforge.net/tracker/?func=detailatid=379133aid=3066682group_id=23629
Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: Applet
Group: v11
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: lili35 (lili35)
Assigned to: Miguel (migueljmol)
Summary: Bug in secondary prediction
Initial Comment:
Jmol seems to have a problem with some secondary structure prediction.
Some amino acids represented in turn in some molecular graphic software (Pymol,
Chimera, Rasmol, VMD...) are represented in beta sheet in Jmol.
You can see it in attachment.
I think it is a bug. How can I fix it ?
--
Comment By: Bob Hanson (hansonr)
Date: 2010-09-17 12:58
Message:
should be = 80 there
--
Comment By: Bob Hanson (hansonr)
Date: 2010-09-17 12:57
Message:
12.1.15 -- I've added
structure SHEET set [-180,-40, 50, 80, -160, -30, 60, 90] # nonsense
numbers here.
meaning define SHEET to be phi=-180 and phi =-40 and psi = 50 and psi
80 OR phi =-160 and phi =-30 and psi =60 and psi = 90
similar --- structure HELIX... structure TURN
I realize this does not solve the issue that strands are not sheets, but
it is what I propose for now. Ages ago Jmol did attempt to use hydrogen
bonding to identify sheets, but this was only for intra-strand sheets,
which was not very satisfactory. We could still do something along those
lines, but really it is so rarely the issue -- mostly we use PDB files that
have all this defined already -- and the calculation is fairly involved to
get all the hydrogen bonds.
Bob
Bob
--
Comment By: Bob Hanson (hansonr)
Date: 2010-09-17 11:02
Message:
I do hate to see you create an all new applet just for this. Why don't we
make it adjustable?
--
Comment By: lili35 (lili35)
Date: 2010-09-17 09:42
Message:
Thanks for your help.
On my website, I will use Jmol to visualize hundred of models like this.
So manually disable structure is not easier.
I prefer reduce phi / psi angle allowed in the function 'isSheet' and
create my own JmolApplet. I do this, it works but I can't build the Applet
with build.xml. I work on a Mac OS 10.6.4 and Eclipse Helios (3.6).
I have this error message :
Buildfile: ~/Documents/workspace/Jmol/build.xml
[taskdef] Could not load definitions from resource
net/sf/antcontrib/antlib.xml. It could not be found.
BUILD FAILED
~/Documents/workspace/Jmol/build.xml:54: Cannot find tools/build-i18n.xml
imported from ~/Documents/workspace/Jmol/build.xml
Can you help me again ? ;-)
--
Comment By: Nobody/Anonymous (nobody)
Date: 2010-09-16 10:02
Message:
It may not be a bug - as you point out, the torsions are 'strand like' -
but isolated segments like this are definitely not sheets. A sheet has at
least two strands, hbonded to each other. In fact, this stretch of chain is
something like a poly-proline helix conformation, I think.
--
Comment By: Bob Hanson (hansonr)
Date: 2010-09-16 09:58
Message:
This is not a bug. Usually Jmol uses the HELIX and SHEET designations in
the PDB file, but this file has no header, so Jmol is doing the calculation
itself. That calculation is simply:
private static boolean isSheet(float psi, float phi) {
return
( (phi = -180) (phi = -10) (psi = 70) (psi = 180) ) ||
( (phi = -180) (phi = -45) (psi = -180) (psi = -130) )
||
( (phi = 140) (phi = 180) (psi = 90) (psi = 180) );
}
In this case we have for phi/psi:
GLU29 -75.46 -41.95
ASN30 -111.74 70.29 *
ILE31 -94.93 109.93 *
PRO32 -52.12 166.21 *
so 30-32 are being tagged as sheet. I'm sure the other programs are using
hydrogen bonding.
If you don't like it, use in this case
structure none {30-32}
cartoons on
Bob
--
Comment By: lili35 (lili35)
Date: 2010-09-15 15:15
Message:
It's done !
--
Comment By: Bob Hanson (hansonr)
Date: 2010-09-15 10:28
Message:
please upload the PDB file.
--
You can respond by visiting:
https://sourceforge.net/tracker/?func=detailatid=379133aid=3066682group_id=23629
--
Start uncovering the many advantages of virtual appliances
and start using them
