Re: [ccp4bb] Coot 'Edit Chi Angles' on Mac misbehaving

[Engin Özkan]

Just to make the point that you are not alone, I have observed the same 
issue on Mac with CCP4-installed Coot 0.8.9.1 using latest OS and 
Xquartz. This started happening with a recent update.



Interestingly, the 'Edit Chi Angles' dialogue now allows us to modify 
non-chi angles as well (not sure if this was intentional), but only for 
some residues. For example, when I click on a Leu or Cys, I am given the 
options to also modify "C <--> CA" and "CA <--> N" torsional angles, 
generally known as psi and phi. But with Asp, I get no such options to 
modify psi and phi. Interestingly, with Glu, the only angles I am 
allowed to modify in the "Edit Chi Angles" dialog are psi and phi angles.



Engin


On 4/26/18 3:19 AM, Chris Richardson wrote:


​We have an issue with the 'Edit Chi Angles' dialogue in Coot on Macs 
using the version of Coot bundled with CCP4.



For some residues - such as Glu - the dialogue only shows the C <--> 
CA angle.  If you tick the 'Add Chi Angles for Hydrogens' box, it adds 
CA <--> N.



I've just compiled Coot on the same Mac using Fink, and the dialogue 
for this version of Coot shows CA <--> CB, CB <--> CG, and CG <--> CD 
angles for the same residue.



The CCP4 version which misbehaves is 0.8.9.1; the working Fink version 
is 0.8.9.  Both are running on OS X 10.11.6.



Has anyone else experienced this?  Any suggestions as to how to fix this?


Regards,


Chris


The Institute of Cancer Research: Royal Cancer Hospital, a charitable 
Company Limited by Guarantee, Registered in England under Company No. 
534147 with its Registered Office at 123 Old Brompton Road, London SW7 
3RP.


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Re: [ccp4bb] Coot 'Edit Chi Angles' on Mac misbehaving

[Charles Ballard - UKRI STFC]

Update 055 should have reverted out ASP, and update 056 (coming real soon now) 
should fix the other issues.

Charles


-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of 
"Weiergräber, Oliver H."
Sent: 26 April 2018 15:06
To: ccp4bb <ccp4bb@jiscmail.ac.uk>
Subject: Re: [ccp4bb] Coot 'Edit Chi Angles' on Mac misbehaving

Indeed, update 54 from Mar 29 seems to have messed up several monomer 
definitions and/or their handling in coot (the version distributed with ccp4):
- GLU and ASP contain lines referencing GLN and ASN, respectively, preventing 
coot from finding any chi angles.
- For GLN, chi angles appear twice in the coot torsion dialog.
- Many amino acid definitions now contain main chain torsion angles, which are 
erroneously listed as chi in coot.

The coot version available from Paul Emsleys website comes with its own version 
of the monomer library, which seems to work fine.

Best
Oliver


  PD Dr. Oliver H. Weiergräber
  Institute of Complex Systems
  ICS-6: Structural Biochemistry
  Tel.: +49 2461 61-2028
  Fax: +49 2461 61-9540





From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Eleanor Dodson 
[176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk]
Sent: Thursday, April 26, 2018 11:49 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Coot 'Edit Chi Angles' on Mac misbehaving

Oops - oh dear - GLN labels should NOT appear in a list devoted to GLU!!


Well spotted..
Eleanor



On 26 April 2018 at 10:34, Chris Richardson 
<chris.richard...@icr.ac.uk<mailto:chris.richard...@icr.ac.uk>> wrote:
Many thanks for explaining where it is going awry.

Looking at GLU.cif in the monomer library that is part of the CCP4 
distribution, it contains the following lines:

 GLN  chi1 N  CA CB CG   180.000   15.000   3
 GLN  chi2 CA CB CG CD   180.000   15.000   3
 GLN  chi3 CB CG CD OE10.000   30.000   2

In the monomer library you link, it has:

 GLU  chi1 N  CA CB CG   180.000   15.000   3
 GLU  chi2 CA CB CG CD   180.000   15.000   3
 GLU  chi3 CB CG CD OE20.000   30.000   2

Which makes more sense.

Thanks again,

Chris

From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>> 
on behalf of Huw Jenkins <h.t.jenk...@me.com<mailto:h.t.jenk...@me.com>>
Sent: 26 April 2018 09:47
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Subject: Re: [ccp4bb] Coot 'Edit Chi Angles' on Mac misbehaving

> On 26 Apr 2018, at 09:19, Chris Richardson 
> <chris.richard...@icr.ac.uk<mailto:chris.richard...@icr.ac.uk>> wrote:
>
> I've just compiled Coot on the same Mac using Fink, and the dialogue for this 
> version of Coot shows CA <--> CB, CB <--> CG, and CG <--> CD angles for the 
> same residue.

>From a quick look at the Fink coot.info<http://coot.info> it appears to get 
>the monomer library from here:

 
http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/refmac/Dictionary/refmac_dictionary_v5.41.tar.gz

Setting $CLIBD_MON to point to this and the 'Edit Chi Angles' dialogue for CCP4 
distributed Coot 0.8.9.1 shows CA <--> CB, CB <--> CG  and CG <--> CD of Glu 14 
A from the RNase tutorial model.



Huw

The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company 
Limited by Guarantee, Registered in England under Company No. 534147 with its 
Registered Office at 123 Old Brompton Road, London SW7 3RP.

This e-mail message is confidential and for use by the addressee only.  If the 
message is received by anyone other than the addressee, please return the 
message to the sender by replying to it and then delete the message from your 
computer and network.





Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 
Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten 
Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian 
M. Schmidt

Re: [ccp4bb] Coot 'Edit Chi Angles' on Mac misbehaving

[Weiergräber, Oliver H.]

Indeed, update 54 from Mar 29 seems to have messed up several monomer 
definitions and/or their handling in coot (the version distributed with ccp4):
- GLU and ASP contain lines referencing GLN and ASN, respectively, preventing 
coot from finding any chi angles.
- For GLN, chi angles appear twice in the coot torsion dialog.
- Many amino acid definitions now contain main chain torsion angles, which are 
erroneously listed as chi in coot.

The coot version available from Paul Emsleys website comes with its own version 
of the monomer library, which seems to work fine.

Best
Oliver


  PD Dr. Oliver H. Weiergräber
  Institute of Complex Systems
  ICS-6: Structural Biochemistry
  Tel.: +49 2461 61-2028
  Fax: +49 2461 61-9540





From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Eleanor Dodson 
[176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk]
Sent: Thursday, April 26, 2018 11:49 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Coot 'Edit Chi Angles' on Mac misbehaving

Oops - oh dear - GLN labels should NOT appear in a list devoted to GLU!!


Well spotted..
Eleanor



On 26 April 2018 at 10:34, Chris Richardson 
<chris.richard...@icr.ac.uk<mailto:chris.richard...@icr.ac.uk>> wrote:
Many thanks for explaining where it is going awry.

Looking at GLU.cif in the monomer library that is part of the CCP4 
distribution, it contains the following lines:

 GLN  chi1 N  CA CB CG   180.000   15.000   3
 GLN  chi2 CA CB CG CD   180.000   15.000   3
 GLN  chi3 CB CG CD OE10.000   30.000   2

In the monomer library you link, it has:

 GLU  chi1 N  CA CB CG   180.000   15.000   3
 GLU  chi2 CA CB CG CD   180.000   15.000   3
 GLU  chi3 CB CG CD OE20.000   30.000   2

Which makes more sense.

Thanks again,

Chris

From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>> 
on behalf of Huw Jenkins <h.t.jenk...@me.com<mailto:h.t.jenk...@me.com>>
Sent: 26 April 2018 09:47
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Subject: Re: [ccp4bb] Coot 'Edit Chi Angles' on Mac misbehaving

> On 26 Apr 2018, at 09:19, Chris Richardson 
> <chris.richard...@icr.ac.uk<mailto:chris.richard...@icr.ac.uk>> wrote:
>
> I've just compiled Coot on the same Mac using Fink, and the dialogue for this 
> version of Coot shows CA <--> CB, CB <--> CG, and CG <--> CD angles for the 
> same residue.

>From a quick look at the Fink coot.info<http://coot.info> it appears to get 
>the monomer library from here:

 
http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/refmac/Dictionary/refmac_dictionary_v5.41.tar.gz

Setting $CLIBD_MON to point to this and the 'Edit Chi Angles' dialogue for CCP4 
distributed Coot 0.8.9.1 shows CA <--> CB, CB <--> CG  and CG <--> CD of Glu 14 
A from the RNase tutorial model.



Huw

The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company 
Limited by Guarantee, Registered in England under Company No. 534147 with its 
Registered Office at 123 Old Brompton Road, London SW7 3RP.

This e-mail message is confidential and for use by the addressee only.  If the 
message is received by anyone other than the addressee, please return the 
message to the sender by replying to it and then delete the message from your 
computer and network.





Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),
Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt

Re: [ccp4bb] Coot 'Edit Chi Angles' on Mac misbehaving

[Eleanor Dodson]

Oops - oh dear - GLN labels should* NOT *appear in a list devoted to GLU!!


Well spotted..
Eleanor



On 26 April 2018 at 10:34, Chris Richardson <chris.richard...@icr.ac.uk>
wrote:

> Many thanks for explaining where it is going awry.
>
> Looking at GLU.cif in the monomer library that is part of the CCP4
> distribution, it contains the following lines:
>
>  GLN  chi1 N  CA CB CG   180.000   15.000   3
>  GLN  chi2 CA CB CG CD   180.000   15.000   3
>  GLN  chi3 CB CG CD OE10.000   30.000   2
>
> In the monomer library you link, it has:
>
>  GLU  chi1 N  CA CB CG   180.000   15.000   3
>  GLU  chi2 CA CB CG CD   180.000   15.000   3
>  GLU  chi3 CB CG CD OE20.000   30.000   2
>
> Which makes more sense.
>
> Thanks again,
>
> Chris
> 
> From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Huw
> Jenkins <h.t.jenk...@me.com>
> Sent: 26 April 2018 09:47
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Coot 'Edit Chi Angles' on Mac misbehaving
>
> > On 26 Apr 2018, at 09:19, Chris Richardson <chris.richard...@icr.ac.uk>
> wrote:
> >
> > I've just compiled Coot on the same Mac using Fink, and the dialogue for
> this version of Coot shows CA <--> CB, CB <--> CG, and CG <--> CD angles
> for the same residue.
>
> From a quick look at the Fink coot.info it appears to get the monomer
> library from here:
>
>  http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/
> refmac/Dictionary/refmac_dictionary_v5.41.tar.gz
>
> Setting $CLIBD_MON to point to this and the 'Edit Chi Angles' dialogue for
> CCP4 distributed Coot 0.8.9.1 shows CA <--> CB, CB <--> CG  and CG <--> CD
> of Glu 14 A from the RNase tutorial model.
>
>
>
> Huw
>
> The Institute of Cancer Research: Royal Cancer Hospital, a charitable
> Company Limited by Guarantee, Registered in England under Company No.
> 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP.
>
> This e-mail message is confidential and for use by the addressee only.  If
> the message is received by anyone other than the addressee, please return
> the message to the sender by replying to it and then delete the message
> from your computer and network.
>

Re: [ccp4bb] Coot 'Edit Chi Angles' on Mac misbehaving

[Chris Richardson]

Many thanks for explaining where it is going awry.

Looking at GLU.cif in the monomer library that is part of the CCP4 
distribution, it contains the following lines:

 GLN  chi1 N  CA CB CG   180.000   15.000   3
 GLN  chi2 CA CB CG CD   180.000   15.000   3
 GLN  chi3 CB CG CD OE10.000   30.000   2

In the monomer library you link, it has:

 GLU  chi1 N  CA CB CG   180.000   15.000   3
 GLU  chi2 CA CB CG CD   180.000   15.000   3
 GLU  chi3 CB CG CD OE20.000   30.000   2

Which makes more sense.

Thanks again,

Chris

From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Huw Jenkins 
<h.t.jenk...@me.com>
Sent: 26 April 2018 09:47
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Coot 'Edit Chi Angles' on Mac misbehaving

> On 26 Apr 2018, at 09:19, Chris Richardson <chris.richard...@icr.ac.uk> wrote:
>
> I've just compiled Coot on the same Mac using Fink, and the dialogue for this 
> version of Coot shows CA <--> CB, CB <--> CG, and CG <--> CD angles for the 
> same residue.

>From a quick look at the Fink coot.info it appears to get the monomer library 
>from here:

 
http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/refmac/Dictionary/refmac_dictionary_v5.41.tar.gz

Setting $CLIBD_MON to point to this and the 'Edit Chi Angles' dialogue for CCP4 
distributed Coot 0.8.9.1 shows CA <--> CB, CB <--> CG  and CG <--> CD of Glu 14 
A from the RNase tutorial model.



Huw

The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company 
Limited by Guarantee, Registered in England under Company No. 534147 with its 
Registered Office at 123 Old Brompton Road, London SW7 3RP.

This e-mail message is confidential and for use by the addressee only.  If the 
message is received by anyone other than the addressee, please return the 
message to the sender by replying to it and then delete the message from your 
computer and network.

Re: [ccp4bb] Coot 'Edit Chi Angles' on Mac misbehaving

[Huw Jenkins]

> On 26 Apr 2018, at 09:19, Chris Richardson  wrote:
> 
> I've just compiled Coot on the same Mac using Fink, and the dialogue for this 
> version of Coot shows CA <--> CB, CB <--> CG, and CG <--> CD angles for the 
> same residue.

From a quick look at the Fink coot.info it appears to get the monomer library 
from here:

 
http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/refmac/Dictionary/refmac_dictionary_v5.41.tar.gz

Setting $CLIBD_MON to point to this and the 'Edit Chi Angles' dialogue for CCP4 
distributed Coot 0.8.9.1 shows CA <--> CB, CB <--> CG  and CG <--> CD of Glu 14 
A from the RNase tutorial model.



Huw

[ccp4bb] Coot 'Edit Chi Angles' on Mac misbehaving

[Chris Richardson]

?We have an issue with the 'Edit Chi Angles' dialogue in Coot on Macs using the 
version of Coot bundled with CCP4.


For some residues - such as Glu - the dialogue only shows the C <--> CA angle.  
If you tick the 'Add Chi Angles for Hydrogens' box, it adds CA <--> N.


I've just compiled Coot on the same Mac using Fink, and the dialogue for this 
version of Coot shows CA <--> CB, CB <--> CG, and CG <--> CD angles for the 
same residue.


The CCP4 version which misbehaves is 0.8.9.1; the working Fink version is 
0.8.9.  Both are running on OS X 10.11.6.


Has anyone else experienced this?  Any suggestions as to how to fix this?


Regards,


Chris

The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company 
Limited by Guarantee, Registered in England under Company No. 534147 with its 
Registered Office at 123 Old Brompton Road, London SW7 3RP.

This e-mail message is confidential and for use by the addressee only.  If the 
message is received by anyone other than the addressee, please return the 
message to the sender by replying to it and then delete the message from your 
computer and network.