subject:"\[ccp4bb\] bond angle deviation listing in refmac log"

Re: [ccp4bb] bond angle deviation listing in refmac log

2022-10-20 Thread Garib Murshadov

Hi Andy

Yes, ARG side chain should not be planar. It was mistakenly restrained to be 
planar. The same rule applies for peptide planes. Planarity should only be 
applied (if ever) for aromatic groups. For ARG side chains the bond is sp2-sp2 
and rotation around this bond is not as prohibited as rotation within aromatic 
rings (as far as I know).

Regards
Garib


> On 21 Oct 2022, at 00:24, Karplus, Andy  wrote:
> 
> HI Robbie and all, 
>  
> Here is further recent analysis regarding the geometry of Arg side chains and 
> recommendations for restraints:
>  
> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7709202/ 
> <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7709202/>
>  
> Best, Andy 
>  
> 
>  
> Dr. P. Andrew Karplus (he, him, his)
> Distinguished Professor of Biochemistry and Biophysics
> NIGMS GCE4All Research Center <http://gce4all.oregonstate.edu/> Director of 
> Communications
> 2133 ALS Building
> Oregon State University
> Corvallis, OR 97331
> ph. 541-737-3200
> andy.karp...@oregonstate.edu <mailto:andy.karp...@oregonstate.edu>
>  
> “Revealing how life works for the benefit of all!”
> http://biochem.oregonstate.edu <http://biochem.oregonstate.edu/>/
> https://www.facebook.com/OSUBB <https://www.facebook.com/OSUBB>
>  
>  
>  
> From: CCP4 bulletin board  <mailto:CCP4BB@JISCMAIL.AC.UK>> on behalf of Robbie Joosten 
> mailto:robbie_joos...@hotmail.com>>
> Reply-To: Robbie Joosten  <mailto:robbie_joos...@hotmail.com>>
> Date: Thursday, October 20, 2022 at 5:53 AM
> To: "CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>" 
> mailto:CCP4BB@JISCMAIL.AC.UK>>
> Subject: Re: [ccp4bb] bond angle deviation listing in refmac log
>  
> [This email originated from outside of OSU. Use caution with links and 
> attachments.]
>  
> Hi Garib,
>  
>> Are these related to the side chain of ARG? In the monomer library sigmas are
>> capped from below - 1.5degree.
>> In the PDB these sigmas might be very small and tiny differences could be 
>> given
>> as outliers.
>> Another reason might be that in the monomer library these two angles are
>> identical (they are considered graph-equivalent, however, rotating around NE-
>> CZ may make them non-equivalent in 3D space):
>> ARG NE CZ NH1 120.052 1.50
>> ARG NE CZ NH2 120.052 1.50
> The chi-5 angle is not really freely rotatable due to the 1.33 bond order. It 
> does give away more than say, a peptide bond with 1.5 bond order. Anyway, NH2 
> and NH1 have E/Z differences if you assume the bond is not freely rotatable.
>  
>> In the PDB they may be considered different with small differences and very
>> small sigmas.
> I'm using
> ARG NE CZ NH1 121.5 1.00
> ARG NE CZ NH2 119.2 0.90
>  
> From 
> https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpubmed.ncbi.nlm.nih.gov%2F27326702%2Fdata=05%7C01%7CAndy.Karplus%40oregonstate.edu%7C07e6e953f28545470f8b08dab299eaf0%7Cce6d05e13c5e4d6287a84c4a2713c113%7C0%7C0%7C638018672137036416%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7Csdata=ORI09%2BMubqLUxmBcaOrrQwGs%2FyiNeBM4ajxSJYDun3s%3Dreserved=0
>  
> <https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpubmed.ncbi.nlm.nih.gov%2F27326702%2Fdata=05%7C01%7CAndy.Karplus%40oregonstate.edu%7C07e6e953f28545470f8b08dab299eaf0%7Cce6d05e13c5e4d6287a84c4a2713c113%7C0%7C0%7C638018672137036416%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7Csdata=ORI09%2BMubqLUxmBcaOrrQwGs%2FyiNeBM4ajxSJYDun3s%3Dreserved=0>
>  
>> I personally do not think that these differences are significant or 
>> important.
>> However, to make pdb validation happy you can change the sigmas and make
>> the angles different. Then NH1 and NH2 will become inequivalent and you have
>> to change your coordinates (it could be done automatically if somebody writes
>> a tiny program)
> Because chi-5 was freely rotatable in O (against convention) there is a check 
> for this in WHAT_CHECK. AFAIK the atom naming is fixed in pdb-redo based on 
> that. We can build in into flipper.
>  
> Cheers,
> Robbie
>  
>>  
>> If the problem is not related with this then I need more info.
>>  
>> Regards
>> Garib
>>  
>>  
>>  
>>On 20 Oct 2022, at 12:33, Bernhard Rupp
>> mailto:hofkristall...@gmail.com> 
>> <mailto:hofkristall...@gmail.com <mailto:hofkristall...@gmail.com>> > wrote:
>>  
>>Hi Fellows/Garib,
>>  
>>I notice unexplained discrepancies between the PDB validation report
>>

Re: [ccp4bb] bond angle deviation listing in refmac log

2022-10-20 Thread Karplus, Andy

HI Robbie and all,

Here is further recent analysis regarding the geometry of Arg side chains and 
recommendations for restraints:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7709202/

Best, Andy

[Black Lives Matter]

Dr. P. Andrew Karplus (he, him, his)
Distinguished Professor of Biochemistry and Biophysics
NIGMS GCE4All Research Center<http://gce4all.oregonstate.edu/> Director of 
Communications
2133 ALS Building
Oregon State University
Corvallis, OR 97331
ph. 541-737-3200
andy.karp...@oregonstate.edu<mailto:andy.karp...@oregonstate.edu>

“Revealing how life works for the benefit of all!”
http://biochem.oregonstate.edu/
https://www.facebook.com/OSUBB



From: CCP4 bulletin board  on behalf of Robbie Joosten 

Reply-To: Robbie Joosten 
Date: Thursday, October 20, 2022 at 5:53 AM
To: "CCP4BB@JISCMAIL.AC.UK" 
Subject: Re: [ccp4bb] bond angle deviation listing in refmac log

[This email originated from outside of OSU. Use caution with links and 
attachments.]

Hi Garib,

Are these related to the side chain of ARG? In the monomer library sigmas are
capped from below - 1.5degree.
In the PDB these sigmas might be very small and tiny differences could be given
as outliers.
Another reason might be that in the monomer library these two angles are
identical (they are considered graph-equivalent, however, rotating around NE-
CZ may make them non-equivalent in 3D space):
ARG NE CZ NH1 120.052 1.50
ARG NE CZ NH2 120.052 1.50
The chi-5 angle is not really freely rotatable due to the 1.33 bond order. It 
does give away more than say, a peptide bond with 1.5 bond order. Anyway, NH2 
and NH1 have E/Z differences if you assume the bond is not freely rotatable.

In the PDB they may be considered different with small differences and very
small sigmas.
I'm using
ARG NE CZ NH1 121.5 1.00
ARG NE CZ NH2 119.2 0.90

From 
https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpubmed.ncbi.nlm.nih.gov%2F27326702%2Fdata=05%7C01%7CAndy.Karplus%40oregonstate.edu%7C07e6e953f28545470f8b08dab299eaf0%7Cce6d05e13c5e4d6287a84c4a2713c113%7C0%7C0%7C638018672137036416%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7Csdata=ORI09%2BMubqLUxmBcaOrrQwGs%2FyiNeBM4ajxSJYDun3s%3Dreserved=0

I personally do not think that these differences are significant or important.
However, to make pdb validation happy you can change the sigmas and make
the angles different. Then NH1 and NH2 will become inequivalent and you have
to change your coordinates (it could be done automatically if somebody writes
a tiny program)
Because chi-5 was freely rotatable in O (against convention) there is a check 
for this in WHAT_CHECK. AFAIK the atom naming is fixed in pdb-redo based on 
that. We can build in into flipper.

Cheers,
Robbie


If the problem is not related with this then I need more info.

Regards
Garib



   On 20 Oct 2022, at 12:33, Bernhard Rupp
mailto:hofkristall...@gmail.com> 
<mailto:hofkristall...@gmail.com<mailto:hofkristall...@gmail.com>> > wrote:

   Hi Fellows/Garib,

   I notice unexplained discrepancies between the PDB validation report
and the Refmac log file:

   a.  If I set in  ‘Monitoring and Output Options’ the angle sigma for
the log output reporting option to the PDB 5 sigma cutoff,

   I get zero angle deviations (i.e., no angle deviation printout at all in 
the
log), even at improbably low sigma levels such as 2.0 or 1.0

   monitor MANY torsion 5.0 distance 5.0 angle 1.0 plane 5.0


   b.  PDB informs me that there are up to 10 sigma outliers on
multiple (and almost exclusively) ARG N-C-N angles (how to fix this we address
later).


   Garib, I can send you a link to the complete log, below the header for
versions (windows) :

   #CCP4I VERSION CCP4Interface 8.0.005

   #CCP4I SCRIPT LOG refmac5
   #CCP4I DATE 20 Oct 2022  13:17:07
   #CCP4I USER 'UNKNOWN'
   #CCP4I PROJECT data_mono
   #CCP4I JOB_ID 13
   #CCP4I SCRATCH C:/Users/br/AppData/Local/Temp
   #CCP4I HOSTNAME BR-WORK
   #CCP4I PID 10064

   

   
   
   



###
   
###
   
###
   ### CCP4 8.0.005: Refmac  version 5.8.0352 : 05/31/22##
   
###

   Thx, BR
   -
   Bernhard Rupp
   k.k. Hofkristallamt
   001 (925) 209-7429
   +43 (676) 571-0536
   b...@ruppweb.org<mailto:b...@ruppweb.org> 
<mailto:b...@ruppweb.org<mailto:b...@ruppweb.org>>
   hofkristall...@gmail.com<mailto:hofkristall...@gmail.com> 
<mailto:hofkristall...@gmail.com<mailto:hofkristall...@gmail.com>>
   
https://nam04.safelin

Re: [ccp4bb] bond angle deviation listing in refmac log

2022-10-20 Thread Robbie Joosten

Hi Garib,

> Are these related to the side chain of ARG? In the monomer library sigmas are
> capped from below - 1.5degree.
> In the PDB these sigmas might be very small and tiny differences could be 
> given
> as outliers.
> Another reason might be that in the monomer library these two angles are
> identical (they are considered graph-equivalent, however, rotating around NE-
> CZ may make them non-equivalent in 3D space):
> ARG NE CZ NH1 120.052 1.50
> ARG NE CZ NH2 120.052 1.50
The chi-5 angle is not really freely rotatable due to the 1.33 bond order. It 
does give away more than say, a peptide bond with 1.5 bond order. Anyway, NH2 
and NH1 have E/Z differences if you assume the bond is not freely rotatable.

> In the PDB they may be considered different with small differences and very
> small sigmas.
I'm using
ARG NE CZ NH1 121.5 1.00
ARG NE CZ NH2 119.2 0.90

From https://pubmed.ncbi.nlm.nih.gov/27326702/

> I personally do not think that these differences are significant or important.
> However, to make pdb validation happy you can change the sigmas and make
> the angles different. Then NH1 and NH2 will become inequivalent and you have
> to change your coordinates (it could be done automatically if somebody writes
> a tiny program)
Because chi-5 was freely rotatable in O (against convention) there is a check 
for this in WHAT_CHECK. AFAIK the atom naming is fixed in pdb-redo based on 
that. We can build in into flipper.

Cheers,
Robbie

> 
> If the problem is not related with this then I need more info.
> 
> Regards
> Garib
> 
> 
> 
>   On 20 Oct 2022, at 12:33, Bernhard Rupp
> mailto:hofkristall...@gmail.com> > wrote:
> 
>   Hi Fellows/Garib,
> 
>   I notice unexplained discrepancies between the PDB validation report
> and the Refmac log file:
> 
>   a.  If I set in  ‘Monitoring and Output Options’ the angle sigma for
> the log output reporting option to the PDB 5 sigma cutoff,
> 
>   I get zero angle deviations (i.e., no angle deviation printout at all 
> in the
> log), even at improbably low sigma levels such as 2.0 or 1.0
> 
>   monitor MANY torsion 5.0 distance 5.0 angle 1.0 plane 5.0
> 
> 
>   b.  PDB informs me that there are up to 10 sigma outliers on
> multiple (and almost exclusively) ARG N-C-N angles (how to fix this we address
> later).
> 
> 
>   Garib, I can send you a link to the complete log, below the header for
> versions (windows) :
> 
>   #CCP4I VERSION CCP4Interface 8.0.005
> 
>   #CCP4I SCRIPT LOG refmac5
>   #CCP4I DATE 20 Oct 2022  13:17:07
>   #CCP4I USER 'UNKNOWN'
>   #CCP4I PROJECT data_mono
>   #CCP4I JOB_ID 13
>   #CCP4I SCRATCH C:/Users/br/AppData/Local/Temp
>   #CCP4I HOSTNAME BR-WORK
>   #CCP4I PID 10064
> 
>   
> 
>   
>   
>   
> 
> 
> 
> ###
>   
> ###
>   
> ###
>   ### CCP4 8.0.005: Refmac  version 5.8.0352 : 05/31/22##
>   
> ###
> 
>   Thx, BR
>   -
>   Bernhard Rupp
>   k.k. Hofkristallamt
>   001 (925) 209-7429
>   +43 (676) 571-0536
>   b...@ruppweb.org 
>   hofkristall...@gmail.com 
>   http://www.hofkristallamt.org/ 
>   -
>   Doors and corners – that’s where they get you
>   -
> 
> 
> 
> 
> 
> 
> 
>   To unsubscribe from the CCP4BB list, click the following link:
>   https://www.jiscmail.ac.uk/cgi-bin/WA-
> JISC.exe?SUBED1=CCP4BB=1
> 
> 
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1




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Re: [ccp4bb] bond angle deviation listing in refmac log

2022-10-20 Thread Garib Murshadov

Are these related to the side chain of ARG? In the monomer library sigmas are 
capped from below - 1.5degree.
In the PDB these sigmas might be very small and tiny differences could be given 
as outliers. 
Another reason might be that in the monomer library these two angles are 
identical (they are considered graph-equivalent, however, rotating around NE-CZ 
may make them non-equivalent in 3D space):
ARG NE CZ NH1 120.052 1.50
ARG NE CZ NH2 120.052 1.50

In the PDB they may be considered different with small differences and very 
small sigmas. 
I personally do not think that these differences are significant or important. 
However, to make pdb validation happy you can change the sigmas and make the 
angles different. Then NH1 and NH2 will become inequivalent and you have to 
change your coordinates (it could be done automatically if somebody writes a 
tiny program)

If the problem is not related with this then I need more info.

Regards
Garib

> On 20 Oct 2022, at 12:33, Bernhard Rupp  wrote:
> 
> Hi Fellows/Garib,
>  
> I notice unexplained discrepancies between the PDB validation report and the 
> Refmac log file:
> If I set in  ‘Monitoring and Output Options’ the angle sigma for the log 
> output reporting option to the PDB 5 sigma cutoff, 
> I get zero angle deviations (i.e., no angle deviation printout at all in the 
> log), even at improbably low sigma levels such as 2.0 or 1.0
>  
> monitor MANY torsion 5.0 distance 5.0 angle 1.0 plane 5.0
>  
> PDB informs me that there are up to 10 sigma outliers on multiple (and almost 
> exclusively) ARG N-C-N angles (how to fix this we address later).
>  
> Garib, I can send you a link to the complete log, below the header for 
> versions (windows) :
> #CCP4I VERSION CCP4Interface 8.0.005
> #CCP4I SCRIPT LOG refmac5
> #CCP4I DATE 20 Oct 2022  13:17:07
> #CCP4I USER 'UNKNOWN'
> #CCP4I PROJECT data_mono
> #CCP4I JOB_ID 13
> #CCP4I SCRATCH C:/Users/br/AppData/Local/Temp
> #CCP4I HOSTNAME BR-WORK
> #CCP4I PID 10064
>  
> 
> 
> 
> 
>  
>  ###
> ###
> ###
> ### CCP4 8.0.005: Refmac  version 5.8.0352 : 05/31/22##
> ###
>  
> Thx, BR
> -
> Bernhard Rupp 
> k.k. Hofkristallamt
> 001 (925) 209-7429
> +43 (676) 571-0536
> b...@ruppweb.org 
> hofkristall...@gmail.com 
> http://www.hofkristallamt.org/    
>   
> -
> Doors and corners – that’s where they get you
> -
>  
>  
>  
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 
> 

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[ccp4bb] bond angle deviation listing in refmac log

2022-10-20 Thread Bernhard Rupp

Hi Fellows/Garib,

 

I notice unexplained discrepancies between the PDB validation report and the
Refmac log file:

a.  If I set in  'Monitoring and Output Options' the angle sigma for the
log output reporting option to the PDB 5 sigma cutoff, 

I get zero angle deviations (i.e., no angle deviation printout at all in the
log), even at improbably low sigma levels such as 2.0 or 1.0

 

monitor MANY torsion 5.0 distance 5.0 angle 1.0 plane 5.0

 

b.  PDB informs me that there are up to 10 sigma outliers on multiple
(and almost exclusively) ARG N-C-N angles (how to fix this we address
later).

 

Garib, I can send you a link to the complete log, below the header for
versions (windows) :

#CCP4I VERSION CCP4Interface 8.0.005

#CCP4I SCRIPT LOG refmac5

#CCP4I DATE 20 Oct 2022  13:17:07

#CCP4I USER 'UNKNOWN'

#CCP4I PROJECT data_mono

#CCP4I JOB_ID 13

#CCP4I SCRATCH C:/Users/br/AppData/Local/Temp

#CCP4I HOSTNAME BR-WORK

#CCP4I PID 10064

 









 

 ###

###

###

### CCP4 8.0.005: Refmac  version 5.8.0352 : 05/31/22##

###

 

Thx, BR

-
Bernhard Rupp 

k.k. Hofkristallamt

001 (925) 209-7429
+43 (676) 571-0536
  b...@ruppweb.org
  hofkristall...@gmail.com
  http://www.hofkristallamt.org/

-
Doors and corners - that's where they get you

-

 

 

 




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Re: [ccp4bb] bond angle deviation listing in refmac log

Re: [ccp4bb] bond angle deviation listing in refmac log

Re: [ccp4bb] bond angle deviation listing in refmac log

Re: [ccp4bb] bond angle deviation listing in refmac log

[ccp4bb] bond angle deviation listing in refmac log

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