Re: [ccp4bb] TYC not linked to previoys amino-acid

2017-10-16 Thread Garib Murshudov 
But it is not L-peptide. And I would not like to make it L-peptide in the 
standard ccp4 dictionary. 
You can add trans link between GLY and TYC. But it would not be nice. The best 
solution is to use TYR and amilate C terminus.

Garib


On 16 Oct 2017, at 07:40, Eleanor Dodson  wrote:

> Thank you Garib..
> 
> 
> So you have to copy the $CLIBD/monomers/t/TYC.cif to your own directory and 
> change the string "non-polymer" to "L-peptide" 
> Then use that as a dictionary entry and indeed that behaves as expected - ie 
> forms the peptide link GLY-TYC
> 
> Eleanor 
> 
> On 16 October 2017 at 12:32, Garib Murshudov  wrote:
> These are default values.
> 
> Decision about standard residue types are made using the info from the 
> dictionary.  In the current version it is like:
> 
> TYC  TYC 'L-TYROSINAMIDE  ' non-polymer25  13 
> .
> 
> I.e. it is not a peptide. Strictly speaking it is not a peptide. It would 
> form standard peptide link, at least on the carboxyl side. 
> These cases should be dealt with different types of links.
> 
> How this residue incorporated into the protein? Is it something like 
> C-terminus amilation? If it is the case then better approach is to use TYR 
> and C-terminus amilation modification. I do not remember how it works, but if 
> it is the case then i can find out.
> 
> 
> Regards
> Garib
> 
> 
> On 16 Oct 2017, at 07:06, Eleanor Dodson  wrote:
> 
>> Very puzzled by this - but now I think I understand .
>> 
>> Can you comment Garib please? 
>> 
>> In refmac there is a list of amino acids to be linked 
>> 
>>   SUBROUTINE GET_STANDARD_RES_TYPE(MDOC,LINE,MONN,ITYPE,IERR)
>>  ...
>> C -
>> C ITYPE = 3 RES_LTYPE( 3) =  'peptide '
>> C
>>   DATA RNAME /'CYS','SER','THR','PRO','ALA','GLY','ASN','ASP'
>>  *   ,'GLU','GLN','HIS','ARG','LYS','MET','ILE','LEU'
>>  *   ,'VAL','PHE','TYR','TRP','TRY','HYP','PCA','SAR'
>>  *   ,'ORN','CSS','CSH','DAR','DPR','NLE','DAS','INI'
>>  *   ,'DGL','DGN','DHI','DIL','DIV','DLI','DSN','DSP'
>>  *   ,'ABA','BMT','MLE','MVA','DVA','MSE','PTR','DAL'
>>  *   ,'DPN','DTR','DTH','TYS','CGU','DCY','ILG','OCS'
>>  *   ,'KCX','SAH','SAM','SEP','LLP','5HP','CSO'  /
>> 
>> 
>> 
>> As you can see TYC is not in this list: 
>> 
>> When I change your TYC to TYS the link is formed properly,  ( I have to 
>> delete the NXT but that shouldnt matter..) 
>> 
>> So either TYC and all other possible peptides should be added to the RNAME 
>> list, or better if the dictionary defines a residue as an L-peptide then 
>> that is how it should be handled.
>> 
>> 
>> But for the present you will have to use that work-around of creating a LINK.
>> 
>> Eleanor
>> C
>> 
>> 
>> 
> 
> Dr Garib N Murshudov
> MRC-LMB
> Francis Crick Avenue
> Cambridge 
> CB2 0QH UK
> Web http://www.mrc-lmb.cam.ac.uk, 
> http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/
> 
> 
> 
> 

Dr Garib N Murshudov
MRC-LMB
Francis Crick Avenue
Cambridge 
CB2 0QH UK
Web http://www.mrc-lmb.cam.ac.uk, 
http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/

[ccp4bb] AW: Re: [ccp4bb] TYC not linked to previoys amino-acid

2017-10-16 Thread Herman . Schreuder 
Dear Eleanor,
The method I proposed works for any amino acid, not just tyrosine. Having an 
amide as a separate residue may sound strange, but is it exactly how our 
chemists treat it as well.
Best,
Herman

Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Eleanor 
Dodson
Gesendet: Montag, 16. Oktober 2017 13:40
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [EXTERNAL] Re: [ccp4bb] TYC not linked to previoys amino-acid

Thank you Garib..


So you have to copy the $CLIBD/monomers/t/TYC.cif to your own directory and 
change the string "non-polymer" to "L-peptide"
Then use that as a dictionary entry and indeed that behaves as expected - ie 
forms the peptide link GLY-TYC
Eleanor

On 16 October 2017 at 12:32, Garib Murshudov 
<ga...@mrc-lmb.cam.ac.uk<mailto:ga...@mrc-lmb.cam.ac.uk>> wrote:
These are default values.

Decision about standard residue types are made using the info from the 
dictionary.  In the current version it is like:

TYC  TYC 'L-TYROSINAMIDE  ' non-polymer25  13 .

I.e. it is not a peptide. Strictly speaking it is not a peptide. It would form 
standard peptide link, at least on the carboxyl side.
These cases should be dealt with different types of links.

How this residue incorporated into the protein? Is it something like C-terminus 
amilation? If it is the case then better approach is to use TYR and C-terminus 
amilation modification. I do not remember how it works, but if it is the case 
then i can find out.


Regards
Garib


On 16 Oct 2017, at 07:06, Eleanor Dodson 
<eleanor.dod...@york.ac.uk<mailto:eleanor.dod...@york.ac.uk>> wrote:


Very puzzled by this - but now I think I understand .
Can you comment Garib please?
In refmac there is a list of amino acids to be linked

  SUBROUTINE GET_STANDARD_RES_TYPE(MDOC,LINE,MONN,ITYPE,IERR)
 ...
C -
C ITYPE = 3 RES_LTYPE( 3) =  'peptide '
C
  DATA RNAME /'CYS','SER','THR','PRO','ALA','GLY','ASN','ASP'
 *   ,'GLU','GLN','HIS','ARG','LYS','MET','ILE','LEU'
 *   ,'VAL','PHE','TYR','TRP','TRY','HYP','PCA','SAR'
 *   ,'ORN','CSS','CSH','DAR','DPR','NLE','DAS','INI'
 *   ,'DGL','DGN','DHI','DIL','DIV','DLI','DSN','DSP'
 *   ,'ABA','BMT','MLE','MVA','DVA','MSE','PTR','DAL'
 *   ,'DPN','DTR','DTH','TYS','CGU','DCY','ILG','OCS'
 *   ,'KCX','SAH','SAM','SEP','LLP','5HP','CSO'  /



As you can see TYC is not in this list:

When I change your TYC to TYS the link is formed properly,  ( I have to delete 
the NXT but that shouldnt matter..)

So either TYC and all other possible peptides should be added to the RNAME 
list, or better if the dictionary defines a residue as an L-peptide then that 
is how it should be handled.


But for the present you will have to use that work-around of creating a LINK.

Eleanor
C


Dr Garib N Murshudov
MRC-LMB
Francis Crick Avenue
Cambridge
CB2 0QH UK
Web 
http://www.mrc-lmb.cam.ac.uk<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mrc-2Dlmb.cam.ac.uk=DwMFaQ=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ=W10d7zbsnGPDr-U5sFcRrFm9Z_H4P4yU_c4Eq6PDyoU=7wCJBN-4XfEuIBGmj18zTJ_uen7yEjYGMZu0BwmWor8=>,
http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/<https://urldefense.proofpoint.com/v2/url?u=http-3A__www2.mrc-2Dlmb.cam.ac.uk_groups_murshudov_=DwMFaQ=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ=W10d7zbsnGPDr-U5sFcRrFm9Z_H4P4yU_c4Eq6PDyoU=w6Pt0lirXdA1Qd-CjTyAP34sQkulOy-qG8ga0OX3HhI=>

Re: [ccp4bb] TYC not linked to previoys amino-acid

2017-10-16 Thread Eleanor Dodson 
Thank you Garib..


So you have to copy the $CLIBD/monomers/t/TYC.cif to your own directory and
change the string "non-polymer" to "L-peptide"
Then use that as a dictionary entry and indeed that behaves as expected -
ie forms the peptide link GLY-TYC

Eleanor

On 16 October 2017 at 12:32, Garib Murshudov 
wrote:

> These are default values.
>
> Decision about standard residue types are made using the info from the
> dictionary.  In the current version it is like:
>
> TYC  TYC 'L-TYROSINAMIDE  ' non-polymer25
>  13 .
>
> I.e. it is not a peptide. Strictly speaking it is not a peptide. It would
> form standard peptide link, at least on the carboxyl side.
> These cases should be dealt with different types of links.
>
> How this residue incorporated into the protein? Is it something like
> C-terminus amilation? If it is the case then better approach is to use TYR
> and C-terminus amilation modification. I do not remember how it works, but
> if it is the case then i can find out.
>
>
> Regards
> Garib
>
>
> On 16 Oct 2017, at 07:06, Eleanor Dodson 
> wrote:
>
> Very puzzled by this - but now I think I understand .
>
> Can you comment Garib please?
>
> In refmac there is a list of amino acids to be linked
>
>   SUBROUTINE GET_STANDARD_RES_TYPE(MDOC,LINE,MONN,ITYPE,IERR)
>  ...
> C -
> C ITYPE = 3 RES_LTYPE( 3) =  'peptide '
> C
>   DATA RNAME /'CYS','SER','THR','PRO','ALA','GLY','ASN','ASP'
>  *   ,'GLU','GLN','HIS','ARG','LYS','MET','ILE','LEU'
>  *   ,'VAL','PHE','TYR','TRP','TRY','HYP','PCA','SAR'
>  *   ,'ORN','CSS','CSH','DAR','DPR','NLE','DAS','INI'
>  *   ,'DGL','DGN','DHI','DIL','DIV','DLI','DSN','DSP'
>  *   ,'ABA','BMT','MLE','MVA','DVA','MSE','PTR','DAL'
>  *   ,'DPN','DTR','DTH','TYS','CGU','DCY','ILG','OCS'
>  *   ,'KCX','SAH','SAM','SEP','LLP','5HP','CSO'  /
>
>
>
> As you can see TYC is not in this list:
>
> When I change your TYC to TYS the link is formed properly,  ( I have to
> delete the NXT but that shouldnt matter..)
>
> So either TYC and all other possible peptides should be added to the RNAME
> list, or better if the dictionary defines a residue as an L-peptide then
> that is how it should be handled.
>
>
> But for the present you will have to use that work-around of creating a
> LINK.
>
> Eleanor
> C
>
>
>
>
> Dr Garib N Murshudov
> MRC-LMB
> Francis Crick Avenue
> Cambridge
> CB2 0QH UK
> Web http://www.mrc-lmb.cam.ac.uk,
> http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/
>
>
>
>