Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] add ligand with AceDRG

[Diana Tomchick]

When you try to use LIG in Phenix it gives you an error message as it doesn’t 
know that LIG is obsoleted.

Diana

Sent from my iPhone

> On Apr 26, 2024, at 10:08 AM, Yong Wang 
> <3c4fc05cc53b-dmarc-requ...@jiscmail.ac.uk> wrote:
>
> EXTERNAL MAIL
>
> Dear all,
>
> Perhaps the issue is that the refinement program should be able to handle the 
> priority of ligand dictionary, i.e. your custom ligand ID and dictionary 
> overrides any existing in the default collection.  I have not had any trouble 
> with LIG or SX1, both existing in PDB ligands.  I also never had any trouble 
> depositing structures containing such ligand ID's, albeit a few years ago.  
> The capable staff at RCSB will always assign a new ligand ID based on its 
> structure, regardless of what ID you have in your pdb file.
>
> Best,
>
> Yong
>
> -Original Message-
> From: CCP4 bulletin board  On Behalf Of Gerard Bricogne
> Sent: Friday, April 26, 2024 11:47 AM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [EXTERNAL] Re: [ccp4bb] add ligand with AceDRG
>
> EXTERNAL EMAIL: Use caution before replying, clicking links, and opening 
> attachments.
>
>
>
>
> Dear Oliver and CCP4BB readers,
>
> This obsoleted LIG came from PDB entry 1JVP deposited in 2001 by Jean-Michel 
> Rondeau working at Novartis. He must simply have been the first person to 
> deposit a structure in which the ligand was called LIG ... . That molecule is 
> now called 89E, but as Phil showed, there are still remnants of its old 
> identity.
>
> Best wishes,
>
> Gerard.
>
> --
>> On Fri, Apr 26, 2024 at 04:31:13PM +0100, Oliver Smart wrote:
>> Hi Stefanie,
>>
>> If you want to try Grade2 (for a non-confidential ligand) then this is
>> easy to do using the Grade Web Server
>>
>> https://urldefense.com/v3/__https://grad/__;!!MznTZTSvDXGV0Co!CIY1cS7S0u6TVzIG6Dh20opNZM2FHbu_xJYD7NwCU3qrUh_75Gd5xd9DbpExqoRdxiNPtuJUy2ls-trztGTScQP12D1gski_Rlab9zxaesA9ZFs$
>> e.globalphasing.org%2F=05%7C02%7CWANG_YONG_Y%40LILLY.COM%7C00daf6
>> fed4844df87c9e08dc66082939%7C18a59a81eea84c30948ad8824cdc2580%7C0%7C0%
>> 7C638497432436392044%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQI
>> joiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C=mvPPcWbmv
>> N%2FCuXXB%2BacAmaHf%2BqZr0O9lCoFxc9p5plk%3D=0
>>
>> We have altered our default "3-letter code" (aka PDB chemical component ID) 
>> to "LIG".
>> The reserved PDB two letter codes 01 to 99 are also fine (as are INH and 
>> DRG).
>> We  understand from users that Grade2 restraint dictionaries work well
>> with REFMAC (as to AceDG) Checking my installation of CCP4 8.0 there are no 
>> distributed dictionaries for LIG, DRG or 01 to 99.
>>
>> There was a PDB component LIG that was obsoleted in 2021
>> https://urldefense.com/v3/__https://www/__;!!MznTZTSvDXGV0Co!CIY1cS7S0u6TVzIG6Dh20opNZM2FHbu_xJYD7NwCU3qrUh_75Gd5xd9DbpExqoRdxiNPtuJUy2ls-trztGTScQP12D1gski_Rlab9zxaEuNjNL0$
>>  .
>> ebi.ac.uk%2Fpdbe%2Fstatic%2Ffiles%2Fpdbechem_v2%2FLIG.cif=05%7C02
>> %7CWANG_YONG_Y%40LILLY.COM%7C00daf6fed4844df87c9e08dc66082939%7C18a59a
>> 81eea84c30948ad8824cdc2580%7C0%7C0%7C638497432436399432%7CUnknown%7CTW
>> FpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6
>> Mn0%3D%7C0%7C%7C%7C=mFCw%2BNkuhOvtx4ozk9IeaBryFaqU6dt0CLQcneSzpm
>> g%3D=0 And there was a restraint dictionary for this
>> distributed with CCP4 7.0.
>>
>> Perhaps you are picking up things from an old CCP4 installation
>>
>> Hope this helps,
>>
>> Oliver
>>
>>
>>
>>
>>>> On 26 Apr 2024, at 11:21, FREITAG-POHL, STEFANIE 
>>>>  wrote:
>>>
>>> Dear all,
>>>
>>> thank you so much for all your suggestions.
>>>
>>> Unfortunately, nothing helped. Whatever 3-letter code I choose Refmac is 
>>> complaining that there is a clash with an already existing ligand (even 
>>> DRG, LIG, numbers) and AceDRG in CCP4i2 insists on 3 letters.
>>>
>>> I am not quite sure how to bypass this issue as I think Refmac is
>>> also insisting on 3-letters for ligands (???)
>>>
>>> I have not tried Grade yet.
>>>
>>> Any advise much appreciated.
>>>
>>> Best wishes,
>>> Stefanie
>>>
>>>
>>>
>>> Dr. Stefanie Freitag-Pohl (she/her)
>>> Durham University
>>> Department of Chemistry
>>> South Road, Durham
>>> DH1 3LE
>>> United Kingdom
>>> 0191 334 2596
>>> stefanie.freitag-p...@durham.ac.uk
>>> <mailto:stefanie.freitag-p...@dur

Re: [ccp4bb] add ligand with AceDRG

[Diana Tomchick]

Use the search tab at the RCSB web site, type in a 3 letter code, and if it has 
been used for a ligand then it will appear as a Chemical Component.

Thanks to Phil, I am on vacation in Mexico and cut and pasting URLs is a pain 
on an iPhone.

Diana


Sent from my iPhone

On Apr 26, 2024, at 9:07 AM, Deborah Harrus  wrote:



Hi Diana,

Could you please clarify where you are searching?

LIG is obsolete and definitely not in use.

Cheers,

Deborah

On 26/04/2024 15:40, Diana Tomchick wrote:
But I think that is a mistake, if you search for LIG in the PDB, it brings up a 
definite ligand that has that 3-letter code.

Diana

Sent from my iPhone

On Apr 26, 2024, at 8:04 AM, Deborah Harrus 
 wrote:



Dear all,

Just to clarify, "LIG" is also a reserved code, so it's safe to use.

See 
https://www.wwpdb.org/news/news?year=2023#656f4404d78e004e766a96c6

Kind regards,

Deborah Harrus

PDBe

On 25/04/2024 16:04, Diana Tomchick wrote:
The PDB has reserved the following codes for unknown ligands:

DRG
INH
01 - 99

Using one of these should not cause you the described problems. I successfully 
used

99

just last week. If you try to use

999 or LIG

these will not work, there are ligands assigned to those codes.


Diana

Sent from my iPhone

On Apr 25, 2024, at 8:03 AM, Nicholas Clark 

 wrote:


EXTERNAL MAIL

Hi Stefanie,

Why can you only use "taken" three letter codes? In the "output monomer" box, 
you should be able to enter whatever you'd like for the "Three letter code for 
output monomer". In the attached image, this is shown as "DRG" but can be 
changed to any 3 letter code of your choice. Obviously, just make sure your 
existing selection does not exist in the PDB.

Best,

Nick Clark



On Thu, Apr 25, 2024 at 8:51 AM Maria Håkansson 
mailto:maria.hakans...@saromics.com>> wrote:
Hi Stefanie,
Can you manually edit the restraints file using TextEdit and find and replace 
and the pdb
file of course?
Other option is to use Grade or Grade2 and the smiles string if you have this 
software installed.
I often find this easier than ccp4i2.

Best regards and good luck!
Maria





On 25 Apr 2024, at 14:01, FREITAG-POHL, STEFANIE 
mailto:stefanie.freitag-p...@durham.ac.uk>> 
wrote:

Hi all,

I have trouble adding a ligand with AceDRG in CCP4i2 into my refinement:

I put in a smilesstring and the ligand is written ok, but since I can only 
chose already 'taken' 3-letter-codes the refinement always crashes as there is 
a clash with existing library entries.
Is there any way around this? How do I add a novel ligand?

Thanks so much for your help.

Best wishes,
Stefanie



Dr. Stefanie Freitag-Pohl (she/her)
Durham University
Department of Chemistry
South Road, Durham
DH1 3LE
United Kingdom
0191 334 2596
stefanie.freitag-p...@durham.ac.uk


To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

Maria Håkansson, PhD,
Principal Scientist

SARomics Biostructures AB
Medicon Village
SE-223 81 Lund, Sweden

Mobile: +46 (0)76 8585706
Web: 
www.saromics.com








To unsubscribe from the CCP4BB list, click the following link:

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] add ligand with AceDRG

[Yong Wang]

Dear all,

Perhaps the issue is that the refinement program should be able to handle the 
priority of ligand dictionary, i.e. your custom ligand ID and dictionary 
overrides any existing in the default collection.  I have not had any trouble 
with LIG or SX1, both existing in PDB ligands.  I also never had any trouble 
depositing structures containing such ligand ID's, albeit a few years ago.  The 
capable staff at RCSB will always assign a new ligand ID based on its 
structure, regardless of what ID you have in your pdb file.

Best,

Yong

-Original Message-
From: CCP4 bulletin board  On Behalf Of Gerard Bricogne
Sent: Friday, April 26, 2024 11:47 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [EXTERNAL] Re: [ccp4bb] add ligand with AceDRG

EXTERNAL EMAIL: Use caution before replying, clicking links, and opening 
attachments.




Dear Oliver and CCP4BB readers,

This obsoleted LIG came from PDB entry 1JVP deposited in 2001 by Jean-Michel 
Rondeau working at Novartis. He must simply have been the first person to 
deposit a structure in which the ligand was called LIG ... . That molecule is 
now called 89E, but as Phil showed, there are still remnants of its old 
identity.

Best wishes,

Gerard.

--
On Fri, Apr 26, 2024 at 04:31:13PM +0100, Oliver Smart wrote:
> Hi Stefanie,
>
> If you want to try Grade2 (for a non-confidential ligand) then this is
> easy to do using the Grade Web Server
>
> https://grad/
> e.globalphasing.org%2F=05%7C02%7CWANG_YONG_Y%40LILLY.COM%7C00daf6
> fed4844df87c9e08dc66082939%7C18a59a81eea84c30948ad8824cdc2580%7C0%7C0%
> 7C638497432436392044%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQI
> joiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C=mvPPcWbmv
> N%2FCuXXB%2BacAmaHf%2BqZr0O9lCoFxc9p5plk%3D=0
>
> We have altered our default "3-letter code" (aka PDB chemical component ID) 
> to "LIG".
> The reserved PDB two letter codes 01 to 99 are also fine (as are INH and DRG).
> We  understand from users that Grade2 restraint dictionaries work well
> with REFMAC (as to AceDG) Checking my installation of CCP4 8.0 there are no 
> distributed dictionaries for LIG, DRG or 01 to 99.
>
> There was a PDB component LIG that was obsoleted in 2021
> https://www/.
> ebi.ac.uk%2Fpdbe%2Fstatic%2Ffiles%2Fpdbechem_v2%2FLIG.cif=05%7C02
> %7CWANG_YONG_Y%40LILLY.COM%7C00daf6fed4844df87c9e08dc66082939%7C18a59a
> 81eea84c30948ad8824cdc2580%7C0%7C0%7C638497432436399432%7CUnknown%7CTW
> FpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6
> Mn0%3D%7C0%7C%7C%7C=mFCw%2BNkuhOvtx4ozk9IeaBryFaqU6dt0CLQcneSzpm
> g%3D=0 And there was a restraint dictionary for this
> distributed with CCP4 7.0.
>
> Perhaps you are picking up things from an old CCP4 installation
>
> Hope this helps,
>
> Oliver
>
>
>
>
> > On 26 Apr 2024, at 11:21, FREITAG-POHL, STEFANIE 
> >  wrote:
> >
> > Dear all,
> >
> > thank you so much for all your suggestions.
> >
> > Unfortunately, nothing helped. Whatever 3-letter code I choose Refmac is 
> > complaining that there is a clash with an already existing ligand (even 
> > DRG, LIG, numbers) and AceDRG in CCP4i2 insists on 3 letters.
> >
> > I am not quite sure how to bypass this issue as I think Refmac is
> > also insisting on 3-letters for ligands (???)
> >
> > I have not tried Grade yet.
> >
> > Any advise much appreciated.
> >
> > Best wishes,
> > Stefanie
> >
> >
> >
> > Dr. Stefanie Freitag-Pohl (she/her)
> > Durham University
> > Department of Chemistry
> > South Road, Durham
> > DH1 3LE
> > United Kingdom
> > 0191 334 2596
> > stefanie.freitag-p...@durham.ac.uk
> > <mailto:stefanie.freitag-p...@durham.ac.uk>
> > From: CCP4 bulletin board  > <mailto:CCP4BB@JISCMAIL.AC.UK>> on behalf of FREITAG-POHL, STEFANIE
> >  > <mailto:stefanie.freitag-p...@durham.ac.uk>>
> > Sent: 25 April 2024 13:01
> > To: CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>
> > mailto:CCP4BB@JISCMAIL.AC.UK>>
> > Subject: [ccp4bb] add ligand with AceDRG
> >
> > [EXTERNAL EMAIL]
> > Hi all,
> >
> > I have trouble adding a ligand with AceDRG in CCP4i2 into my refinement:
> >
> > I put in a smilesstring and the ligand is written ok, but since I can only 
> > chose already 'taken' 3-letter-codes the refinement always crashes as there 
> > is a clash with existing library entries.
> > Is there any way around this? How do I add a novel ligand?
> >
> > Thanks so much for your help.
> >
> > Best wishes,
> > Stefanie
> >
> >
> >
> > Dr. Stefanie Freitag-Pohl (she/her)
> 

Re: [ccp4bb] add ligand with AceDRG

[Gerard Bricogne]

Dear Oliver and CCP4BB readers,

This obsoleted LIG came from PDB entry 1JVP deposited in 2001 by Jean-Michel
Rondeau working at Novartis. He must simply have been the first person to
deposit a structure in which the ligand was called LIG ... . That molecule
is now called 89E, but as Phil showed, there are still remnants of its old
identity.

Best wishes,

Gerard.

--
On Fri, Apr 26, 2024 at 04:31:13PM +0100, Oliver Smart wrote:
> Hi Stefanie,
> 
> If you want to try Grade2 (for a non-confidential ligand) then this is easy 
> to do using the Grade Web Server
> 
> https://grade.globalphasing.org/
> 
> We have altered our default "3-letter code” (aka PDB chemical component ID) 
> to “LIG”. 
> The reserved PDB two letter codes 01 to 99 are also fine (as are INH and 
> DRG). 
> We  understand from users that Grade2 restraint dictionaries work well with 
> REFMAC (as to AceDG)
> Checking my installation of CCP4 8.0 there are no distributed dictionaries 
> for LIG, DRG or 01 to 99.
> 
> There was a PDB component LIG that was obsoleted in 2021 
> https://www.ebi.ac.uk/pdbe/static/files/pdbechem_v2/LIG.cif
> And there was a restraint dictionary for this distributed with CCP4 7.0.
> 
> Perhaps you are picking up things from an old CCP4 installation
> 
> Hope this helps,
> 
> Oliver 
> 
> 
> 
> 
> > On 26 Apr 2024, at 11:21, FREITAG-POHL, STEFANIE 
> >  wrote:
> > 
> > Dear all,
> > 
> > thank you so much for all your suggestions.
> > 
> > Unfortunately, nothing helped. Whatever 3-letter code I choose Refmac is 
> > complaining that there is a clash with an already existing ligand (even 
> > DRG, LIG, numbers) and AceDRG in CCP4i2 insists on 3 letters.
> > 
> > I am not quite sure how to bypass this issue as I think Refmac is also 
> > insisting on 3-letters for ligands (???)
> > 
> > I have not tried Grade yet.
> > 
> > Any advise much appreciated.
> > 
> > Best wishes,
> > Stefanie
> > 
> > 
> > 
> > Dr. Stefanie Freitag-Pohl (she/her)
> > Durham University
> > Department of Chemistry
> > South Road, Durham
> > DH1 3LE
> > United Kingdom
> > 0191 334 2596
> > stefanie.freitag-p...@durham.ac.uk 
> > <mailto:stefanie.freitag-p...@durham.ac.uk>
> > From: CCP4 bulletin board  > <mailto:CCP4BB@JISCMAIL.AC.UK>> on behalf of FREITAG-POHL, STEFANIE 
> >  > <mailto:stefanie.freitag-p...@durham.ac.uk>>
> > Sent: 25 April 2024 13:01
> > To: CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK> 
> > mailto:CCP4BB@JISCMAIL.AC.UK>>
> > Subject: [ccp4bb] add ligand with AceDRG
> >  
> > [EXTERNAL EMAIL]
> > Hi all,
> > 
> > I have trouble adding a ligand with AceDRG in CCP4i2 into my refinement:
> > 
> > I put in a smilesstring and the ligand is written ok, but since I can only 
> > chose already 'taken' 3-letter-codes the refinement always crashes as there 
> > is a clash with existing library entries.
> > Is there any way around this? How do I add a novel ligand?
> > 
> > Thanks so much for your help.
> > 
> > Best wishes,
> > Stefanie
> > 
> > 
> > 
> > Dr. Stefanie Freitag-Pohl (she/her)
> > Durham University
> > Department of Chemistry
> > South Road, Durham
> > DH1 3LE
> > United Kingdom
> > 0191 334 2596
> > stefanie.freitag-p...@durham.ac.uk 
> > <mailto:stefanie.freitag-p...@durham.ac.uk>
> > 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
> 
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> 
> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing 
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This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
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Re: [ccp4bb] add ligand with AceDRG

[Oliver Smart]

Hi Stefanie,

If you want to try Grade2 (for a non-confidential ligand) then this is easy to 
do using the Grade Web Server

https://grade.globalphasing.org/

We have altered our default "3-letter code” (aka PDB chemical component ID) to 
“LIG”. 
The reserved PDB two letter codes 01 to 99 are also fine (as are INH and DRG). 
We  understand from users that Grade2 restraint dictionaries work well with 
REFMAC (as to AceDG)
Checking my installation of CCP4 8.0 there are no distributed dictionaries for 
LIG, DRG or 01 to 99.

There was a PDB component LIG that was obsoleted in 2021 
https://www.ebi.ac.uk/pdbe/static/files/pdbechem_v2/LIG.cif
And there was a restraint dictionary for this distributed with CCP4 7.0.

Perhaps you are picking up things from an old CCP4 installation

Hope this helps,

Oliver 




> On 26 Apr 2024, at 11:21, FREITAG-POHL, STEFANIE 
>  wrote:
> 
> Dear all,
> 
> thank you so much for all your suggestions.
> 
> Unfortunately, nothing helped. Whatever 3-letter code I choose Refmac is 
> complaining that there is a clash with an already existing ligand (even DRG, 
> LIG, numbers) and AceDRG in CCP4i2 insists on 3 letters.
> 
> I am not quite sure how to bypass this issue as I think Refmac is also 
> insisting on 3-letters for ligands (???)
> 
> I have not tried Grade yet.
> 
> Any advise much appreciated.
> 
> Best wishes,
> Stefanie
> 
> 
> 
> Dr. Stefanie Freitag-Pohl (she/her)
> Durham University
> Department of Chemistry
> South Road, Durham
> DH1 3LE
> United Kingdom
> 0191 334 2596
> stefanie.freitag-p...@durham.ac.uk <mailto:stefanie.freitag-p...@durham.ac.uk>
> From: CCP4 bulletin board  <mailto:CCP4BB@JISCMAIL.AC.UK>> on behalf of FREITAG-POHL, STEFANIE 
>  <mailto:stefanie.freitag-p...@durham.ac.uk>>
> Sent: 25 April 2024 13:01
> To: CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK> 
> mailto:CCP4BB@JISCMAIL.AC.UK>>
> Subject: [ccp4bb] add ligand with AceDRG
>  
> [EXTERNAL EMAIL]
> Hi all,
> 
> I have trouble adding a ligand with AceDRG in CCP4i2 into my refinement:
> 
> I put in a smilesstring and the ligand is written ok, but since I can only 
> chose already 'taken' 3-letter-codes the refinement always crashes as there 
> is a clash with existing library entries.
> Is there any way around this? How do I add a novel ligand?
> 
> Thanks so much for your help.
> 
> Best wishes,
> Stefanie
> 
> 
> 
> Dr. Stefanie Freitag-Pohl (she/her)
> Durham University
> Department of Chemistry
> South Road, Durham
> DH1 3LE
> United Kingdom
> 0191 334 2596
> stefanie.freitag-p...@durham.ac.uk <mailto:stefanie.freitag-p...@durham.ac.uk>
> 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] add ligand with AceDRG

[Deborah Harrus]

Thanks for the feedback, I will let PDBe developers know that this is 
causing confusion and that LIG should not return results.


Kind regards,

Deborah

On 26/04/2024 16:11, Garib Murshudov wrote:

On this website:
https://www.ebi.ac.uk/pdbe-srv/pdbechem/

If you search for LIG it returns a ligand. With small letters it says:


         The chemical component you are trying to view (LIG) has
  been obsoleted. You have been redirected to the component which
  superceded it.


On RCSB website it does not return anything. Perhaps, on the PDBe 
website it could also not return anything.


Regards
Garib



On 26 Apr 2024, at 16:07, Deborah Harrus  wrote:

Hi Diana,

Could you please clarify where you are searching?

LIG is obsolete and definitely not in use.

Cheers,

Deborah

On 26/04/2024 15:40, Diana Tomchick wrote:
But I think that is a mistake, if you search for LIG in the PDB, it 
brings up a definite ligand that has that 3-letter code.


Diana

Sent from my iPhone


On Apr 26, 2024, at 8:04 AM, Deborah Harrus  wrote:



Dear all,

Just to clarify, "LIG" is also a reserved code, so it's safe to use.

See https://www.wwpdb.org/news/news?year=2023#656f4404d78e004e766a96c6

Kind regards,

Deborah Harrus

PDBe

On 25/04/2024 16:04, Diana Tomchick wrote:

The PDB has reserved the following codes for unknown ligands:

DRG
INH
01 - 99

Using one of these should not cause you the described problems. I 
successfully used


99

just last week. If you try to use

999 or LIG

these will not work, there are ligands assigned to those codes.


Diana

Sent from my iPhone

On Apr 25, 2024, at 8:03 AM, Nicholas Clark 
 wrote:




EXTERNAL MAIL


Hi Stefanie,

Why can you only use "taken" three letter codes? In the "output 
monomer" box, you should be able to enter whatever you'd like for 
the "Three letter code for output monomer". In the attached 
image, this is shown as "DRG" but can be changed to any 3 letter 
code of your choice. Obviously, just make sure your existing 
selection does not exist in the PDB.


Best,

Nick Clark



On Thu, Apr 25, 2024 at 8:51 AM Maria Håkansson 
 wrote:


Hi Stefanie,
Can you manually edit the restraints file using TextEdit and
find and replace and the pdb
file of course?
Other option is to use Grade or Grade2 and the smiles string
if you have this software installed.
I often find this easier than ccp4i2.

Best regards and good luck!
Maria






On 25 Apr 2024, at 14:01, FREITAG-POHL, STEFANIE
 wrote:

Hi all,

I have trouble adding a ligand with AceDRG in CCP4i2 into my
refinement:

I put in a smilesstring and the ligand is written ok, but
since I can only chose already 'taken' 3-letter-codes the
refinement always crashes as there is a clash with existing
library entries.
Is there any way around this? How do I add a novel ligand?

Thanks so much for your help.

Best wishes,
Stefanie



Dr. Stefanie Freitag-Pohl (she/her)
Durham University
Department of Chemistry
South Road, Durham
DH1 3LE
United Kingdom
0191 334 2596
stefanie.freitag-p...@durham.ac.uk


To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1




Maria Håkansson, PhD,
Principal Scientist

SARomics Biostructures AB
Medicon Village
SE-223 81 Lund, Sweden

Mobile: +46 (0)76 8585706
Web: www.saromics.com










To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

Re: [ccp4bb] add ligand with AceDRG

[Phil Jeffrey]

Indeed, as Diana points out:

PDB's own components.cif defines LIG as:

_chem_comp.id   LIG
_chem_comp.name "3-PYRIDIN-4-YL-2,4-DIHYDRO-INDENO[1,2-.C.]PYRAZOLE"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula   "C15 H11 N3"

So they probably should fix that.  Also that chem_comp.name seems to be 
associated with a variety of ligand IDs with different formulae and also 
turns up as a synonym of others.  Things seem to be a little wayward in 
there.


Phil Jeffrey
Princeton


On 4/26/24 10:40 AM, Diana Tomchick wrote:
But I think that is a mistake, if you search for LIG in the PDB, it 
brings up a definite ligand that has that 3-letter code.


Diana

Sent from my iPhone


On Apr 26, 2024, at 8:04 AM, Deborah Harrus  wrote:



Dear all,

Just to clarify, "LIG" is also a reserved code, so it's safe to use.

See https://www.wwpdb.org/news/news?year=2023#656f4404d78e004e766a96c6

Kind regards,

Deborah Harrus

PDBe





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Re: [ccp4bb] add ligand with AceDRG

[Garib Murshudov]

On this website:
https://www.ebi.ac.uk/pdbe-srv/pdbechem/ 


If you search for LIG it returns a ligand. With small letters it says:

   The chemical component you are trying to view (LIG) has been obsoleted. 
You have been redirected to the component which superceded it.


On RCSB website it does not return anything. Perhaps, on the PDBe website it 
could also not return anything.

Regards
Garib


> On 26 Apr 2024, at 16:07, Deborah Harrus  wrote:
> 
> Hi Diana,
> 
> Could you please clarify where you are searching?
> 
> LIG is obsolete and definitely not in use.
> 
> Cheers,
> 
> Deborah
> 
> On 26/04/2024 15:40, Diana Tomchick wrote:
>> But I think that is a mistake, if you search for LIG in the PDB, it brings 
>> up a definite ligand that has that 3-letter code. 
>> 
>> Diana
>> 
>> Sent from my iPhone
>> 
>>> On Apr 26, 2024, at 8:04 AM, Deborah Harrus  
>>>  wrote:
>>> 
>>> 
>>> Dear all,
>>> 
>>> Just to clarify, "LIG" is also a reserved code, so it's safe to use.
>>> 
>>> See https://www.wwpdb.org/news/news?year=2023#656f4404d78e004e766a96c6 
>>> 
>>> Kind regards,
>>> 
>>> Deborah Harrus
>>> 
>>> PDBe
>>> 
>>> On 25/04/2024 16:04, Diana Tomchick wrote:
 The PDB has reserved the following codes for unknown ligands:
 
 DRG
 INH
 01 - 99
 
 Using one of these should not cause you the described problems. I 
 successfully used 
 
 99
 
 just last week. If you try to use
 
 999 or LIG
 
 these will not work, there are ligands assigned to those codes.
 
 
 Diana
 
 Sent from my iPhone
 
> On Apr 25, 2024, at 8:03 AM, Nicholas Clark 
>  
>  wrote:
> 
> 
> EXTERNAL MAIL
> 
> 
> Hi Stefanie,
> 
> Why can you only use "taken" three letter codes? In the "output monomer" 
> box, you should be able to enter whatever you'd like for the "Three 
> letter code for output monomer". In the attached image, this is shown as 
> "DRG" but can be changed to any 3 letter code of your choice. Obviously, 
> just make sure your existing selection does not exist in the PDB. 
> 
> Best,
> 
> Nick Clark
> 
> 
> 
> On Thu, Apr 25, 2024 at 8:51 AM Maria Håkansson 
> mailto:maria.hakans...@saromics.com>> 
> wrote:
> Hi Stefanie,
> Can you manually edit the restraints file using TextEdit and find and 
> replace and the pdb
> file of course?
> Other option is to use Grade or Grade2 and the smiles string if you have 
> this software installed.
> I often find this easier than ccp4i2.
> 
> Best regards and good luck!
> Maria
> 
> 
> 
> 
> 
>> On 25 Apr 2024, at 14:01, FREITAG-POHL, STEFANIE 
>> > > wrote:
>> 
>> Hi all,
>> 
>> I have trouble adding a ligand with AceDRG in CCP4i2 into my refinement:
>> 
>> I put in a smilesstring and the ligand is written ok, but since I can 
>> only chose already 'taken' 3-letter-codes the refinement always crashes 
>> as there is a clash with existing library entries.
>> Is there any way around this? How do I add a novel ligand?
>> 
>> Thanks so much for your help.
>> 
>> Best wishes,
>> Stefanie
>> 
>> 
>> 
>> Dr. Stefanie Freitag-Pohl (she/her)
>> Durham University
>> Department of Chemistry
>> South Road, Durham
>> DH1 3LE
>> United Kingdom
>> 0191 334 2596
>> stefanie.freitag-p...@durham.ac.uk 
>> 
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 
>> 
> Maria Håkansson, PhD,
> Principal Scientist
> 
> SARomics Biostructures AB
> Medicon Village
> SE-223 81 Lund, Sweden
> 
> Mobile: +46 (0)76 8585706
> Web: www.saromics.com 
> 

Re: [ccp4bb] add ligand with AceDRG

[Deborah Harrus]

Hi Diana,

Could you please clarify where you are searching?

LIG is obsolete and definitely not in use.

Cheers,

Deborah

On 26/04/2024 15:40, Diana Tomchick wrote:
But I think that is a mistake, if you search for LIG in the PDB, it 
brings up a definite ligand that has that 3-letter code.


Diana

Sent from my iPhone


On Apr 26, 2024, at 8:04 AM, Deborah Harrus  wrote:



Dear all,

Just to clarify, "LIG" is also a reserved code, so it's safe to use.

See https://www.wwpdb.org/news/news?year=2023#656f4404d78e004e766a96c6

Kind regards,

Deborah Harrus

PDBe

On 25/04/2024 16:04, Diana Tomchick wrote:

The PDB has reserved the following codes for unknown ligands:

DRG
INH
01 - 99

Using one of these should not cause you the described problems. I 
successfully used


99

just last week. If you try to use

999 or LIG

these will not work, there are ligands assigned to those codes.


Diana

Sent from my iPhone

On Apr 25, 2024, at 8:03 AM, Nicholas Clark 
 wrote:




EXTERNAL MAIL


Hi Stefanie,

Why can you only use "taken" three letter codes? In the "output 
monomer" box, you should be able to enter whatever you'd like for 
the "Three letter code for output monomer". In the attached image, 
this is shown as "DRG" but can be changed to any 3 letter code of 
your choice. Obviously, just make sure your existing selection does 
not exist in the PDB.


Best,

Nick Clark



On Thu, Apr 25, 2024 at 8:51 AM Maria Håkansson 
 wrote:


Hi Stefanie,
Can you manually edit the restraints file using TextEdit and
find and replace and the pdb
file of course?
Other option is to use Grade or Grade2 and the smiles string if
you have this software installed.
I often find this easier than ccp4i2.

Best regards and good luck!
Maria






On 25 Apr 2024, at 14:01, FREITAG-POHL, STEFANIE
 wrote:

Hi all,

I have trouble adding a ligand with AceDRG in CCP4i2 into my
refinement:

I put in a smilesstring and the ligand is written ok, but
since I can only chose already 'taken' 3-letter-codes the
refinement always crashes as there is a clash with existing
library entries.
Is there any way around this? How do I add a novel ligand?

Thanks so much for your help.

Best wishes,
Stefanie



Dr. Stefanie Freitag-Pohl (she/her)
Durham University
Department of Chemistry
South Road, Durham
DH1 3LE
United Kingdom
0191 334 2596
stefanie.freitag-p...@durham.ac.uk


To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1




Maria Håkansson, PhD,
Principal Scientist

SARomics Biostructures AB
Medicon Village
SE-223 81 Lund, Sweden

Mobile: +46 (0)76 8585706
Web: www.saromics.com










To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1






--
Nicholas D. Clark (He/Him)
PhD Candidate
Malkowski Lab
University at Buffalo
Department of Structural Biology
Jacob's School of Medicine & Biomedical Sciences
955 Main Street, RM 5130
Buffalo, NY 14203



To unsubscribe from the CCP4BB list, click the following link:

Re: [ccp4bb] add ligand with AceDRG

[Diana Tomchick]

But I think that is a mistake, if you search for LIG in the PDB, it brings up a 
definite ligand that has that 3-letter code.

Diana

Sent from my iPhone

On Apr 26, 2024, at 8:04 AM, Deborah Harrus  wrote:



Dear all,

Just to clarify, "LIG" is also a reserved code, so it's safe to use.

See 
https://www.wwpdb.org/news/news?year=2023#656f4404d78e004e766a96c6

Kind regards,

Deborah Harrus

PDBe

On 25/04/2024 16:04, Diana Tomchick wrote:
The PDB has reserved the following codes for unknown ligands:

DRG
INH
01 - 99

Using one of these should not cause you the described problems. I successfully 
used

99

just last week. If you try to use

999 or LIG

these will not work, there are ligands assigned to those codes.


Diana

Sent from my iPhone

On Apr 25, 2024, at 8:03 AM, Nicholas Clark 

 wrote:


EXTERNAL MAIL

Hi Stefanie,

Why can you only use "taken" three letter codes? In the "output monomer" box, 
you should be able to enter whatever you'd like for the "Three letter code for 
output monomer". In the attached image, this is shown as "DRG" but can be 
changed to any 3 letter code of your choice. Obviously, just make sure your 
existing selection does not exist in the PDB.

Best,

Nick Clark



On Thu, Apr 25, 2024 at 8:51 AM Maria Håkansson 
mailto:maria.hakans...@saromics.com>> wrote:
Hi Stefanie,
Can you manually edit the restraints file using TextEdit and find and replace 
and the pdb
file of course?
Other option is to use Grade or Grade2 and the smiles string if you have this 
software installed.
I often find this easier than ccp4i2.

Best regards and good luck!
Maria





On 25 Apr 2024, at 14:01, FREITAG-POHL, STEFANIE 
mailto:stefanie.freitag-p...@durham.ac.uk>> 
wrote:

Hi all,

I have trouble adding a ligand with AceDRG in CCP4i2 into my refinement:

I put in a smilesstring and the ligand is written ok, but since I can only 
chose already 'taken' 3-letter-codes the refinement always crashes as there is 
a clash with existing library entries.
Is there any way around this? How do I add a novel ligand?

Thanks so much for your help.

Best wishes,
Stefanie



Dr. Stefanie Freitag-Pohl (she/her)
Durham University
Department of Chemistry
South Road, Durham
DH1 3LE
United Kingdom
0191 334 2596
stefanie.freitag-p...@durham.ac.uk


To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

Maria Håkansson, PhD,
Principal Scientist

SARomics Biostructures AB
Medicon Village
SE-223 81 Lund, Sweden

Mobile: +46 (0)76 8585706
Web: 
www.saromics.com








To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1


--
Nicholas D. Clark (He/Him)
PhD Candidate
Malkowski Lab
University at Buffalo
Department of Structural Biology
Jacob's School of Medicine & Biomedical Sciences
955 Main Street, RM 5130
Buffalo, NY 14203



To unsubscribe from the CCP4BB list, click the following link:

Re: [ccp4bb] add ligand with AceDRG

[Deborah Harrus]

Dear all,

Just to clarify, "LIG" is also a reserved code, so it's safe to use.

See https://www.wwpdb.org/news/news?year=2023#656f4404d78e004e766a96c6

Kind regards,

Deborah Harrus

PDBe

On 25/04/2024 16:04, Diana Tomchick wrote:

The PDB has reserved the following codes for unknown ligands:

DRG
INH
01 - 99

Using one of these should not cause you the described problems. I 
successfully used


99

just last week. If you try to use

999 or LIG

these will not work, there are ligands assigned to those codes.


Diana

Sent from my iPhone

On Apr 25, 2024, at 8:03 AM, Nicholas Clark 
 wrote:




EXTERNAL MAIL


Hi Stefanie,

Why can you only use "taken" three letter codes? In the "output 
monomer" box, you should be able to enter whatever you'd like for the 
"Three letter code for output monomer". In the attached image, this 
is shown as "DRG" but can be changed to any 3 letter code of your 
choice. Obviously, just make sure your existing selection does not 
exist in the PDB.


Best,

Nick Clark



On Thu, Apr 25, 2024 at 8:51 AM Maria Håkansson 
 wrote:


Hi Stefanie,
Can you manually edit the restraints file using TextEdit and find
and replace and the pdb
file of course?
Other option is to use Grade or Grade2 and the smiles string if
you have this software installed.
I often find this easier than ccp4i2.

Best regards and good luck!
Maria






On 25 Apr 2024, at 14:01, FREITAG-POHL, STEFANIE
 wrote:

Hi all,

I have trouble adding a ligand with AceDRG in CCP4i2 into my
refinement:

I put in a smilesstring and the ligand is written ok, but since
I can only chose already 'taken' 3-letter-codes the refinement
always crashes as there is a clash with existing library entries.
Is there any way around this? How do I add a novel ligand?

Thanks so much for your help.

Best wishes,
Stefanie



Dr. Stefanie Freitag-Pohl (she/her)
Durham University
Department of Chemistry
South Road, Durham
DH1 3LE
United Kingdom
0191 334 2596
stefanie.freitag-p...@durham.ac.uk


To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1




Maria Håkansson, PhD,
Principal Scientist

SARomics Biostructures AB
Medicon Village
SE-223 81 Lund, Sweden

Mobile: +46 (0)76 8585706
Web: www.saromics.com










To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1






--
Nicholas D. Clark (He/Him)
PhD Candidate
Malkowski Lab
University at Buffalo
Department of Structural Biology
Jacob's School of Medicine & Biomedical Sciences
955 Main Street, RM 5130
Buffalo, NY 14203



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 
 



CAUTION: This email originated from outside UTSW. Please be cautious 
of links or attachments, and validate the sender's 

Re: [ccp4bb] add ligand with AceDRG

[Garib Murshudov]

Thank you Paul. I did not think about it.

Stefanie, could you please send the log file to me?

Regards
Garib


> On 26 Apr 2024, at 14:17, Paul Emsley  wrote:
> 
> 
> On 25/04/2024 13:01, FREITAG-POHL, STEFANIE wrote:
>> 
>> 
>> 
>> I have trouble adding a ligand with AceDRG in CCP4i2 into my refinement:
>> 
>> I put in a smilesstring and the ligand is written ok, but since I can only 
>> chose already 'taken' 3-letter-codes the refinement always crashes as there 
>> is a clash with existing library entries.
> 
> I suspect that the issue is not what you think it is.
> 
> Look at the refmac log and tell us the refmac command line and the failure 
> message.
> 
> 
> 
> Paul.
> 
> 
> 
> 
> 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] add ligand with AceDRG

[Paul Emsley]

On 25/04/2024 13:01, FREITAG-POHL, STEFANIE wrote:



I have trouble adding a ligand with AceDRG in CCP4i2 into my refinement:

I put in a smilesstring and the ligand is written ok, but since I can 
only chose already 'taken' 3-letter-codes the refinement always 
crashes as there is a clash with existing library entries.



I suspect that the issue is not what you think it is.

Look at the refmac log and tell us the refmac command line and the 
failure message.



Paul.




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Re: [ccp4bb] add ligand with AceDRG

[Cyprian Cukier]

Dear Stefanie,

We routinely use DRG or LIG or numbers in running refmac and do not see the 
issue. Maybe check if .cif and .pdb file has the same code for the compound and 
also, if the issue is not coming from other molecule in the structure?

Another option would to be try a different computer to make sure that it is not 
related to your ccp4 installation.

Best regards
Cyprian

Cyprian Cukier, Ph.D.
Head of Structural Biology
Selvita S.A.


From: CCP4 bulletin board  On Behalf Of Garib Murshudov
Sent: Friday, April 26, 2024 1:48 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] add ligand with AceDRG


CAUTION: External Sender. Please do not click on links or open attachments from 
senders you do not trust.
Refmac by itself should not care about duplicated residue names in the monomer 
library. It takes the last monomer. There should be something on the interface 
preventing this.

Longer than three letters should be available from the next release of ccp4. 
New acedrg and Refmacat should be able to deal with them. Ccp4i2 might not be 
ready.

Regards
Garib



On 26 Apr 2024, at 11:21, FREITAG-POHL, STEFANIE 
mailto:stefanie.freitag-p...@durham.ac.uk>> 
wrote:

Dear all,

thank you so much for all your suggestions.

Unfortunately, nothing helped. Whatever 3-letter code I choose Refmac is 
complaining that there is a clash with an already existing ligand (even DRG, 
LIG, numbers) and AceDRG in CCP4i2 insists on 3 letters.

I am not quite sure how to bypass this issue as I think Refmac is also 
insisting on 3-letters for ligands (???)

I have not tried Grade yet.

Any advise much appreciated.

Best wishes,
Stefanie



Dr. Stefanie Freitag-Pohl (she/her)
Durham University
Department of Chemistry
South Road, Durham
DH1 3LE
United Kingdom
0191 334 2596
stefanie.freitag-p...@durham.ac.uk<mailto:stefanie.freitag-p...@durham.ac.uk>

From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
on behalf of FREITAG-POHL, STEFANIE 
mailto:stefanie.freitag-p...@durham.ac.uk>>
Sent: 25 April 2024 13:01
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> 
mailto:CCP4BB@JISCMAIL.AC.UK>>
Subject: [ccp4bb] add ligand with AceDRG

[EXTERNAL EMAIL]
Hi all,

I have trouble adding a ligand with AceDRG in CCP4i2 into my refinement:

I put in a smilesstring and the ligand is written ok, but since I can only 
chose already 'taken' 3-letter-codes the refinement always crashes as there is 
a clash with existing library entries.
Is there any way around this? How do I add a novel ligand?

Thanks so much for your help.

Best wishes,
Stefanie



Dr. Stefanie Freitag-Pohl (she/her)
Durham University
Department of Chemistry
South Road, Durham
DH1 3LE
United Kingdom
0191 334 2596
stefanie.freitag-p...@durham.ac.uk<mailto:stefanie.freitag-p...@durham.ac.uk>


To unsubscribe from the CCP4BB list, click the following link:
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Re: [ccp4bb] add ligand with AceDRG

[Garib Murshudov]

Refmac by itself should not care about duplicated residue names in the monomer 
library. It takes the last monomer. There should be something on the interface 
preventing this.

Longer than three letters should be available from the next release of ccp4. 
New acedrg and Refmacat should be able to deal with them. Ccp4i2 might not be 
ready.

Regards
Garib


> On 26 Apr 2024, at 11:21, FREITAG-POHL, STEFANIE 
>  wrote:
> 
> Dear all,
> 
> thank you so much for all your suggestions.
> 
> Unfortunately, nothing helped. Whatever 3-letter code I choose Refmac is 
> complaining that there is a clash with an already existing ligand (even DRG, 
> LIG, numbers) and AceDRG in CCP4i2 insists on 3 letters.
> 
> I am not quite sure how to bypass this issue as I think Refmac is also 
> insisting on 3-letters for ligands (???)
> 
> I have not tried Grade yet.
> 
> Any advise much appreciated.
> 
> Best wishes,
> Stefanie
> 
> 
> 
> Dr. Stefanie Freitag-Pohl (she/her)
> Durham University
> Department of Chemistry
> South Road, Durham
> DH1 3LE
> United Kingdom
> 0191 334 2596
> stefanie.freitag-p...@durham.ac.uk <mailto:stefanie.freitag-p...@durham.ac.uk>
> From: CCP4 bulletin board  <mailto:CCP4BB@JISCMAIL.AC.UK>> on behalf of FREITAG-POHL, STEFANIE 
>  <mailto:stefanie.freitag-p...@durham.ac.uk>>
> Sent: 25 April 2024 13:01
> To: CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK> 
> mailto:CCP4BB@JISCMAIL.AC.UK>>
> Subject: [ccp4bb] add ligand with AceDRG
>  
> [EXTERNAL EMAIL]
> Hi all,
> 
> I have trouble adding a ligand with AceDRG in CCP4i2 into my refinement:
> 
> I put in a smilesstring and the ligand is written ok, but since I can only 
> chose already 'taken' 3-letter-codes the refinement always crashes as there 
> is a clash with existing library entries.
> Is there any way around this? How do I add a novel ligand?
> 
> Thanks so much for your help.
> 
> Best wishes,
> Stefanie
> 
> 
> 
> Dr. Stefanie Freitag-Pohl (she/her)
> Durham University
> Department of Chemistry
> South Road, Durham
> DH1 3LE
> United Kingdom
> 0191 334 2596
> stefanie.freitag-p...@durham.ac.uk <mailto:stefanie.freitag-p...@durham.ac.uk>
> To unsubscribe from the CCP4BB list, click the following link:
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Re: [ccp4bb] add ligand with AceDRG

[FREITAG-POHL, STEFANIE]

Dear all,

thank you so much for all your suggestions.

Unfortunately, nothing helped. Whatever 3-letter code I choose Refmac is 
complaining that there is a clash with an already existing ligand (even DRG, 
LIG, numbers) and AceDRG in CCP4i2 insists on 3 letters.

I am not quite sure how to bypass this issue as I think Refmac is also 
insisting on 3-letters for ligands (???)

I have not tried Grade yet.

Any advise much appreciated.

Best wishes,
Stefanie




Dr. Stefanie Freitag-Pohl (she/her)

Durham University

Department of Chemistry

South Road, Durham

DH1 3LE

United Kingdom

0191 334 2596

stefanie.freitag-p...@durham.ac.uk<mailto:stefanie.freitag-p...@durham.ac.uk>


From: CCP4 bulletin board  on behalf of FREITAG-POHL, 
STEFANIE 
Sent: 25 April 2024 13:01
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] add ligand with AceDRG

[EXTERNAL EMAIL]
Hi all,

I have trouble adding a ligand with AceDRG in CCP4i2 into my refinement:

I put in a smilesstring and the ligand is written ok, but since I can only 
chose already 'taken' 3-letter-codes the refinement always crashes as there is 
a clash with existing library entries.
Is there any way around this? How do I add a novel ligand?

Thanks so much for your help.

Best wishes,
Stefanie




Dr. Stefanie Freitag-Pohl (she/her)

Durham University

Department of Chemistry

South Road, Durham

DH1 3LE

United Kingdom

0191 334 2596

stefanie.freitag-p...@durham.ac.uk<mailto:stefanie.freitag-p...@durham.ac.uk>



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Re: [ccp4bb] add ligand with AceDRG

[Diana Tomchick]

The PDB has reserved the following codes for unknown ligands:

DRG
INH
01 - 99

Using one of these should not cause you the described problems. I successfully 
used

99

just last week. If you try to use

999 or LIG

these will not work, there are ligands assigned to those codes.


Diana

Sent from my iPhone

On Apr 25, 2024, at 8:03 AM, Nicholas Clark 
 wrote:


EXTERNAL MAIL

Hi Stefanie,

Why can you only use "taken" three letter codes? In the "output monomer" box, 
you should be able to enter whatever you'd like for the "Three letter code for 
output monomer". In the attached image, this is shown as "DRG" but can be 
changed to any 3 letter code of your choice. Obviously, just make sure your 
existing selection does not exist in the PDB.

Best,

Nick Clark



On Thu, Apr 25, 2024 at 8:51 AM Maria Håkansson 
mailto:maria.hakans...@saromics.com>> wrote:
Hi Stefanie,
Can you manually edit the restraints file using TextEdit and find and replace 
and the pdb
file of course?
Other option is to use Grade or Grade2 and the smiles string if you have this 
software installed.
I often find this easier than ccp4i2.

Best regards and good luck!
Maria





On 25 Apr 2024, at 14:01, FREITAG-POHL, STEFANIE 
mailto:stefanie.freitag-p...@durham.ac.uk>> 
wrote:

Hi all,

I have trouble adding a ligand with AceDRG in CCP4i2 into my refinement:

I put in a smilesstring and the ligand is written ok, but since I can only 
chose already 'taken' 3-letter-codes the refinement always crashes as there is 
a clash with existing library entries.
Is there any way around this? How do I add a novel ligand?

Thanks so much for your help.

Best wishes,
Stefanie



Dr. Stefanie Freitag-Pohl (she/her)
Durham University
Department of Chemistry
South Road, Durham
DH1 3LE
United Kingdom
0191 334 2596
stefanie.freitag-p...@durham.ac.uk


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Maria Håkansson, PhD,
Principal Scientist

SARomics Biostructures AB
Medicon Village
SE-223 81 Lund, Sweden

Mobile: +46 (0)76 8585706
Web: 
www.saromics.com








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--
Nicholas D. Clark (He/Him)
PhD Candidate
Malkowski Lab
University at Buffalo
Department of Structural Biology
Jacob's School of Medicine & Biomedical Sciences
955 Main Street, RM 5130
Buffalo, NY 14203



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Re: [ccp4bb] add ligand with AceDRG

[Fei Long]

Hi Stefanie,

If you could run from command-lines, it will be easy to solve this 
problem.


try from command-line, type
acedrg -i "your_smiles_string" -r your_3_letter_code -o 
your_out_file_name


For example,
acedrg -i "C[C@@H](C(=O)O)N" -r UNL -o UNL

You will get a file called UNL.cif, which should be ok for the 
refinement.


Best wishes,

Fei




On 2024-04-25 13:01, FREITAG-POHL, STEFANIE wrote:

Hi all,

 I have trouble adding a ligand with AceDRG in CCP4i2 into my
refinement:

 I put in a smilesstring and the ligand is written ok, but since I can
only chose already 'taken' 3-letter-codes the refinement always
crashes as there is a clash with existing library entries.
 Is there any way around this? How do I add a novel ligand?

 Thanks so much for your help.

 Best wishes,
 Stefanie

Dr. Stefanie Freitag-Pohl (she/her)

Durham University

Department of Chemistry

South Road, Durham

DH1 3LE

United Kingdom

0191 334 2596

stefanie.freitag-p...@durham.ac.uk

-

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--
Dr. Fei Long
Structural Studies Division
UKRI Laboratory of Molecular Biology
Francis Crick Avenue,
Cambridge Biomedical Campus,
Cambridge
CB2 0QH UK
Email:fl...@mrc-lmb.cam.ac.uk



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Re: [ccp4bb] add ligand with AceDRG

[Nicholas Clark]

Hi Stefanie,

Why can you only use "taken" three letter codes? In the "output monomer"
box, you should be able to enter whatever you'd like for the "Three letter
code for output monomer". In the attached image, this is shown as "DRG" but
can be changed to any 3 letter code of your choice. Obviously, just make
sure your existing selection does not exist in the PDB.

Best,

Nick Clark
[image: AdeDRG_jobwindow.png]

On Thu, Apr 25, 2024 at 8:51 AM Maria Håkansson <
maria.hakans...@saromics.com> wrote:

> Hi Stefanie,
> Can you manually edit the restraints file using TextEdit and find and
> replace and the pdb
> file of course?
> Other option is to use Grade or Grade2 and the smiles string if you have
> this software installed.
> I often find this easier than ccp4i2.
>
> Best regards and good luck!
> Maria
>
>
>
>
>
> On 25 Apr 2024, at 14:01, FREITAG-POHL, STEFANIE <
> stefanie.freitag-p...@durham.ac.uk> wrote:
>
> Hi all,
>
> I have trouble adding a ligand with AceDRG in CCP4i2 into my refinement:
>
> I put in a smilesstring and the ligand is written ok, but since I can only
> chose already 'taken' 3-letter-codes the refinement always crashes as there
> is a clash with existing library entries.
> Is there any way around this? How do I add a novel ligand?
>
> Thanks so much for your help.
>
> Best wishes,
> Stefanie
>
>
>
> Dr. Stefanie Freitag-Pohl (she/her)
> Durham University
> Department of Chemistry
> South Road, Durham
> DH1 3LE
> United Kingdom
> 0191 334 2596
> stefanie.freitag-p...@durham.ac.uk
>
> --
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> 
>
>
> Maria Håkansson, PhD,
> Principal Scientist
>
> SARomics Biostructures AB
> Medicon Village
> SE-223 81 Lund, Sweden
>
> Mobile: +46 (0)76 8585706
> Web: www.saromics.com
>
>
>
>
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> 
>


-- 
Nicholas D. Clark (He/Him)
PhD Candidate
Malkowski Lab
University at Buffalo
Department of Structural Biology
Jacob's School of Medicine & Biomedical Sciences
955 Main Street, RM 5130
Buffalo, NY 14203



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Re: [ccp4bb] add ligand with AceDRG

[Maria Håkansson]

Hi Stefanie,
Can you manually edit the restraints file using TextEdit and find and replace 
and the pdb
file of course?
Other option is to use Grade or Grade2 and the smiles string if you have this 
software installed.
I often find this easier than ccp4i2.

Best regards and good luck!
Maria





> On 25 Apr 2024, at 14:01, FREITAG-POHL, STEFANIE 
>  wrote:
> 
> Hi all,
> 
> I have trouble adding a ligand with AceDRG in CCP4i2 into my refinement:
> 
> I put in a smilesstring and the ligand is written ok, but since I can only 
> chose already 'taken' 3-letter-codes the refinement always crashes as there 
> is a clash with existing library entries.
> Is there any way around this? How do I add a novel ligand?
> 
> Thanks so much for your help.
> 
> Best wishes,
> Stefanie
> 
> 
> 
> Dr. Stefanie Freitag-Pohl (she/her)
> Durham University
> Department of Chemistry
> South Road, Durham
> DH1 3LE
> United Kingdom
> 0191 334 2596
> stefanie.freitag-p...@durham.ac.uk 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

Maria Håkansson, PhD,
Principal Scientist

SARomics Biostructures AB
Medicon Village
SE-223 81 Lund, Sweden

Mobile: +46 (0)76 8585706
Web: www.saromics.com








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Re: [ccp4bb] add ligand with AceDRG

[Andy Purkiss]

Hi Stefanie,

In CCP4Cloud, the equivalent task will generate the files using a 'free', 
unused code, if nothing is entered in the relevant box. However, not sure if 
CCP4I2's task will do the same, but worth trying.

Hope this helps,

Andy


From: CCP4 bulletin board  on behalf of FREITAG-POHL, 
STEFANIE 
Sent: 25 April 2024 13:01
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] add ligand with AceDRG


External Sender: Use caution.

Hi all,

I have trouble adding a ligand with AceDRG in CCP4i2 into my refinement:

I put in a smilesstring and the ligand is written ok, but since I can only 
chose already 'taken' 3-letter-codes the refinement always crashes as there is 
a clash with existing library entries.
Is there any way around this? How do I add a novel ligand?

Thanks so much for your help.

Best wishes,
Stefanie




Dr. Stefanie Freitag-Pohl (she/her)

Durham University

Department of Chemistry

South Road, Durham

DH1 3LE

United Kingdom

0191 334 2596

stefanie.freitag-p...@durham.ac.uk<mailto:stefanie.freitag-p...@durham.ac.uk>



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[ccp4bb] add ligand with AceDRG

[FREITAG-POHL, STEFANIE]

Hi all,

I have trouble adding a ligand with AceDRG in CCP4i2 into my refinement:

I put in a smilesstring and the ligand is written ok, but since I can only 
chose already 'taken' 3-letter-codes the refinement always crashes as there is 
a clash with existing library entries.
Is there any way around this? How do I add a novel ligand?

Thanks so much for your help.

Best wishes,
Stefanie




Dr. Stefanie Freitag-Pohl (she/her)

Durham University

Department of Chemistry

South Road, Durham

DH1 3LE

United Kingdom

0191 334 2596

stefanie.freitag-p...@durham.ac.uk



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