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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[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



To unsubscribe from the CCP4BB list, click the following link:
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[ccp4bb] Babinets scaling in Refmac

[FREITAG-POHL, STEFANIE]

Hi,

I just upgraded to CCP4-8.0.002 and found that if I refine in Refmac with 
Babinets scaling my maps look not correct.
Is that a known problem?

Best wishes, Stefanie



Dr. Stefanie Freitag-Pohl

Durham University

Department of Chemistry

South Road, Durham

DH1 3LE

United Kingdom

0191 334 3619

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



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