Re: [ccp4bb] replacement for Scientific Linux

2024-04-26 Thread Kay Diederichs 
Hi Harry,

same here. Actually we skipped RHEL8 and its alternatives, so moved directly 
from CentOS7 to Rocky9. We are happy with that decision.

Best wishes,
Kay

On Fri, 26 Apr 2024 15:57:46 +, Andy Purkiss  
wrote:

>Hi Harry,
>
>We've been migrating to Rocky Linux as it is built on RHEL in a similar way to 
>Scientific Linux. Most things compiled on Centos 7 (our default for a while) 
>work in Rocky Linux version 9. For compilers etc., I use the Software 
>Collections / devtoolsets to run later versions than the default OS.
>
>Hope this helps,
>
>Andy
>
>
>From: CCP4 bulletin board  on behalf of Harry Powell 
><193323b1e616-dmarc-requ...@jiscmail.ac.uk>
>Sent: 26 April 2024 16:46
>To: CCP4BB@JISCMAIL.AC.UK 
>Subject: [ccp4bb] replacement for Scientific Linux
>
>
>External Sender: Use caution.
>
>
>Hi folks
>
>For many years I�ve been using Scientific Linux as my OS of choice (when not 
>using my Mac) - but it�s been discontinued. SL was based on RHEL, and had 
>useful things like a less-buggy Fortran/C/C++ compiler than that released by 
>RH.
>
>What do people here recommend as a replacement?
>
>Harry
>
>
>To unsubscribe from the CCP4BB list, click the following link:
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Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] add ligand with AceDRG

2024-04-26 Thread 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
>>> 
>>> From: CCP4 bulletin board >> > on behalf of FREITAG-POHL, STEFANIE
>>> >> >
>>> Sent: 25 April 2024 13:01
>>> To: 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

Re: [ccp4bb] add ligand with AceDRG

2024-04-26 Thread 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


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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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Re: [ccp4bb] replacement for Scientific Linux

2024-04-26 Thread Tim Gruene 
Hi Harry,

I started using Debian about 10-15 years ago, and never changed my
opinion since. I had tested various others before, like redhat, suse,
ubuntu etc. The stable version of Debian is indeed very stable, as
there are no version changes, only bug fixes etc. The new release
is about every three years, and upgrading does not break the system
(with rpm based systems I remember quite frequent re-installs,
because the system got messed up). The long-term support is indeed very
long.

The main repositories of Debian
include a great number of scientific / crystallographic packages, e.g.
raster3d, pymol, clipper-, ccp4-, mmdb2-libraries and what not.

Due to the philosophy of sticking to a version, and only to bug fixes
and security releases, Debian is often not affected by security holes,
e.g. the SHELX server was save from heart-bleed when it came out,
because heart-bleed require more modern versions of whatever library
was affected (SSL?). Same is true for the recent foul version of XZ.

Debian is POSIX compliant, so it doesn't mess around with standards,
and for configuration you can rely on what you find on the web. There
is a saying 'even a chicken can install Debian, as you only need to hit
Enter', which is not far from true.

Cheers,
Tim


On Fri, 26 Apr 2024 16:46:17 +0100 Harry Powell
<193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:

> Hi folks
> 
> For many years I’ve been using Scientific Linux as my OS of choice
> (when not using my Mac) - but it’s been discontinued. SL was based on
> RHEL, and had useful things like a less-buggy Fortran/C/C++ compiler
> than that released by RH.
> 
> What do people here recommend as a replacement? 
> 
> Harry
> 
> 
> 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 list hosted by www.jiscmail.ac.uk, terms & conditions are
> available at https://www.jiscmail.ac.uk/policyandsecurity/



-- 
Tim Gruene
Head of the Centre for X-ray Structure Analysis
Faculty of Chemistry
University of Vienna

Phone: +43-1-4277-70202

GPG Key ID = A46BEE1A



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pgp4iZKUGAxYg.pgp
Description: OpenPGP digital signature

[ccp4bb] Staff Scientist Position to Manage Protein Purification Facility at Ohio State

2024-04-26 Thread Bell, Charles 
Dear Colleagues,

The Department of Biological Chemistry and Pharmacology at The Ohio State 
University has recently obtained 5 years of generous funding to equip and staff 
a facility for expression and purification of proteins for structural analysis 
by cryo-EM, x-ray crystallography, and NMR spectroscopy. We are seeking 
applications for a Staff Scientist position to manage the facility. The ideal 
candidate has a PhD in Biochemistry or related discipline, and extensive 
experience in protein expression and purification from bacterial, insect, and 
mammalian cell lines. If interested, please apply here: R102685: Research 
Senior 
Associate,
 and feel free to contact me directly if you have any questions.

Cheers,

-Chuck Bell

Charles E. Bell
Professor, Dept. of Biological Chemistry and Pharmacology
Director, Ohio State Biochemistry Program: https://osbp.osu.edu/
The Ohio State University College of Medicine
Tel: 614-688-3115
Website: 
https://medicine.osu.edu/find-faculty/non-clinical/bcpharm/charles-e-bell





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Re: [ccp4bb] replacement for Scientific Linux

2024-04-26 Thread Jonathan Clinger 
If you want to keep as close to scientific linux as possible, I would
suggest Alma or Rocky Linux. Those were the two options my group considered
when the writing was on the wall for scientific linux and we were ramping
up our workstations. We ended up going with Alma, but I'm not sure it is
any better than Rocky. We'll have to wait and see how much they diverge
over time.

If you are ok with moving to something more different, Ubuntu or one of its
derivations would probably do just fine.

Cheers! -Jonathan Clinger

On Fri, Apr 26, 2024 at 9:58 AM Jon Cooper <
488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:

> Hello Harry
>
> Any of the top 50 on distrowatch.com will basically be fine and the next
> 20 or so on the list will probably be fine. Then you start getting into the
> twilight zone. I am sure that will help greatly to narrow down your choice
> ;-0
>
> Best wishes, Jon Cooper. jon.b.coo...@protonmail.com
>
> Sent from Proton Mail mobile
>
>
>
>  Original Message 
> On 26 Apr 2024, 16:46, Harry Powell <
> 193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
>
>
> Hi folks For many years I’ve been using Scientific Linux as my OS of
> choice (when not using my Mac) - but it’s been discontinued. SL was based
> on RHEL, and had useful things like a less-buggy Fortran/C/C++ compiler
> than that released by RH. What do people here recommend as a replacement?
> Harry
>  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
> list hosted by www.jiscmail.ac.uk, terms & conditions are available at
> https://www.jiscmail.ac.uk/policyandsecurity/
> --
>
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>



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[ccp4bb] Deadline extended - ECM34 - Symposium on Serial crystallography and dynamics/room temperature

2024-04-26 Thread Daniele de Sanctis 
Dear all,

A gentle reminder for the ECM  "M3  Serial crystallography and
dynamics/room temperature"

Please note that the general deadline for abstract submission has been
extended to May 7th.

Best regards

Anna and Daniele

On Tue, Apr 9, 2024 at 10:12 AM Daniele de Sanctis 
wrote:

> Dear colleagues,
>
> The ECM34 (https://www.ecm34.org/) is going to be organized in Padova,
> Italy, from the 26th to 30th of August. As chairpersons of the  "M3  Serial
> crystallography and dynamics/room temperature"  we are looking forward to
> receiving your contributions.
>
> We remind you that the deadline for abstract submission is on the 30th of
> April. https://www.ecm34.org/abstracts
>
> Best regards
>
> Anna and Daniele
>
>
> ---
> Daniele de Sanctis, PhD
> Structural Biology Group
> ESRF - The European Synchrotron
> Grenoble, France
> Tel 33 (0)4 76 88 2869
>
> http://www.esrf.eu/id29
>



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Re: [ccp4bb] replacement for Scientific Linux

2024-04-26 Thread Jon Cooper 
Hello Harry

Any of the top 50 on distrowatch.com will basically be fine and the next 20 or 
so on the list will probably be fine. Then you start getting into the twilight 
zone. I am sure that will help greatly to narrow down your choice ;-0

Best wishes, Jon Cooper. jon.b.coo...@protonmail.com

Sent from Proton Mail mobile

 Original Message 
On 26 Apr 2024, 16:46, Harry Powell wrote:

> Hi folks For many years I’ve been using Scientific Linux as my OS of choice 
> (when not using my Mac) - but it’s been discontinued. SL was based on RHEL, 
> and had useful things like a less-buggy Fortran/C/C++ compiler than that 
> released by RH. What do people here recommend as a replacement? Harry 
>  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 list hosted by 
> www.jiscmail.ac.uk, terms & conditions are available at 
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Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] add ligand with AceDRG

2024-04-26 Thread 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
> > 
> > From: CCP4 bulletin board  > > on behalf of FREITAG-POHL, STEFANIE
> >  > >
> > Sent: 25 April 2024 13:01
> > To: 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
> > 
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://ww/
> > w.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1
> > ata=05%7C02%7CWANG_YONG_Y%40LILLY.COM%7C00daf6fed4844df87c9e08dc6608
> > 2939%7C18a59a81eea84c30948ad8824cdc2580%7C0%7C0%7C638497432436403543
> >

Re: [ccp4bb] replacement for Scientific Linux

2024-04-26 Thread Andy Purkiss 
Hi Harry,

We've been migrating to Rocky Linux as it is built on RHEL in a similar way to 
Scientific Linux. Most things compiled on Centos 7 (our default for a while) 
work in Rocky Linux version 9. For compilers etc., I use the Software 
Collections / devtoolsets to run later versions than the default OS.

Hope this helps,

Andy


From: CCP4 bulletin board  on behalf of Harry Powell 
<193323b1e616-dmarc-requ...@jiscmail.ac.uk>
Sent: 26 April 2024 16:46
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] replacement for Scientific Linux


External Sender: Use caution.


Hi folks

For many years I’ve been using Scientific Linux as my OS of choice (when not 
using my Mac) - but it’s been discontinued. SL was based on RHEL, and had 
useful things like a less-buggy Fortran/C/C++ compiler than that released by RH.

What do people here recommend as a replacement?

Harry


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

2024-04-26 Thread 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 
> > 
> > From: CCP4 bulletin board  > > on behalf of FREITAG-POHL, STEFANIE 
> >  > >
> > Sent: 25 April 2024 13:01
> > To: 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 
> > 
> > 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:
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> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing 
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[ccp4bb] replacement for Scientific Linux

2024-04-26 Thread Harry Powell 
Hi folks

For many years I’ve been using Scientific Linux as my OS of choice (when not 
using my Mac) - but it’s been discontinued. SL was based on RHEL, and had 
useful things like a less-buggy Fortran/C/C++ compiler than that released by RH.

What do people here recommend as a replacement? 

Harry


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 list 
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Re: [ccp4bb] add ligand with AceDRG

2024-04-26 Thread 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 
> From: CCP4 bulletin board  > on behalf of FREITAG-POHL, STEFANIE 
>  >
> Sent: 25 April 2024 13:01
> To: 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 
> 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

2024-04-26 Thread 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:
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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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Re: [ccp4bb] add ligand with AceDRG

2024-04-26 Thread 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

2024-04-26 Thread 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

2024-04-26 Thread 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










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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

2024-04-26 Thread 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

2024-04-26 Thread 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

2024-04-26 Thread 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] COOT 1.1 and DNA mutation

2024-04-26 Thread Paul Emsley 

On 26/04/2024 02:44, Paul Emsley wrote:



On 25/04/2024 16:07, Simon Vecchioni wrote:



Paul,

Many thanks for fixing the [simple mutate] button for DNA in 
v1.1.08--works like a charm!


I would ask about two other DNA features--
1) The [add terminal residue] button seems unresponsive for DNA,


I see what you mean. From the terminal output it seems to want to try 
to add a residue via a peptide bond.


I have made a note of this bug.


and is often quite useful;


OK.

This has been fixed and is in the HEAD of main (I will be busy with 
other things for the next few weeks so there won't be a release soon).


You will probably need some local refinement/regularization to anneal 
the phosphodiester link.



Paul.



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Re: [ccp4bb] add ligand with AceDRG

2024-04-26 Thread 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

2024-04-26 Thread 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

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>>
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


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

2024-04-26 Thread 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 
> From: CCP4 bulletin board  > on behalf of FREITAG-POHL, STEFANIE 
>  >
> Sent: 25 April 2024 13:01
> To: 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 
> 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

2024-04-26 Thread 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


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



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[ccp4bb] Postdoctoral Position - Institut de Biologie Structurale (IBS/PATBAC) - Grenoble - France

2024-04-26 Thread Carlos CONTRERAS-MARTEL 

Dear CCP4 community,

a postdoctoral research position financed by the National Research 
Agency is on offer by the Bacterial Pathogenesis Group (DR Andréa 
DESSEN) at the IBS (Institut de Biologie Structurale) in Grenoble. Our 
group focuses on the study of the various mechanisms used by the 
bacteria to initiate an infection and concentrates on the bacterial 
cell-wall, virulence factors and secretion systems.


See details in :

https://emploi.cnrs.fr/Offres/CDD/UMR5075-CYNDAV-062/Default.aspx

--
 Carlos CONTRERAS MARTEL, Ph.D.
 (CRHC CNRS)

 carlos.contreras-mar...@ibs.fr

 "Bacterial Pathogenesis Group"
Institut de Biologie Structurale
 UMR5075 CEA-CNRS-UGA

  IBS (PATBAC)
  Campus EPN
  71, avenue des Martyrs
  CS 10090
  38044 Grenoble CEDEX 9
  FRANCE


 tel : (+33) (0)4 57 42 86 41

http://www.ibs.fr/groupes/groupe-pathogenie-bacterienne/?lang=fr
http://www.ibs.fr/groups/bacterial-pathogenesis-group/?lang=en



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