Re: [ccp4bb] Fwd: Please register - Phenix Workshops - April 7 & 14

[rini chaturvedi]

Dear Dr Moriarty,

Thank you so much.

Looking forward for this meeting.

Kind regards,
Rini Chaturvedi



On Thu, Apr 8, 2021 at 12:11 AM Nigel Moriarty  wrote:

> Rini
>
> It appears you are 30 minutes out but it is still early. Phenix Workshops
> will be recorded. As with the last two virtual workshops, they will be
> posted on YouTube. A simple search there will reveal all.
>
> Cheers
>
> Nigel
>
> ---
> Nigel W. Moriarty
> Building 33R0349, Molecular Biophysics and Integrated Bioimaging
> Lawrence Berkeley National Laboratory
> Berkeley, CA 94720-8235
> Phone : 510-486-5709 Email : nwmoria...@lbl.gov
> Fax   : 510-486-5909  Web  : CCI.LBL.gov
> ORCID : orcid.org/-0001-8857-9464
>
>
> On Wed, Apr 7, 2021 at 2:31 AM rini chaturvedi 
> wrote:
>
>> Dear Dr Moriarty,
>>
>> Thank you for sharing the Phenix workshop link.
>>
>> Will it be possible for the recording of the sessions to be shared in the
>> CCP4BB mail?
>>
>> The given time for the workshop i.e *3.45 pm PDT* which will be around *3.45
>> am* in India (*IST*) and it would be difficult for us to be available at
>> that time
>>
>> Kindly let us know if that is a possibility from your end.
>>
>> Kind regards,
>> Rini Chaturvedi
>> Molecular Medicine
>> ICGEB, New Delhi
>>
>>
>> On Mon, Apr 5, 2021 at 10:45 PM Nigel Moriarty 
>> wrote:
>>
>>> Forward in case it was not circulated. Sorry if it's a repeat.
>>>
>>> Cheers
>>>
>>> Nigel
>>>
>>> ---
>>> Nigel W. Moriarty
>>> Building 33R0349, Molecular Biophysics and Integrated Bioimaging
>>> Lawrence Berkeley National Laboratory
>>> Berkeley, CA 94720-8235
>>> Phone : 510-486-5709 Email : nwmoria...@lbl.gov
>>> Fax   : 510-486-5909  Web  : CCI.LBL.gov
>>> ORCID : orcid.org/-0001-8857-9464
>>>
>>>
>>> -- Forwarded message -
>>> From: Paul Adams 
>>> Date: Wed, Mar 31, 2021 at 2:08 PM
>>> Subject: Please register - Phenix Workshops - April 7 & 14
>>> To: PHENIX user mailing list 
>>> Cc: Nigel Moriarty , Ashley Dawn ,
>>> CCP4BB@JISCMAIL.AC.UK 
>>>
>>>
>>> Dear Colleagues,
>>>
>>> The Phenix developers will be holding an online *Phenix User Workshop on
>>> the 7th and 14th of April at 4-9pm PDT.* These times will work best for
>>> researchers in Asia and Australasia.
>>>
>>> The format of the workshop will be demos of the use of Phenix programs
>>> combined with slides to explain the theory. We expect an interactive
>>> meeting where attendees can ask questions for the Phenix team to answer.
>>>
>>> The workshop will cover aspects of macromolecular crystallography
>>> in Phenix, with the final emphasis based on the applicants’ research
>>> interests. To apply please fill out this form
>>> . We will make every effort to
>>> accommodate all applicants, but may need to defer some requests to a
>>> future workshop if demand is high. We are hoping this workshop will be a
>>> success, in which case we plan to host more in the future.
>>>
>>> *AGENDA:*
>>> *7 APR *
>>>
>>>- 3.45pm - Start of Zoom session (for people to debug any issues)
>>>- 4.00pm - Paul Adams - Phenix Overview
>>>- 4.30pm - Tom Terwilliger - Map Improvement
>>>- 5.45pm - Tom Terwilliger - Model Building
>>>- 7.00pm - Question/Answer session
>>>
>>> *14 APR *
>>>
>>>- 3.45pm - Start of Zoom session (for people to debug any issues)
>>>- 4.00pm - Pavel Afonine - Real Space Refine
>>>- 5.15pm - Nigel Moriarty - Ligands and Restraints
>>>- 6.00pm - Jane Richardson - Validation
>>>- 7.00pm - Question/Answer session
>>>
>>>
>>> Cheers,
>>> The Phenix Developer Team
>>>
>>> --
>>> Paul Adams
>>> Division Director, Molecular Biophysics & Integrated Bioimaging, LBL (
>>> http://biosciences.lbl.gov/divisions/mbib)
>>> Principal Investigator, Computational Crystallography Initiative, LBL (
>>> http://cci.lbl.gov)
>>> Vice President for Technology, the Joint BioEnergy Institute (
>>> http://www.jbei.org)
>>> Principal Investigator, ALS-ENABLE, Advanced Light Source (
>>> http://als-enable.lbl.gov)
>>> Division Deputy for Biosciences, Advanced Light Source (
>>> https://als.lbl.gov)
>>> Laboratory Research Manager, ENIGMA Science Focus Area (
>>> http://enigma.lbl.gov)
>>> Adjunct Professor, Department of Bioengineering, U.C. Berkeley (
>>> http://bioeng.berkeley.edu)
>>> Adjunct Professor, Comparative Biochemistry, U.C. Berkeley (
>>> http://compbiochem.berkeley.edu)
>>>
>>> Building 33, Room 347
>>> Building 978, Room 4126
>>> Building 977, Room 180C
>>> Tel: 1-510-486-4225
>>> http://cci.lbl.gov/paul
>>>
>>> Lawrence Berkeley Laboratory
>>> 1 Cyclotron Road
>>> BLDG 33R0345
>>> Berkeley, CA 94720, USA.
>>>
>>> Executive Assistant: Ashley Dawn [ ashleyd...@lbl.gov
>>>  ] [ 1-510-486-5455 ]
>>>
>>> --
>>>
>>> To unsubscribe from the CCP4BB list, click the following link:
>>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>>>
>>

#

[ccp4bb] First Regional Structural Biology Meeting for Balkans and South-East Mediterranean area, Friday May 14th, 2021

[Evangelia D. Chrysina]

Dear Colleagues,



With this message I would like to announce the *“**First Regional
Structural Biology meeting** for** Balkans and the South-East Mediterranean*
* area”*, jointly organized by iNEXT-Discovery partners NHRF and NKI, to be
held online on *Friday afternoon, May 14th, 2021*.



The aim of the meeting is to:

-increase awareness of EU-wide iNEXT-Discovery and Instruct-ERIC
structural biology services

-emphasize on possibilities for remote access

-broaden the structural biology user community

-strengthen awareness and cooperation between European stakeholders



An overview of *structural biology research in the European Research Area* will
be presented by Prof. Anastassis Perrakis, Prof. Sir David Stuart, Prof.
Harald Schwalbe, Dr Andreas Holtel and Prof. Yannis Ioannidis followed by *open
discussion to stimulate the engagement of key stakeholders in Structural
Biology at Regional level*. The *target group* of the meeting is scientists
from academia and industry, research administrators and decision-makers
from Balkans and Southern Mediterranean countries.



We therefore, invite you to actively participate in shaping the structural
biology future in the South East Europe and the Mediterranean Area since this
virtual meeting will also serve to prepare a physical meeting later in the
project.



Please find more information on the event and the agenda at the following
link:

https://inext-discovery.eu/events/first-regional-structural-biology-meeting-balkans-and-the-south-east-mediterranean/

or register at
https://zoom.us/meeting/register/tJAsd-GhpzgjE9db7CXW_hlcqIAB88t4Crzc



Also on behalf of the iNEXT-Discovery Coordinator, Prof. Anastassis
Perrakis and the organizing committee



Best regards,

Evangelia Chrysina



p.s. This meeting is supported by iNEXT-Discovery (grant no. 871037) an EU
H2020 project for stimulating the use of structural biology research in
Europe.



-- 
Dr Evangelia D. Chrysina
Senior Researcher, ICB-NHRF
Docent (Assoc. Prof.) in Medical Science-Biomedicine, Örebro University,
Sweden
Structural Biologist- PhD in Biochemistry, Univ. of Bath, UK -  Marie Curie
Alumna
Chemical Engineer-National Technical University of Athens (NTUA), Greece
--
National Hellenic Research Foundation (NHRF)
Institute of Chemical Biology (ICB)
48, Vassileos Constantinou Avenue
Athens GR-11635, Greece, E-mail: echrys...@eie.gr, ec...@tee.gr
Tel. 00302107273851, 00306937443207
Fax 00302107273831



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

Re: [ccp4bb] Fwd: Please register - Phenix Workshops - April 7 & 14

[Nigel Moriarty]

Rini

It appears you are 30 minutes out but it is still early. Phenix Workshops
will be recorded. As with the last two virtual workshops, they will be
posted on YouTube. A simple search there will reveal all.

Cheers

Nigel

---
Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709 Email : nwmoria...@lbl.gov
Fax   : 510-486-5909  Web  : CCI.LBL.gov
ORCID : orcid.org/-0001-8857-9464


On Wed, Apr 7, 2021 at 2:31 AM rini chaturvedi 
wrote:

> Dear Dr Moriarty,
>
> Thank you for sharing the Phenix workshop link.
>
> Will it be possible for the recording of the sessions to be shared in the
> CCP4BB mail?
>
> The given time for the workshop i.e *3.45 pm PDT* which will be around *3.45
> am* in India (*IST*) and it would be difficult for us to be available at
> that time
>
> Kindly let us know if that is a possibility from your end.
>
> Kind regards,
> Rini Chaturvedi
> Molecular Medicine
> ICGEB, New Delhi
>
>
> On Mon, Apr 5, 2021 at 10:45 PM Nigel Moriarty  wrote:
>
>> Forward in case it was not circulated. Sorry if it's a repeat.
>>
>> Cheers
>>
>> Nigel
>>
>> ---
>> Nigel W. Moriarty
>> Building 33R0349, Molecular Biophysics and Integrated Bioimaging
>> Lawrence Berkeley National Laboratory
>> Berkeley, CA 94720-8235
>> Phone : 510-486-5709 Email : nwmoria...@lbl.gov
>> Fax   : 510-486-5909  Web  : CCI.LBL.gov
>> ORCID : orcid.org/-0001-8857-9464
>>
>>
>> -- Forwarded message -
>> From: Paul Adams 
>> Date: Wed, Mar 31, 2021 at 2:08 PM
>> Subject: Please register - Phenix Workshops - April 7 & 14
>> To: PHENIX user mailing list 
>> Cc: Nigel Moriarty , Ashley Dawn ,
>> CCP4BB@JISCMAIL.AC.UK 
>>
>>
>> Dear Colleagues,
>>
>> The Phenix developers will be holding an online *Phenix User Workshop on
>> the 7th and 14th of April at 4-9pm PDT.* These times will work best for
>> researchers in Asia and Australasia.
>>
>> The format of the workshop will be demos of the use of Phenix programs
>> combined with slides to explain the theory. We expect an interactive
>> meeting where attendees can ask questions for the Phenix team to answer.
>>
>> The workshop will cover aspects of macromolecular crystallography
>> in Phenix, with the final emphasis based on the applicants’ research
>> interests. To apply please fill out this form
>> . We will make every effort to
>> accommodate all applicants, but may need to defer some requests to a
>> future workshop if demand is high. We are hoping this workshop will be a
>> success, in which case we plan to host more in the future.
>>
>> *AGENDA:*
>> *7 APR *
>>
>>- 3.45pm - Start of Zoom session (for people to debug any issues)
>>- 4.00pm - Paul Adams - Phenix Overview
>>- 4.30pm - Tom Terwilliger - Map Improvement
>>- 5.45pm - Tom Terwilliger - Model Building
>>- 7.00pm - Question/Answer session
>>
>> *14 APR *
>>
>>- 3.45pm - Start of Zoom session (for people to debug any issues)
>>- 4.00pm - Pavel Afonine - Real Space Refine
>>- 5.15pm - Nigel Moriarty - Ligands and Restraints
>>- 6.00pm - Jane Richardson - Validation
>>- 7.00pm - Question/Answer session
>>
>>
>> Cheers,
>> The Phenix Developer Team
>>
>> --
>> Paul Adams
>> Division Director, Molecular Biophysics & Integrated Bioimaging, LBL (
>> http://biosciences.lbl.gov/divisions/mbib)
>> Principal Investigator, Computational Crystallography Initiative, LBL (
>> http://cci.lbl.gov)
>> Vice President for Technology, the Joint BioEnergy Institute (
>> http://www.jbei.org)
>> Principal Investigator, ALS-ENABLE, Advanced Light Source (
>> http://als-enable.lbl.gov)
>> Division Deputy for Biosciences, Advanced Light Source (
>> https://als.lbl.gov)
>> Laboratory Research Manager, ENIGMA Science Focus Area (
>> http://enigma.lbl.gov)
>> Adjunct Professor, Department of Bioengineering, U.C. Berkeley (
>> http://bioeng.berkeley.edu)
>> Adjunct Professor, Comparative Biochemistry, U.C. Berkeley (
>> http://compbiochem.berkeley.edu)
>>
>> Building 33, Room 347
>> Building 978, Room 4126
>> Building 977, Room 180C
>> Tel: 1-510-486-4225
>> http://cci.lbl.gov/paul
>>
>> Lawrence Berkeley Laboratory
>> 1 Cyclotron Road
>> BLDG 33R0345
>> Berkeley, CA 94720, USA.
>>
>> Executive Assistant: Ashley Dawn [ ashleyd...@lbl.gov  ]
>> [ 1-510-486-5455 ]
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>>
>



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

Re: [ccp4bb] Omit maps in phenix and ccp4

[Nigel Moriarty]

Hari

I'm happy to take a closer look if you send me the files directly.

Phenix has an omit map known as the Polder map that takes care of the
solvent masking.

Cheers

Nigel

---
Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709 Email : nwmoria...@lbl.gov
Fax   : 510-486-5909  Web  : CCI.LBL.gov
ORCID : orcid.org/-0001-8857-9464


On Wed, Apr 7, 2021 at 7:49 AM Bernhard Rupp 
wrote:

> > setting occupancies of omitted atoms to zero has the danger of leaving a
> hole
>
>
>
> Not quite. We probably need Garib to confirm this, but I tried this many
> times, and if in refmac the occupancy is really zero (0.00), then this does
> not happen, and the ligand is treated as not present. An occupancy of 0.02
> however, already suffices to have the solvent excluded and the fo component
> from the solvent shows up nicely.
>
>
>
> The effect is indeed dramatic, cf. Figure 2 (and F1 for more fun with the
> same ligand)
>
> https://febs.onlinelibrary.wiley.com/doi/epdf/10./febs.14320
>
>
>
> Best, BR
>
> *From:* CCP4 bulletin board  *On Behalf Of *Dirk
> Kostrewa
> *Sent:* Wednesday, April 7, 2021 03:59
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* Re: [ccp4bb] Omit maps in phenix and ccp4
>
>
>
> Dear Eleanor,
>
> setting occupancies of omitted atoms to zero has the danger of leaving a
> hole with the shape of these atoms in the bulk solvent mask, leading to
> positive difference density just because of the missing bulk solvent
> density. Since the days of X-PLOR, I always removed the omitted atoms. I
> never tried this with REFMAC5, though.
>
> Cheers,
>
> Dirk.
>
> On 07.04.21 11:46, Eleanor Dodson wrote:
>
> Well - I use COOT for this sort of task, and dont trust the automated
> tools.
>
> my procedure is
>
> load COOT - probably after a refinement cycle
>
> set occupancy of ligand(s) to 0.00 ( Measures - residue information -
> change occupancy)
>
> Look at the environment critically . eg if an ARG or other bulky side
> chain nearby , or waters etc selectively set occupancies to 0.00
>
>
>
> Doo some more cycles of refinement with this coordinate set to remove any
> memory of the ligand.
>
>
>
> Look at the map - if the ligand and other zero occ atoms is still in the
> right place reinstate them, or try to reinterpret density..
>
> Eleanor
>
>
>
>
>
>
>
> On Wed, 7 Apr 2021 at 08:39, Bjarte Aarmo Lund  wrote:
>
> Dear Hari,
>
>
>
> With regards to 1) Is 15 the number of atoms in your molecule? Or is it
> the number of hydrogens? The CIF file may have the wrong residue name or
> lack the hydrogens depending on how you built the ligand-protein complex.
>
> There is also a phenixbb for phenix questions,
> http://www.phenix-online.org/mailman/listinfo/phenixbb
>
>
>
>
>
> Kind regards,
>
>
>
> Bjarte Aarmo Lund
>
> Postdoc
>
> UiT The Arctic University of Norway
>
>
>
> *From:* CCP4 bulletin board  *On Behalf Of *Hari
> shankar
> *Sent:* Wednesday, April 7, 2021 08:47
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* [ccp4bb] Omit maps in phenix and ccp4
>
>
>
>
> Dear All,
>
>
>
> I have a ligand-protein complex and I wish to calculate different kinds of
> omit maps (say, composite omit maps, simulated annealing maps, other
> unbiased fo-fc maps ). I wish to omit the ligand and 3.5 angstrom 3D space
> around it. I have tried phenix for this purpose but get this error message
> consistently.
>
>
>
> "Fatal problems interpreting model file: no of atoms with unknown
> nonbonded energy type symbols: 15 Please edit the model file to resolve the
> problems and/of supply a CIF file with matching restraint definitions,
> along with apply_cif_modification and apply_cif_link parameter definitions
> if necessary."
>
>
>
> This error occurs despite supplying the CIF file for the ligand. I have
> tried to remake the CIF/PDB files from SMILES strings, by drawing the
> molecule in both ccp4 (acedrug) as well as phenix (elBOW and Readyset go).
> Nothing seems to work.
>
>
>
> 1. Is there something I have missed out that can solve this issue?
>
> 2. Is there a program in CCP4i that can be used to generate the required
> omit maps?
>
> 3. In general, how do I omit 3.5 ang of the space around the ligand during
> this map calculations?
>
>
> Thank you so much for your time.
> Hari
>
>
>
>
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>
> --
>
>
>
> ***
>
> Dirk Kostrewa
>
> Gene Center Munich
>
> Department o

Re: [ccp4bb] Omit maps in phenix and ccp4

[Bernhard Rupp]

> setting occupancies of omitted atoms to zero has the danger of leaving a hole 

 

Not quite. We probably need Garib to confirm this, but I tried this many times, 
and if in refmac the occupancy is really zero (0.00), then this does not 
happen, and the ligand is treated as not present. An occupancy of 0.02 however, 
already suffices to have the solvent excluded and the fo component from the 
solvent shows up nicely. 

 

The effect is indeed dramatic, cf. Figure 2 (and F1 for more fun with the same 
ligand)

https://febs.onlinelibrary.wiley.com/doi/epdf/10./febs.14320

 

Best, BR

From: CCP4 bulletin board  On Behalf Of Dirk Kostrewa
Sent: Wednesday, April 7, 2021 03:59
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Omit maps in phenix and ccp4

 

Dear Eleanor,

setting occupancies of omitted atoms to zero has the danger of leaving a hole 
with the shape of these atoms in the bulk solvent mask, leading to positive 
difference density just because of the missing bulk solvent density. Since the 
days of X-PLOR, I always removed the omitted atoms. I never tried this with 
REFMAC5, though.

Cheers,

Dirk.

On 07.04.21 11:46, Eleanor Dodson wrote:

Well - I use COOT for this sort of task, and dont trust the automated tools. 

my procedure is

load COOT - probably after a refinement cycle

set occupancy of ligand(s) to 0.00 ( Measures - residue information - change 
occupancy) 

Look at the environment critically . eg if an ARG or other bulky side chain 
nearby , or waters etc selectively set occupancies to 0.00

 

Doo some more cycles of refinement with this coordinate set to remove any 
memory of the ligand.

 

Look at the map - if the ligand and other zero occ atoms is still in the right 
place reinstate them, or try to reinterpret density..

Eleanor

 

 

 

On Wed, 7 Apr 2021 at 08:39, Bjarte Aarmo Lund mailto:bjarte.l...@uit.no> > wrote:

Dear Hari,

 

With regards to 1) Is 15 the number of atoms in your molecule? Or is it the 
number of hydrogens? The CIF file may have the wrong residue name or lack the 
hydrogens depending on how you built the ligand-protein complex. 

There is also a phenixbb for phenix questions, 
http://www.phenix-online.org/mailman/listinfo/phenixbb

 

 

Kind regards,

 

Bjarte Aarmo Lund

Postdoc

UiT The Arctic University of Norway

 

From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK> 
> On Behalf Of Hari shankar
Sent: Wednesday, April 7, 2021 08:47
To: CCP4BB@JISCMAIL.AC.UK  
Subject: [ccp4bb] Omit maps in phenix and ccp4

 


Dear All,

 

I have a ligand-protein complex and I wish to calculate different kinds of omit 
maps (say, composite omit maps, simulated annealing maps, other unbiased fo-fc 
maps ). I wish to omit the ligand and 3.5 angstrom 3D space around it. I have 
tried phenix for this purpose but get this error message consistently. 

 

"Fatal problems interpreting model file: no of atoms with unknown nonbonded 
energy type symbols: 15 Please edit the model file to resolve the problems 
and/of supply a CIF file with matching restraint definitions, along with 
apply_cif_modification and apply_cif_link parameter definitions if necessary."

 

This error occurs despite supplying the CIF file for the ligand. I have tried 
to remake the CIF/PDB files from SMILES strings, by drawing the molecule in 
both ccp4 (acedrug) as well as phenix (elBOW and Readyset go). Nothing seems to 
work. 

 

1. Is there something I have missed out that can solve this issue?

2. Is there a program in CCP4i that can be used to generate the required omit 
maps? 

3. In general, how do I omit 3.5 ang of the space around the ligand during this 
map calculations?


Thank you so much for your time. 
Hari

 

 

 

  _  

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

 

  _  

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

 

  _  

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

-- 
 
***
Dirk Kostrewa
Gene Center Munich
Department of Biochemistry, AG Hopfner
Ludwig-Maximilians-Universität München
Feodor-Lynen-Str. 25
D-81377 Munich
Germany
Phone:  +49-89-2180-76845
Fax:+49-89-2180-76998
E-mail: dirk.kostr...@lmu.de  
kostr...@genzentrum.lmu.de  
WWW:www.genzentrum.lmu.de  
***

 

  _  

To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac

Re: [ccp4bb] Omit maps in phenix and ccp4

[Eleanor Dodson]

Hmm - yes.
For refmac the default scaling is:

2) Mask based bulk solvent correction.  It is activated using the following
keywords to build a mask based bulk solvent correction:

scale type simple

solvent yes

The solvent mask is generated with default parameters to mask the whole
model : vdwprobe 1.2 ionprobe 0.8 rashrink 0.8


I am not sure whether the mask is built taking into account atoms with occ
= 0.00 or not..


Will ask the experts.



But what happens to scaling when you do an OMIT map?



Scaling is often a problem, especially at limited resolution. I like to
look at a plot of  v  which you can find in REFMAC outputs if
you know where to look, but often the scaling procedure is shrouded in
mystery..

Eleanor




On Wed, 7 Apr 2021 at 11:59, Dirk Kostrewa <
dirk.kostr...@lrz.uni-muenchen.de> wrote:

> Dear Eleanor,
>
> setting occupancies of omitted atoms to zero has the danger of leaving a
> hole with the shape of these atoms in the bulk solvent mask, leading to
> positive difference density just because of the missing bulk solvent
> density. Since the days of X-PLOR, I always removed the omitted atoms. I
> never tried this with REFMAC5, though.
>
> Cheers,
>
> Dirk.
> On 07.04.21 11:46, Eleanor Dodson wrote:
>
> Well - I use COOT for this sort of task, and dont trust the automated
> tools.
> my procedure is
> load COOT - probably after a refinement cycle
> set occupancy of ligand(s) to 0.00 ( Measures - residue information -
> change occupancy)
> Look at the environment critically . eg if an ARG or other bulky side
> chain nearby , or waters etc selectively set occupancies to 0.00
>
> Doo some more cycles of refinement with this coordinate set to remove any
> memory of the ligand.
>
> Look at the map - if the ligand and other zero occ atoms is still in the
> right place reinstate them, or try to reinterpret density..
> Eleanor
>
>
>
> On Wed, 7 Apr 2021 at 08:39, Bjarte Aarmo Lund  wrote:
>
>> Dear Hari,
>>
>>
>>
>> With regards to 1) Is 15 the number of atoms in your molecule? Or is it
>> the number of hydrogens? The CIF file may have the wrong residue name or
>> lack the hydrogens depending on how you built the ligand-protein complex.
>>
>> There is also a phenixbb for phenix questions,
>> http://www.phenix-online.org/mailman/listinfo/phenixbb
>>
>>
>>
>>
>>
>> Kind regards,
>>
>>
>>
>> Bjarte Aarmo Lund
>>
>> Postdoc
>>
>> UiT The Arctic University of Norway
>>
>>
>>
>> *From:* CCP4 bulletin board  * On Behalf Of *Hari
>> shankar
>> *Sent:* Wednesday, April 7, 2021 08:47
>> *To:* CCP4BB@JISCMAIL.AC.UK
>> *Subject:* [ccp4bb] Omit maps in phenix and ccp4
>>
>>
>>
>>
>> Dear All,
>>
>>
>>
>> I have a ligand-protein complex and I wish to calculate different kinds
>> of omit maps (say, composite omit maps, simulated annealing maps, other
>> unbiased fo-fc maps ). I wish to omit the ligand and 3.5 angstrom 3D space
>> around it. I have tried phenix for this purpose but get this error message
>> consistently.
>>
>>
>>
>> "Fatal problems interpreting model file: no of atoms with unknown
>> nonbonded energy type symbols: 15 Please edit the model file to resolve the
>> problems and/of supply a CIF file with matching restraint definitions,
>> along with apply_cif_modification and apply_cif_link parameter definitions
>> if necessary."
>>
>>
>>
>> This error occurs despite supplying the CIF file for the ligand. I have
>> tried to remake the CIF/PDB files from SMILES strings, by drawing the
>> molecule in both ccp4 (acedrug) as well as phenix (elBOW and Readyset go).
>> Nothing seems to work.
>>
>>
>>
>> 1. Is there something I have missed out that can solve this issue?
>>
>> 2. Is there a program in CCP4i that can be used to generate the required
>> omit maps?
>>
>> 3. In general, how do I omit 3.5 ang of the space around the ligand
>> during this map calculations?
>>
>>
>> Thank you so much for your time.
>> Hari
>>
>>
>>
>>
>>
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>
> --
>
> ***
> Dirk Kostrewa
> Gene Center Munich
> Department of Biochemistry, AG Hopfner
> Ludwig-Maximilians-Universität München
> Feodor-Lynen-Str. 25
> D-81377 Munich
> Germany
> Phone:  +49-89-2180-76845
> Fax:+49-89-2180-76998
> E-mail: dirk.kostr...@lmu.de
> kostr...@genzentrum.lmu.de
> WWW:www.genzentrum.lmu.de
> ***
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscma

Re: [ccp4bb] Omit maps in phenix and ccp4

[Dirk Kostrewa]

Dear Eleanor,

setting occupancies of omitted atoms to zero has the danger of leaving a 
hole with the shape of these atoms in the bulk solvent mask, leading to 
positive difference density just because of the missing bulk solvent 
density. Since the days of X-PLOR, I always removed the omitted atoms. I 
never tried this with REFMAC5, though.


Cheers,

Dirk.

On 07.04.21 11:46, Eleanor Dodson wrote:
Well - I use COOT for this sort of task, and dont trust the automated 
tools.

my procedure is
load COOT - probably after a refinement cycle
set occupancy of ligand(s) to 0.00 ( Measures - residue information - 
change occupancy)
Look at the environment critically . eg if an ARG or other bulky side 
chain nearby , or waters etc selectively set occupancies to 0.00


Doo some more cycles of refinement with this coordinate set to remove 
any memory of the ligand.


Look at the map - if the ligand and other zero occ atoms is still in 
the right place reinstate them, or try to reinterpret density..

Eleanor



On Wed, 7 Apr 2021 at 08:39, Bjarte Aarmo Lund > wrote:


Dear Hari,

With regards to 1) Is 15 the number of atoms in your molecule? Or
is it the number of hydrogens? The CIF file may have the wrong
residue name or lack the hydrogens depending on how you built the
ligand-protein complex.

There is also a phenixbb for phenix questions,
http://www.phenix-online.org/mailman/listinfo/phenixbb


Kind regards,

Bjarte Aarmo Lund

Postdoc

UiT The Arctic University of Norway

*From:* CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> *On Behalf Of *Hari shankar
*Sent:* Wednesday, April 7, 2021 08:47
*To:* CCP4BB@JISCMAIL.AC.UK 
*Subject:* [ccp4bb] Omit maps in phenix and ccp4


Dear All,

I have a ligand-protein complex and I wish to calculate different
kinds of omit maps (say, composite omit maps, simulated annealing
maps, other unbiased fo-fc maps ). I wish to omit the ligand and
3.5 angstrom 3D space around it. I have tried phenix for this
purpose but get this error message consistently.

"Fatal problems interpreting model file: no of atoms with unknown
nonbonded energy type symbols: 15 Please edit the model file to
resolve the problems and/of supply a CIF file with matching
restraint definitions, along with apply_cif_modification and
apply_cif_link parameter definitions if necessary."

This error occurs despite supplying the CIF file for the ligand. I
have tried to remake the CIF/PDB files from SMILES strings, by
drawing the molecule in both ccp4 (acedrug) as well as phenix
(elBOW and Readyset go). Nothing seems to work.

1. Is there something I have missed out that can solve this issue?

2. Is there a program in CCP4i that can be used to generate the
required omit maps?

3. In general, how do I omit 3.5 ang of the space around the
ligand during this map calculations?


Thank you so much for your time.
Hari



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





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





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




--

***
Dirk Kostrewa
Gene Center Munich
Department of Biochemistry, AG Hopfner
Ludwig-Maximilians-Universität München
Feodor-Lynen-Str. 25
D-81377 Munich
Germany
Phone:  +49-89-2180-76845
Fax:+49-89-2180-76998
E-mail: dirk.kostr...@lmu.de
kostr...@genzentrum.lmu.de
WWW:www.genzentrum.lmu.de
***




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

Re: [ccp4bb] Omit maps in phenix and ccp4

[Eleanor Dodson]

Well - I use COOT for this sort of task, and dont trust the automated tools.
my procedure is
load COOT - probably after a refinement cycle
set occupancy of ligand(s) to 0.00 ( Measures - residue information -
change occupancy)
Look at the environment critically . eg if an ARG or other bulky side chain
nearby , or waters etc selectively set occupancies to 0.00

Doo some more cycles of refinement with this coordinate set to remove any
memory of the ligand.

Look at the map - if the ligand and other zero occ atoms is still in the
right place reinstate them, or try to reinterpret density..
Eleanor



On Wed, 7 Apr 2021 at 08:39, Bjarte Aarmo Lund  wrote:

> Dear Hari,
>
>
>
> With regards to 1) Is 15 the number of atoms in your molecule? Or is it
> the number of hydrogens? The CIF file may have the wrong residue name or
> lack the hydrogens depending on how you built the ligand-protein complex.
>
> There is also a phenixbb for phenix questions,
> http://www.phenix-online.org/mailman/listinfo/phenixbb
>
>
>
>
>
> Kind regards,
>
>
>
> Bjarte Aarmo Lund
>
> Postdoc
>
> UiT The Arctic University of Norway
>
>
>
> *From:* CCP4 bulletin board  * On Behalf Of *Hari
> shankar
> *Sent:* Wednesday, April 7, 2021 08:47
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* [ccp4bb] Omit maps in phenix and ccp4
>
>
>
>
> Dear All,
>
>
>
> I have a ligand-protein complex and I wish to calculate different kinds of
> omit maps (say, composite omit maps, simulated annealing maps, other
> unbiased fo-fc maps ). I wish to omit the ligand and 3.5 angstrom 3D space
> around it. I have tried phenix for this purpose but get this error message
> consistently.
>
>
>
> "Fatal problems interpreting model file: no of atoms with unknown
> nonbonded energy type symbols: 15 Please edit the model file to resolve the
> problems and/of supply a CIF file with matching restraint definitions,
> along with apply_cif_modification and apply_cif_link parameter definitions
> if necessary."
>
>
>
> This error occurs despite supplying the CIF file for the ligand. I have
> tried to remake the CIF/PDB files from SMILES strings, by drawing the
> molecule in both ccp4 (acedrug) as well as phenix (elBOW and Readyset go).
> Nothing seems to work.
>
>
>
> 1. Is there something I have missed out that can solve this issue?
>
> 2. Is there a program in CCP4i that can be used to generate the required
> omit maps?
>
> 3. In general, how do I omit 3.5 ang of the space around the ligand during
> this map calculations?
>
>
> Thank you so much for your time.
> Hari
>
>
>
>
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>



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

Re: [ccp4bb] Fwd: Please register - Phenix Workshops - April 7 & 14

[rini chaturvedi]

Dear Dr Moriarty,

Thank you for sharing the Phenix workshop link.

Will it be possible for the recording of the sessions to be shared in the
CCP4BB mail?

The given time for the workshop i.e *3.45 pm PDT* which will be around *3.45
am* in India (*IST*) and it would be difficult for us to be available at
that time

Kindly let us know if that is a possibility from your end.

Kind regards,
Rini Chaturvedi
Molecular Medicine
ICGEB, New Delhi


On Mon, Apr 5, 2021 at 10:45 PM Nigel Moriarty  wrote:

> Forward in case it was not circulated. Sorry if it's a repeat.
>
> Cheers
>
> Nigel
>
> ---
> Nigel W. Moriarty
> Building 33R0349, Molecular Biophysics and Integrated Bioimaging
> Lawrence Berkeley National Laboratory
> Berkeley, CA 94720-8235
> Phone : 510-486-5709 Email : nwmoria...@lbl.gov
> Fax   : 510-486-5909  Web  : CCI.LBL.gov
> ORCID : orcid.org/-0001-8857-9464
>
>
> -- Forwarded message -
> From: Paul Adams 
> Date: Wed, Mar 31, 2021 at 2:08 PM
> Subject: Please register - Phenix Workshops - April 7 & 14
> To: PHENIX user mailing list 
> Cc: Nigel Moriarty , Ashley Dawn ,
> CCP4BB@JISCMAIL.AC.UK 
>
>
> Dear Colleagues,
>
> The Phenix developers will be holding an online *Phenix User Workshop on
> the 7th and 14th of April at 4-9pm PDT.* These times will work best for
> researchers in Asia and Australasia.
>
> The format of the workshop will be demos of the use of Phenix programs
> combined with slides to explain the theory. We expect an interactive
> meeting where attendees can ask questions for the Phenix team to answer.
>
> The workshop will cover aspects of macromolecular crystallography
> in Phenix, with the final emphasis based on the applicants’ research
> interests. To apply please fill out this form
> . We will make every effort to
> accommodate all applicants, but may need to defer some requests to a
> future workshop if demand is high. We are hoping this workshop will be a
> success, in which case we plan to host more in the future.
>
> *AGENDA:*
> *7 APR *
>
>- 3.45pm - Start of Zoom session (for people to debug any issues)
>- 4.00pm - Paul Adams - Phenix Overview
>- 4.30pm - Tom Terwilliger - Map Improvement
>- 5.45pm - Tom Terwilliger - Model Building
>- 7.00pm - Question/Answer session
>
> *14 APR *
>
>- 3.45pm - Start of Zoom session (for people to debug any issues)
>- 4.00pm - Pavel Afonine - Real Space Refine
>- 5.15pm - Nigel Moriarty - Ligands and Restraints
>- 6.00pm - Jane Richardson - Validation
>- 7.00pm - Question/Answer session
>
>
> Cheers,
> The Phenix Developer Team
>
> --
> Paul Adams
> Division Director, Molecular Biophysics & Integrated Bioimaging, LBL (
> http://biosciences.lbl.gov/divisions/mbib)
> Principal Investigator, Computational Crystallography Initiative, LBL (
> http://cci.lbl.gov)
> Vice President for Technology, the Joint BioEnergy Institute (
> http://www.jbei.org)
> Principal Investigator, ALS-ENABLE, Advanced Light Source (
> http://als-enable.lbl.gov)
> Division Deputy for Biosciences, Advanced Light Source (
> https://als.lbl.gov)
> Laboratory Research Manager, ENIGMA Science Focus Area (
> http://enigma.lbl.gov)
> Adjunct Professor, Department of Bioengineering, U.C. Berkeley (
> http://bioeng.berkeley.edu)
> Adjunct Professor, Comparative Biochemistry, U.C. Berkeley (
> http://compbiochem.berkeley.edu)
>
> Building 33, Room 347
> Building 978, Room 4126
> Building 977, Room 180C
> Tel: 1-510-486-4225
> http://cci.lbl.gov/paul
>
> Lawrence Berkeley Laboratory
> 1 Cyclotron Road
> BLDG 33R0345
> Berkeley, CA 94720, USA.
>
> Executive Assistant: Ashley Dawn [ ashleyd...@lbl.gov  ]
> [ 1-510-486-5455 ]
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>



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

Re: [ccp4bb] Omit maps in phenix and ccp4

[Bjarte Aarmo Lund]

Dear Hari,

With regards to 1) Is 15 the number of atoms in your molecule? Or is it the 
number of hydrogens? The CIF file may have the wrong residue name or lack the 
hydrogens depending on how you built the ligand-protein complex.
There is also a phenixbb for phenix questions, 
http://www.phenix-online.org/mailman/listinfo/phenixbb


Kind regards,

Bjarte Aarmo Lund
Postdoc
UiT The Arctic University of Norway

From: CCP4 bulletin board  On Behalf Of Hari shankar
Sent: Wednesday, April 7, 2021 08:47
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Omit maps in phenix and ccp4


Dear All,

I have a ligand-protein complex and I wish to calculate different kinds of omit 
maps (say, composite omit maps, simulated annealing maps, other unbiased fo-fc 
maps ). I wish to omit the ligand and 3.5 angstrom 3D space around it. I have 
tried phenix for this purpose but get this error message consistently.

"Fatal problems interpreting model file: no of atoms with unknown nonbonded 
energy type symbols: 15 Please edit the model file to resolve the problems 
and/of supply a CIF file with matching restraint definitions, along with 
apply_cif_modification and apply_cif_link parameter definitions if necessary."

This error occurs despite supplying the CIF file for the ligand. I have tried 
to remake the CIF/PDB files from SMILES strings, by drawing the molecule in 
both ccp4 (acedrug) as well as phenix (elBOW and Readyset go). Nothing seems to 
work.

1. Is there something I have missed out that can solve this issue?
2. Is there a program in CCP4i that can be used to generate the required omit 
maps?
3. In general, how do I omit 3.5 ang of the space around the ligand during this 
map calculations?

Thank you so much for your time.
Hari





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



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

Re: [ccp4bb] Omit maps in phenix and ccp4

[Paul Emsley]

On 07/04/2021 07:46, Hari shankar wrote:



I have a ligand-protein complex and I wish to calculate different kinds of omit maps (say, composite omit 
maps, simulated annealing maps, other unbiased fo-fc maps ). I wish to omit the ligand and 3.5 angstrom 3D 
space around it. I have tried phenix for this purpose but get this error message consistently.


"Fatal problems interpreting model file: no of atoms with unknown nonbonded energy type symbols: 15 Please 
edit the model file to resolve the problems and/of supply a CIF file with matching restraint definitions, 
along with apply_cif_modification and apply_cif_link parameter definitions if necessary."


This error occurs despite supplying the CIF file for the ligand. I have tried to remake the CIF/PDB files 
from SMILES strings, by drawing the molecule in both ccp4 (acedrug) as well as phenix (elBOW and Readyset 
go). Nothing seems to work.


1. Is there something I have missed out that can solve this issue?
2. Is there a program in CCP4i that can be used to generate the required omit 
maps?
3. In general, how do I omit 3.5 ang of the space around the ligand during this 
map calculations?



Let's imagine that you'd like to use refmac.

1: By drawing the ligand [1] or by other means, create a mmCIF restraints file
2: Using Coot or other means, fit the ligand (it doesn't need to be exact) and 
add the ligand to the protein
3: Refine a couple of cycles with refmac (to test that it comprehends the 
ligand)
4: If fine, calculate SFs with refmac (0 cycles) excluding the ligand and other 
residues that you desire
   using keywords: refinement exclude all from A 1001 to A 1 10001 # for example

https://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/refmac/refmac_keywords.html

Paul

[1] Lidia is part of Coot for the record



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

Re: [ccp4bb] cryptic error message trying to use LigPlot on an unknown ligand

[Tim Gruene]

Dear Fred,

the error message looks like ligplot was started through a script, that
uses an environment variable, which is not set, soemthing like

${MYLIGPLOTDIR}/components.cif

In case MYLIGPLOTDIR is not set, you would get this sort of error
messages.

Best,
Tim

On Tue, 6 Apr 2021 15:47:21 +0200 Fred Vellieux
 wrote:

> Hi folks,
> 
> I'm trying to run Ligplot on a PDB file that contains a residue with 
> type UNL (Unknown Ligand). I hadn't been using LigPlot for perhaps 2 
> years now (which means that I had to reinstall, with an expired
> license, and get familiar with it again). I get the following error
> message (rather cryptic):
> 
> Calling HBADD ...
> Running HBADD
> Het Group Dictionary: /components.cif
> Temporary PDB file: /tmp/lig7141158588178475829/ligplus.pdb
> Command:  /LigPlus/lib/exe_linux/hbadd 
> /tmp/lig7141158588178475829/ligplus.pdb /components.cif -wkdir 
> /tmp/lig7141158588178475829/
> java.io.IOException: Cannot run program
> "/LigPlus/lib/exe_linux/hbadd": error=2, No such file or directory
> Other event: state
> 
> Would anyone know what to make out of this message ? Otherwise is
> there another piece of software (called "app" nowadays) that could
> provide me with similar drawings ?
> 
> At some stage I ran PRODRG, introduced the cif file in the file 
> components.cif used by LigPlot (LigPlus). I also replaced the
> coordinate files by those returned by the PRODRG run. Always with the
> same cryptic error message provided by the software (oops, app).
> 
> Thanks,
> 
> Fred.
> 



-- 
--
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



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


pgptBBuocNNr3.pgp
Description: OpenPGP digital signature