[ccp4bb] MhRe: [ccp4bb] xds crashes

[Bret Church]

Iu

W BRET CHURCH
Sydney Pharmacy School A15
THE UNIVERSITY OF SYDNEY

E bret.chu...@sydney.edu.au | W http://sydney.edu.au


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From: CCP4 bulletin board  on behalf of Demetres D. 
Leonidas <8f316b2a2e17-dmarc-requ...@jiscmail.ac.uk>
Sent: Tuesday, November 29, 2022 6:34:49 PM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] xds crashes

Dear Kay,

after some digging and help from Max Nanao we found that the problem
was the memory.  It was fulling rapidly. The workaround was to:

1. unzip the cbf files prior to processing

2. use maximum number of jobs 1

3. use number of processors 4

4. run xds_par

Many thanks for all your help

Demetres

On 11/29/2022 9:03 AM, Kay Diederichs wrote:
> Dear Demetres,
>
> I agree with what James says: this is the operating system trying to to 
> prevent, in an over-zealous way, the
> forking of too many or too big (in terms of memory) processes.
> In other words, XDS hasn't changed, but the operating system changed - it 
> applies different limits to its processes.
> Your friendly system administrator should try to find out exactly which 
> limit(s) changed, and reset the value(s).
> Perhaps a hint is in the Release Notes of Ubuntu 22.04 ?
>
> Pls report here when you've found it - currently you are the only one 
> reporting it.
>
> Best wishes,
> Kay
>
>
> On Mon, 28 Nov 2022 12:06:43 -0800, James Holton  wrote:
>
>> Sounds like your kernel might think "forkxds" is creating a "fork
>> bomb".  Too many sub-processes firing off in too short a time triggers
>> this.  On one of my systems, I fixed it by editing
>> /etc/security/limits.d/20-nproc.conf so that users are allowed ~10x more
>> pids than normal.  This tends to prevent these mysterious "Killed" errors.
>>
>> HTH?
>>
>> -James Holton
>> MAD Scientist
>>
>>
>> On 11/28/2022 7:44 AM, Demetres D. Leonidas wrote:
>>> Dear all,
>>>
>>> I do not know if this is the right list and I would like to apologize
>>> if it is not.
>>>
>>> We have repeatedly experienced xds crashes in machines running ubuntu
>>> 22.04.1 with the following message repeated several times at the
>>> INTEGRATE step
>>>
>>> /usr/local/bin/forkxds: line 60:  3427 Done echo "$itask"
>>>
>>>3428 Killed  | $amain
>>>
>>> We are trying to process data from P13 at EMBL-Hamburg.
>>>
>>> We are running XDS version Jan 10, 2022 BUILT=20220820
>>>
>>> Any ideas ?
>>>
>>> Demetres
>>>
>> 
>>
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--
---
Dr. Demetres D. Leonidas
Professor in Biochemistry
Department of Biochemistry & Biotechnology
University of Thessaly
Biopolis 41500 Larissa, Greece
-
Tel. +302410 565278
Tel. +302410 565297 (Lab)
Tel. +304210 565263 (X-ray)
Fax. +302410 565290
E-mail: ddleoni...@bio.uth.gr
ORCID ID orcid.org/-0002-3874-2523
---


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Re: [ccp4bb] xds crashes

[Demetres D. Leonidas]

Dear Kay,

after some digging and help from Max Nanao we found that the problem  
was the memory.  It was fulling rapidly. The workaround was to:


1. unzip the cbf files prior to processing

2. use maximum number of jobs 1

3. use number of processors 4

4. run xds_par

Many thanks for all your help

Demetres

On 11/29/2022 9:03 AM, Kay Diederichs wrote:

Dear Demetres,

I agree with what James says: this is the operating system trying to to 
prevent, in an over-zealous way, the
forking of too many or too big (in terms of memory) processes.
In other words, XDS hasn't changed, but the operating system changed - it 
applies different limits to its processes.
Your friendly system administrator should try to find out exactly which 
limit(s) changed, and reset the value(s).
Perhaps a hint is in the Release Notes of Ubuntu 22.04 ?

Pls report here when you've found it - currently you are the only one reporting 
it.

Best wishes,
Kay


On Mon, 28 Nov 2022 12:06:43 -0800, James Holton  wrote:


Sounds like your kernel might think "forkxds" is creating a "fork
bomb".  Too many sub-processes firing off in too short a time triggers
this.  On one of my systems, I fixed it by editing
/etc/security/limits.d/20-nproc.conf so that users are allowed ~10x more
pids than normal.  This tends to prevent these mysterious "Killed" errors.

HTH?

-James Holton
MAD Scientist


On 11/28/2022 7:44 AM, Demetres D. Leonidas wrote:

Dear all,

I do not know if this is the right list and I would like to apologize
if it is not.

We have repeatedly experienced xds crashes in machines running ubuntu
22.04.1 with the following message repeated several times at the
INTEGRATE step

/usr/local/bin/forkxds: line 60:  3427 Done echo "$itask"

   3428 Killed  | $amain

We are trying to process data from P13 at EMBL-Hamburg.

We are running XDS version Jan 10, 2022 BUILT=20220820

Any ideas ?

Demetres




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--
---
Dr. Demetres D. Leonidas
Professor in Biochemistry
Department of Biochemistry & Biotechnology
University of Thessaly
Biopolis 41500 Larissa, Greece
-
Tel. +302410 565278
Tel. +302410 565297 (Lab)
Tel. +304210 565263 (X-ray)
Fax. +302410 565290
E-mail: ddleoni...@bio.uth.gr
ORCID ID orcid.org/-0002-3874-2523
---


--
Αυτό το email έχει ελεγχθεί για ιούς από το Avast antivirus.
www.avast.com



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] xds crashes

[Kay Diederichs]

Dear Demetres,

I agree with what James says: this is the operating system trying to to 
prevent, in an over-zealous way, the 
forking of too many or too big (in terms of memory) processes.
In other words, XDS hasn't changed, but the operating system changed - it 
applies different limits to its processes.
Your friendly system administrator should try to find out exactly which 
limit(s) changed, and reset the value(s).
Perhaps a hint is in the Release Notes of Ubuntu 22.04 ?

Pls report here when you've found it - currently you are the only one reporting 
it.

Best wishes,
Kay


On Mon, 28 Nov 2022 12:06:43 -0800, James Holton  wrote:

>Sounds like your kernel might think "forkxds" is creating a "fork
>bomb".  Too many sub-processes firing off in too short a time triggers
>this.  On one of my systems, I fixed it by editing
>/etc/security/limits.d/20-nproc.conf so that users are allowed ~10x more
>pids than normal.  This tends to prevent these mysterious "Killed" errors.
>
>HTH?
>
>-James Holton
>MAD Scientist
>
>
>On 11/28/2022 7:44 AM, Demetres D. Leonidas wrote:
>> Dear all,
>>
>> I do not know if this is the right list and I would like to apologize
>> if it is not.
>>
>> We have repeatedly experienced xds crashes in machines running ubuntu
>> 22.04.1 with the following message repeated several times at the
>> INTEGRATE step
>>
>> /usr/local/bin/forkxds: line 60:  3427 Done echo "$itask"
>>
>>   3428 Killed  | $amain
>>
>> We are trying to process data from P13 at EMBL-Hamburg.
>>
>> We are running XDS version Jan 10, 2022 BUILT=20220820
>>
>> Any ideas ?
>>
>> Demetres
>>
>
>
>
>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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Re: [ccp4bb] Question about CCP4 monomer dictionaries

[stephen.c...@rc-harwell.ac.uk]

Dear Boaz,

You're quite right, in my haste to reply last night I only related part of the 
discussion relating to peroxide.  In a bid to identify the diatomic ligand, 
which appears on oxygen exposure,  I quoted the peroxide bond length as being 
too long, then went on to say it is much more like dioxygen in 
oxyhaemoglobin/myoglobin and referenced structures from yourself and Simon 
Phillips.

Best wishes,
Steve


Dr Stephen Carr
Research Complex at Harwell (RCaH)
Rutherford Appleton Laboratory
Harwell Oxford
Didcot
Oxon OX11 0FA
United Kingdom
Email stephen.c...@rc-harwell.ac.uk
tel 01235 567717

From: Boaz Shaanan 
Sent: 28 November 2022 23:33
To: Carr, Stephen (MRC,RAL,RCAH) 
Subject: Re: [ccp4bb] Question about CCP4 monomer dictionaries

Hi stephen,

I obviously don't have the full context of your case, but I am not sure why you 
invoked peroxide as a reference for the O-O bond length in the context of 
oxygen-metal complex. In my good old oxy haemoglobin structure (1HHO) the O-O 
bond length in Fe-O-O  is 1.22 A. It's also worth checking MbO2 with Fe and 
various metals which are most likely higher resolution structures.

 I could of course be completely wrong line of thought.

Cheers,

 Boaz



Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel

E-mail: bshaa...@bgu.ac.il
Phone: 972-8-647-2220
Fax:   972-8-647-2992 or 972-8-646-1710





From: CCP4 bulletin board  on behalf of 
stephen.c...@rc-harwell.ac.uk <8f3604def7f0-dmarc-requ...@jiscmail.ac.uk>
Sent: Monday, November 28, 2022 10:03 PM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] Question about CCP4 monomer dictionaries

Dear BB,

Thank you for all the helpful responses. To give a bit more context to my 
question, I have a 1.2 A structure with a diatomic ligand bound to a metal at 
the active site, which we believe is an oxygen species.  The bond length is 
1.22 A and I made a comment in the discussion that this was unlikely to be a 
peroxide species as the bond length was shorter than the 1.48 A typically 
observed.  The referee has questioned the validity of the 1.48 A, which led to 
my original question.

Best wishes,
Steve

PS I have tried Raman spectroscopy with no definitive result.

Dr Stephen Carr
Research Complex at Harwell (RCaH)
Rutherford Appleton Laboratory
Harwell Oxford
Didcot
Oxon OX11 0FA
United Kingdom
Email stephen.c...@rc-harwell.ac.uk
tel 01235 567717

From: Paul Emsley 
Sent: 28 November 2022 19:20
To: Carr, Stephen (MRC,RAL,RCAH) 
Subject: Re: [ccp4bb] Question about CCP4 monomer dictionaries



On 28/11/2022 17:29, 
stephen.c...@rc-harwell.ac.uk wrote:
Dear CCPBB,

I have a question regarding the origin of the monomer libraries in CCP4.  I ask 
because I have quoted the bond length listed in the monomer library describing 
peroxide in a manuscript and a referee has asked for a reference since they 
seem to disagree with the quoted value of ~1.48 A. My understanding is that 
parameters describing bond length, angles etc are derived from structures in 
the CSD is this the case?  Is there an appropriate reference out there 
somewhere?


When you say "peroxide," I presume that you mean H2O2. The entry for
that in the monomer library is PEO. The bond length between the oxygen
atoms in PEO is 1.461A.  Perhaps your referee is thinking of the

peroxide ion, which indeed would have a different bond length (1.15).

Both PEO and PER would, to my mind, be susceptible to radiation damage,

so one wonders what is actually in the crystal. To address question, one

would make an "Fearly-Flate" map.


One can (in principle) dig into the Acedrg table of bond lengths to examine how 
many

examples, of this sort of chemistry exist (I did it a few years ago), but I 
don't recall

now how to do it for this example.


Regards,

Paul.



This email and any attachments may contain confidential, copyrightand or 
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Re: [ccp4bb] Question about CCP4 monomer dictionaries

[Jessica Bruhn]

Hi Steve,

You could cite this book:

Müller, P., Herbst-Irmer, R., Spek, A.L., Schneider, T.R., and Sawaya M.R.
(2007) Crystal Structure Refinement: A Crystallographer's Guide to SHELXL.
IUCr Texts on Crystallography. J Am Chem Soc. 129, 451–451.

It also lists the expected bond length for a single bond between two
oxygens as 1.48 Ang in Table 12.5.

Kind regards,
Jessica

On Mon, Nov 28, 2022 at 12:04 PM stephen.c...@rc-harwell.ac.uk <
8f3604def7f0-dmarc-requ...@jiscmail.ac.uk> wrote:

> Dear BB,
>
> Thank you for all the helpful responses. To give a bit more context to my
> question, I have a 1.2 A structure with a diatomic ligand bound to a metal
> at the active site, which we believe is an oxygen species.  The bond length
> is 1.22 A and I made a comment in the discussion that this was unlikely to
> be a peroxide species as the bond length was shorter than the 1.48 A
> typically observed.  The referee has questioned the validity of the 1.48 A,
> which led to my original question.
>
> Best wishes,
> Steve
>
> PS I have tried Raman spectroscopy with no definitive result.
>
> Dr Stephen Carr
> Research Complex at Harwell (RCaH)
> Rutherford Appleton Laboratory
> Harwell Oxford
> Didcot
> Oxon OX11 0FA
> United Kingdom
> Email stephen.c...@rc-harwell.ac.uk
> tel 01235 567717
> --
> *From:* Paul Emsley 
> *Sent:* 28 November 2022 19:20
> *To:* Carr, Stephen (MRC,RAL,RCAH) 
> *Subject:* Re: [ccp4bb] Question about CCP4 monomer dictionaries
>
>
>
> On 28/11/2022 17:29, stephen.c...@rc-harwell.ac.uk wrote:
>
> Dear CCPBB,
>
> I have a question regarding the origin of the monomer libraries in CCP4.
> I ask because I have quoted the bond length listed in the monomer library
> describing peroxide in a manuscript and a referee has asked for a reference
> since they seem to disagree with the quoted value of ~1.48 A. My
> understanding is that parameters describing bond length, angles etc are
> derived from structures in the CSD is this the case?  Is there an
> appropriate reference out there somewhere?
>
>
> When you say "peroxide," I presume that you mean H2O2. The entry for
> that in the monomer library is PEO. The bond length between the oxygen
> atoms in PEO is 1.461A.  Perhaps your referee is thinking of the
>
> peroxide ion, which indeed would have a different bond length (1.15).
>
> Both PEO and PER would, to my mind, be susceptible to radiation damage,
>
> so one wonders what is actually in the crystal. To address question, one
>
> would make an "Fearly-Flate" map.
>
>
> One can (in principle) dig into the Acedrg table of bond lengths to
> examine how many
>
> examples, of this sort of chemistry exist (I did it a few years ago), but
> I don't recall
>
> now how to do it for this example.
>
>
> Regards,
>
> Paul.
>
>
>
> This email and any attachments may contain confidential, copyrightand or
> privileged material, and are for the use of the intended addressee only. If
> you are not the intended addressee or an authorized recipient of the
> addressee, please notify us of receipt by returning the e-mail and do not
> use, copy, retain, distribute or disclose the information in or attached to
> this email.
>
>
>
> Any views or opinions presented are solely those of the author and do not
> necessarily represent those of the Research Complex at Harwell.
>
>
>
> There is no guarantee that this email or any attachments are free from
> viruses and we cannot accept liability for any damage which you may sustain
> as a result of software viruses which may be transmitted in or with the
> message.
>
>
>
> We use an electronic filing system. Please send electronic versions of
> documents, unless paper is specifically requested.
>
>
>
> This email may have a protective marking, for an explanation, please see:
>
>
> http://www.mrc.ac.uk/About/informationandstandards/documentmarking/index.htm
> .
>
> --
>
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Re: [ccp4bb] xds crashes

[James Holton]

Sounds like your kernel might think "forkxds" is creating a "fork 
bomb".  Too many sub-processes firing off in too short a time triggers 
this.  On one of my systems, I fixed it by editing 
/etc/security/limits.d/20-nproc.conf so that users are allowed ~10x more 
pids than normal.  This tends to prevent these mysterious "Killed" errors.


HTH?

-James Holton
MAD Scientist


On 11/28/2022 7:44 AM, Demetres D. Leonidas wrote:

Dear all,

I do not know if this is the right list and I would like to apologize 
if it is not.


We have repeatedly experienced xds crashes in machines running ubuntu 
22.04.1 with the following message repeated several times at the 
INTEGRATE step


/usr/local/bin/forkxds: line 60:  3427 Done echo "$itask"

  3428 Killed  | $amain

We are trying to process data from P13 at EMBL-Hamburg.

We are running XDS version Jan 10, 2022 BUILT=20220820

Any ideas ?

Demetres





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https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

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Re: [ccp4bb] Question about CCP4 monomer dictionaries

[stephen.c...@rc-harwell.ac.uk]

Dear BB,

Thank you for all the helpful responses. To give a bit more context to my 
question, I have a 1.2 A structure with a diatomic ligand bound to a metal at 
the active site, which we believe is an oxygen species.  The bond length is 
1.22 A and I made a comment in the discussion that this was unlikely to be a 
peroxide species as the bond length was shorter than the 1.48 A typically 
observed.  The referee has questioned the validity of the 1.48 A, which led to 
my original question.

Best wishes,
Steve

PS I have tried Raman spectroscopy with no definitive result.

Dr Stephen Carr
Research Complex at Harwell (RCaH)
Rutherford Appleton Laboratory
Harwell Oxford
Didcot
Oxon OX11 0FA
United Kingdom
Email stephen.c...@rc-harwell.ac.uk
tel 01235 567717

From: Paul Emsley 
Sent: 28 November 2022 19:20
To: Carr, Stephen (MRC,RAL,RCAH) 
Subject: Re: [ccp4bb] Question about CCP4 monomer dictionaries



On 28/11/2022 17:29, 
stephen.c...@rc-harwell.ac.uk wrote:
Dear CCPBB,

I have a question regarding the origin of the monomer libraries in CCP4.  I ask 
because I have quoted the bond length listed in the monomer library describing 
peroxide in a manuscript and a referee has asked for a reference since they 
seem to disagree with the quoted value of ~1.48 A. My understanding is that 
parameters describing bond length, angles etc are derived from structures in 
the CSD is this the case?  Is there an appropriate reference out there 
somewhere?


When you say "peroxide," I presume that you mean H2O2. The entry for
that in the monomer library is PEO. The bond length between the oxygen
atoms in PEO is 1.461A.  Perhaps your referee is thinking of the

peroxide ion, which indeed would have a different bond length (1.15).

Both PEO and PER would, to my mind, be susceptible to radiation damage,

so one wonders what is actually in the crystal. To address question, one

would make an "Fearly-Flate" map.


One can (in principle) dig into the Acedrg table of bond lengths to examine how 
many

examples, of this sort of chemistry exist (I did it a few years ago), but I 
don't recall

now how to do it for this example.


Regards,

Paul.



This email and any attachments may contain confidential, copyright and or 
privileged material, and are for the use of the intended addressee only. If you 
are not the intended addressee or an authorized recipient of the addressee, 
please notify us of receipt by returning the e-mail and do not use, copy, 
retain, distribute or disclose the information in or attached to this email.

Any views or opinions presented are solely those of the author and do not 
necessarily represent those of the Research Complex at Harwell.

There is no guarantee that this email or any attachments are free from viruses 
and we cannot accept liability for any damage which you may sustain as a result 
of software viruses which may be transmitted in or with the message.

We use an electronic filing system. Please send electronic versions of 
documents, unless paper is specifically requested.

This email may have a protective marking, for an explanation, please see:
http://www.mrc.ac.uk/About/informationandstandards/documentmarking/index.htm.




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[ccp4bb] occupancy factors for alternate conformations and alternate ligands

[Michael Colaneri]

Dear colleagues,
If I have alternate ligands overlapping in the same electron density or 
alternate conformations of the protein chain overlapping in the same electron 
density, how accurate are the occupancy factors?  (Res 2A - temp factors are 
fine)
Thanks, Mike Colaneri



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Re: [ccp4bb] Question about CCP4 monomer dictionaries

[Lucrezia Catapano MRC-LMB]

Dear Stephen,

The current monomer library is, for the most part, generated
by running AceDRG - for non-metal containing entries at least.

AceDRG [1,2] derives atom types using the cif files in the
Crystallography Open Database [3], not the CSD.

You can see which version of Acedrg has been using by examing the
_pdbx_chem_comp_description_generator block in the cif file.

[1] Fei Long, Robert A Nicholls, Paul Emsley, Saulius Gražulis, Andrius 
Merkys, Antanas Vaitkus and Garib N Murshudov "ACEDRG: A stereo-chemical 
description generator for ligands" Acta Cryst. (2017), D73, 112-122.
[2] Fei Long, Robert A Nicholls, Paul Emsley, Saulius Gražulis, Andrius 
Merkys, Antanas Vaitkus and Garib N Murshudov "Validation and extraction 
of stereochemical information fromsmall molecular databases" Acta Cryst. 
(2017), D73, 103-111
[3] Gražulis, S., Chateigner, D., Downs, R. T., Yokochi, A. F. T., 
Quirós, M., Lutterotti, L., Manakova, E., Butkus, J., Moeck, P. & Le 
Bail, A. "Crystallography Open Database (COD): an open-access collection 
of crystal structures and platform for world-wide collaboration" J. 
Appl. Cryst. (2009) 42, 726–729.


Best regards
Lucrezia


On 2022-11-28 17:29, stephen.c...@rc-harwell.ac.uk wrote:

Dear CCPBB,

 I have a question regarding the origin of the monomer libraries in
CCP4.  I ask because I have quoted the bond length listed in the
monomer library describing peroxide in a manuscript and a referee has
asked for a reference since they seem to disagree with the quoted
value of ~1.48 A. My understanding is that parameters describing bond
length, angles etc are derived from structures in the CSD is this the
case?  Is there an appropriate reference out there somewhere?

 Thanks very much in advance,
 Steve

Dr Stephen Carr
Research Complex at Harwell (RCaH)
Rutherford Appleton Laboratory
Harwell Oxford
Didcot
Oxon OX11 0FA
United Kingdom
Email stephen.c...@rc-harwell.ac.uk
tel 01235 567717

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[ccp4bb] Reminder - Tenure Track Position in Cryo-EM

[Martin Lawrence]

Dear CCP4 Community,

Montana State University (MSU) invites applications for a tenure-track
faculty position in cryogenic electron microscopy.  The position is
formally a joint appointment between the Department of Chemistry and
Biochemistry, and the Department of Microbiology and Cell Biology.  The
candidate will join an active structural biology group with existing
expertise in X-ray crystallography, NMR and mass spectrometry, and developing
expertise in cryo-EM.

The TEM Core  facility
at MSU houses a 200 kV Talos Arctica microscope equipped with a Gatan K3
camera, and a 120 kV Spirit for screening purposes.  Potential applicants
with expertise in single particle analysis and/or cryo-electron tomography
are encouraged to apply.  Review of applications will begin November 28th and
continue until the position is filled.  So, if you are interested in this
position, please submit your applications as soon as possible.

Montana State University maintains a highly collaborative,
interdisciplinary environment with research programs broadly focused in
multiple areas, including  metalloproteins and metals in biology, innate
and acquired immunity, virology, pathogen microbiology, host/pathogen
interactions, microbial biofilms, cell and developmental biology and
neurobiology/neuroscience.  There are numerous opportunities for
collaborations in these areas.

Montana State University is located in the Northern Rocky Mountain
community of Bozeman Montana, immediately north of Yellowstone National
Park.  Bozeman is regularly recognized for its high quality of life,
including its outdoor, cultural and educational amenities:
http://www.montana.edu/about-msu/bozeman/
.

For further details and to apply, please visit:
https://jobs.montana.edu/postings/33131

For inquiries and additional questions, please contact:

Martin Lawrence
lawre...@montana.edu

Martin Lawrence
Professor of Chemistry and Biochemistry
Montana State University
Bozeman, MT
406-994-5382



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Re: [ccp4bb] Question about CCP4 monomer dictionaries

[Boaz Shaanan]

Hi Stephen,
On top of Roberto's reply I was wondering whether the resolution of your 
structure and the ensuing s.d. of the bond length was taken into account by the 
refree.
Cheers,
Boaz

Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben Gurion University
Beer Sheva, Israel

On Nov 28, 2022 19:29, "stephen.c...@rc-harwell.ac.uk" 
<8f3604def7f0-dmarc-requ...@jiscmail.ac.uk> wrote:
Dear CCPBB,

I have a question regarding the origin of the monomer libraries in CCP4.  I ask 
because I have quoted the bond length listed in the monomer library describing 
peroxide in a manuscript and a referee has asked for a reference since they 
seem to disagree with the quoted value of ~1.48 A. My understanding is that 
parameters describing bond length, angles etc are derived from structures in 
the CSD is this the case?  Is there an appropriate reference out there 
somewhere?

Thanks very much in advance,
Steve


Dr Stephen Carr
Research Complex at Harwell (RCaH)
Rutherford Appleton Laboratory
Harwell Oxford
Didcot
Oxon OX11 0FA
United Kingdom
Email stephen.c...@rc-harwell.ac.uk
tel 01235 567717
This email and any attachments may contain confidential, copyrightand or 
privileged material, and are for the use of the intended addressee only. If you 
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Re: [ccp4bb] Question about CCP4 monomer dictionaries

[Steiner, Roberto]

Hi Stephen

A value of 1.48 A sounds reasonable to me. For H2O2
https://cccbdb.nist.gov/exp2x.asp?casno=7722841=0
Also in the paper below we have the structure of a peroxide derivative pretty 
much at atomic resolution and the O-O distance refined at 1.47 A
Bui et al. Direct evidence for a peroxide intermediate and a reactive 
enzyme-substrate-dioxygen configuration in a cofactor-free 
oxidase.
Angew Chem Int Ed Engl. 2014 Dec 8;53(50):13710-4. doi: 10.1002/anie.201405485. 
Epub 2014 Oct 14.

HTH

Best wishes
Roberto

__
Professor Roberto A Steiner
www.steinerlab.org
https://twitter.com/steiner_lab


roberto.stei...@kcl.ac.uk
Randall Centre for Cell and Molecular Biophysics
Faculty of Life Sciences and Medicine
King's College London
Room 3.10A
New Hunt's House, Guy's Campus
SE1 1UL, London, UK
Phone 0044 20 78488216
Fax0044 20 78486435

roberto.stei...@unipd.it
Dipartimento di Scienze Biomediche
Università degli Studi di Padova
Viale G. Colombo 3
35131 Padova, Italia
Telefono 0039 049 8276409

Responses to emails are not expected outside of your normal working hours.


From: CCP4 bulletin board  on behalf of 
"stephen.c...@rc-harwell.ac.uk" <8f3604def7f0-dmarc-requ...@jiscmail.ac.uk>
Reply to: "stephen.c...@rc-harwell.ac.uk" 
Date: Monday, 28 November 2022 at 18:29
To: "CCP4BB@JISCMAIL.AC.UK" 
Subject: [ccp4bb] Question about CCP4 monomer dictionaries

You don't often get email from 8f3604def7f0-dmarc-requ...@jiscmail.ac.uk. 
Learn why this is important
Dear CCPBB,

I have a question regarding the origin of the monomer libraries in CCP4.  I ask 
because I have quoted the bond length listed in the monomer library describing 
peroxide in a manuscript and a referee has asked for a reference since they 
seem to disagree with the quoted value of ~1.48 A. My understanding is that 
parameters describing bond length, angles etc are derived from structures in 
the CSD is this the case?  Is there an appropriate reference out there 
somewhere?

Thanks very much in advance,
Steve


Dr Stephen Carr
Research Complex at Harwell (RCaH)
Rutherford Appleton Laboratory
Harwell Oxford
Didcot
Oxon OX11 0FA
United Kingdom
Email stephen.c...@rc-harwell.ac.uk
tel 01235 567717
This email and any attachments may contain confidential, copyrightand or 
privileged material, and are for the use of the intended addressee only. If you 
are not the intended addressee or an authorized recipient of the addressee, 
please notify us of receipt by returning the e-mail and do not use, copy, 
retain, distribute or disclose the information in or attached to this email.

Any views or opinions presented are solely those of the author and do not 
necessarily represent those of the Research Complex at Harwell.

There is no guarantee that this email or any attachments are free from viruses 
and we cannot accept liability for any damage which you may sustain as a result 
of software viruses which may be transmitted in or with the message.

We use an electronic filing system. Please send electronic versions of 
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[ccp4bb] Question about CCP4 monomer dictionaries

[stephen.c...@rc-harwell.ac.uk]

Dear CCPBB,

I have a question regarding the origin of the monomer libraries in CCP4.  I ask 
because I have quoted the bond length listed in the monomer library describing 
peroxide in a manuscript and a referee has asked for a reference since they 
seem to disagree with the quoted value of ~1.48 A. My understanding is that 
parameters describing bond length, angles etc are derived from structures in 
the CSD is this the case?  Is there an appropriate reference out there 
somewhere?

Thanks very much in advance,
Steve


Dr Stephen Carr
Research Complex at Harwell (RCaH)
Rutherford Appleton Laboratory
Harwell Oxford
Didcot
Oxon OX11 0FA
United Kingdom
Email stephen.c...@rc-harwell.ac.uk
tel 01235 567717

This email and any attachments may contain confidential, copyright and or 
privileged material, and are for the use of the intended addressee only. If you 
are not the intended addressee or an authorized recipient of the addressee, 
please notify us of receipt by returning the e-mail and do not use, copy, 
retain, distribute or disclose the information in or attached to this email.

Any views or opinions presented are solely those of the author and do not 
necessarily represent those of the Research Complex at Harwell.

There is no guarantee that this email or any attachments are free from viruses 
and we cannot accept liability for any damage which you may sustain as a result 
of software viruses which may be transmitted in or with the message.

We use an electronic filing system. Please send electronic versions of 
documents, unless paper is specifically requested.

This email may have a protective marking, for an explanation, please see:
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[ccp4bb] Fill-your-own-model with AlphaFill and other updates

[Robbie Joosten]

Dear bulletin boarders,

The previous version of this post did not come through. Apologies if this turns 
out to be a double post.

To celebrate the publication of our AlphaFill paper 
(https://www.nature.com/articles/s41592-022-01685-y), we have released a new 
version of our https://alphafill.eu website. It has some (we hope) useful new 
features:
- AlphaFold V3 and V4 entries (all Uniprot entries) are now available. When you 
ask for them, the AlphaFold model is downloaded through the 3D-Beacons system 
and filled on-the-fly.
- You can download AlphaFill entries with your personal selection of 
transplants. The download button is above the transplant selection boxes.
- Fill-your-own-model is now available for any structure model (computational 
or experimental). Just upload a valid mmCIF or PDB file and it will look for 
potential ligands ions and cofactors. This feature is completely new and 
constructive feedback is always appreciated. 

All the best,
Maarten, Ida, Robbie and Tassos



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[ccp4bb] xds crashes

[Demetres D. Leonidas]

Dear all,

I do not know if this is the right list and I would like to apologize if 
it is not.


We have repeatedly experienced xds crashes in machines running ubuntu 
22.04.1 with the following message repeated several times at the 
INTEGRATE step


/usr/local/bin/forkxds: line 60:  3427 Done echo "$itask"

  3428 Killed  | $amain

We are trying to process data from P13 at EMBL-Hamburg.

We are running XDS version Jan 10, 2022 BUILT=20220820

Any ideas ?

Demetres

--
---
Dr. Demetres D. Leonidas
Professor in Biochemistry
Department of Biochemistry & Biotechnology
University of Thessaly
Biopolis 41500 Larissa, Greece
-
Tel. +302410 565278
Tel. +302410 565297 (Lab)
Tel. +304210 565263 (X-ray)
Fax. +302410 565290
E-mail: ddleoni...@bio.uth.gr
ORCID ID orcid.org/-0002-3874-2523
---


--
Αυτό το email έχει ελεγχθεί για ιούς από το Avast antivirus.
www.avast.com



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[ccp4bb] Postdoctoral position in structural biology, Bethesda, MD

[Pazgier, Marzena]

There is an immediate opportunity to join a research team at the Uniformed
Services University of the Health Sciences (USU, https://www.usuhs.edu/) in
Bethesda, Maryland, to provide the molecular underpinnings of the adaptive
immune responses to HIV-1 and SARS-Cov-2 with the ultimate goal of
developing new protein/antibody-based therapies and new vaccines. Strong
research interests and experience in structural biology/ immunology,
including molecular cloning, protein/antibody/envelope glycoprotein
expression, protein engineering, X-ray crystallography and/or Cryo-EM are
required for this position. Qualified candidates should have a doctorate in
structural biology, chemistry, biochemistry, immunology or a
closely-related field. Candidates at any career stage are invited.


Candidates need to be highly motivated individuals who enjoy working as
part of a dynamic, collaborative and multidisciplinary team. Preference
will be given to candidates with exceptionally strong experimental skills,
a strong record of peer-reviewed publications, and a demonstrated
commitment to basic and translational research.


USU is in Bethesda, MD directly across the street from the NIH, and is
therefore part of an extraordinarily vibrant local biomedical research
community. Our research projects take advantage of recently established
Core facilities for Nextgen sequencing, Bioinformatics and Structural
Biology analyses. USU has a strongly collaborative environment, with weekly
Immunology data club and journal club meetings, as well as regular research
seminars featuring local and invited speakers.


For more information, please contact Dr. Pazgier at
marzena.pazg...@usuhs.edu.



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