Re: [ccp4bb] RAXIS and X-ray generator available now..

[Robert Stroud]

Is anyone interested in acquiring a home X-ray source system including a Rigaku 
generator, Haskris water cooler and pump, Haskris cryogenic cooler, MSC 
X-stream crystal cooler, RAXIS IV detector, OSMIC mirrors, etc?  The system has 
not been used in some time but all worked well previously. We need the space 
ASAP for other applications.
best wishes,

Robert Stroud, UCSF
str...@msg.ucsf.edu 
https://msg.ucsf.edu/people/robert-stroud-ma-phd 

mobile 415 987 7535
skype: rstroud9502












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Re: [ccp4bb] Dimple anomalous peaks

[Gildea, Richard (DLSLtd,RAL,LSCI)]

Dear Evgenii,

The dimple --anode option uses AnoDe [1, 2] to calculate the anomalous 
difference maps, so the anomalous map phases are in the output file anode.pha, 
not in final.mtz, which is generated by refmac. You can run the script 
anom-coot.sh to view the difference map in coot, or manually load the anode.pha 
and final.pdb yourself.

Cheers,

Richard

[1] http://shelx.uni-goettingen.de/anode.php
[2] http://scripts.iucr.org/cgi-bin/paper?fs5005
Dr Richard Gildea
Data Analysis Scientist
Tel: +441235 77 8078

Diamond Light Source Ltd.
Diamond House
Harwell Science & Innovation Campus
Didcot
Oxfordshire
OX11 0DE

From: CCP4 bulletin board  on behalf of Eugene Osipov 

Sent: 03 December 2019 12:35
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] Dimple anomalous peaks

Dear Richard,
yes, it has I(+)/I(-) and corresponding sigmas. I tried the command you've 
specified - final mtz still contains only "normal" maps but now I see anomalous 
phases in anode.pha
In order to get difference anomalous maps I still have to run refmac5 with
LABIN F+=F(+) SIGF+=SIGF(+) F-=F(-) SIGF-=SIGF(-) FREE=FreeR_flag
Is it possible to specify in dimple which columns I want it to use during 
restrained refinement, either F/SIGF or anomalous pairs F+/SIGF+ and F-/SIGF-?
May be it is possible to modify source code to tell dimple to run refmac5 with 
specified LABINs?
Kind regards,
Evgenii


вт, 3 дек. 2019 г. в 12:31, Gildea, Richard (DLSLtd,RAL,LSCI) 
mailto:richard.gil...@diamond.ac.uk>>:
Dear Evgenii,

Does your input mtz file contain I(+)/I(-) and SIGI(+)/SIGI(-) columns? Dimple 
runs shelxc to obtain the input reflection file for anode, which requires 
anomalous intensities as input.

I.e. it essentially runs the following commands:

$ mtz2sca AUTOMATIC_DEFAULT_free.mtz anode.sca

$ shelxc anode << EOF
SAD anode.sca
CELL 57.9066 57.9066 150.3051 90.0 90.0 90.0
SPAG P 41 21 2
EOF

$ cp dimple/final.pdb anode.pdb

$ anode anode

At Diamond we run dimple --anode on the free.mtz file generated by xia2, which 
contains the following columns:

label#valid  %valid min max type
F 32162  99.75%0.01 3130.76 F: amplitude
SIGF  32162  99.75%0.01  102.51 Q: standard deviation
DANO  31745  98.46% -271.19  227.37 D: anomalous difference
SIGDANO   31745  98.46%0.00  124.40 Q: standard deviation
F(+)  31777  98.55%0.01 3130.76 G: F(+) or F(-)
SIGF(+)   31777  98.55%0.01  102.51 L: standard deviation
F(-)  27431  85.08%0.02 2758.00 G: F(+) or F(-)
SIGF(-)   27431  85.08%0.01   91.95 L: standard deviation
ISYM  32243 100.00%   -1.002.00 Y: M/ISYM, packed partial/reject 
flag and symmetry number
IMEAN 32162  99.75%   -0.31  780.55 J: intensity
SIGIMEAN  32162  99.75%0.00   24.65 Q: standard deviation
I(+)  31777  98.55%   -0.48  780.55 K: I(+) or I(-)
SIGI(+)   31777  98.55%0.00   24.65 M: standard deviation
I(-)  27431  85.08%   -0.44  609.14 K: I(+) or I(-)
SIGI(-)   27431  85.08%0.00   16.78 M: standard deviation

E.g.:

$ dimple AUTOMATIC_DEFAULT_free.mtz 1RQW dimple --anode -fpng

Cheers,

Richard

Dr Richard Gildea
Data Analysis Scientist
Tel: +441235 77 8078

Diamond Light Source Ltd.
Diamond House
Harwell Science & Innovation Campus
Didcot
Oxfordshire
OX11 0DE

From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
on behalf of Eugene Osipov mailto:e.m.osi...@gmail.com>>
Sent: 03 December 2019 10:22
To: CCP4BB@JISCMAIL.AC.UK 
mailto:CCP4BB@JISCMAIL.AC.UK>>
Subject: [ccp4bb] Dimple anomalous peaks

Dear CCP4 community,
I can't figure out how to tell Dimple to use F(+)/F(-) columns and search for 
anomalous peaks.
I was trying to run dimple in the next form:
dimple -R free.mtz --anode --fcolumn F output.mtz test.pdb dimple_dir
In the output mtz  I get only 2Fo-Fc and Fo-Fc maps. When I try to use 
--fcolumn F(+) I gen an error.
My mtz file contains both averaged F/SIGF, anomalous pairs F(+)/F(-) and their 
differences in DANO.
Can someone tell how to calculate anomalous difference maps from dimple run?
Thanks in advance,
--
Evgenii Osipov
Laboratory for Biocrystallography,
Department of Pharmaceutical Sciences,
KU Leuven O&N2



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--

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are not the intended addressee or an authorised 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 the e-mail.
Any opinions expressed within this e-mail are those of the individual and not 
necessarily of Diamond Light Source Ltd.

[ccp4bb] International School of Crystallography - 55th Course: Structural Drug Design

[Scapin, Giovanna]

Dear all

OK I lied it wasn't the last reminder.

We would like to let you all know that the registrations for the 55th Course of 
the International School of Crystallography (Structural Drug Design) to be held 
in the beautiful town of Erice (Italy) May 29 - June 6, 2020 
(www.crystalerice.org) has been extended to Monday 
December 9, 2019.

The International School of Crystallography has been active since 1974, and 
over the years has brought together a remarkable number of scientists from many 
different countries.  Applicants may be able to apply for financial support, 
and we will try to provide as many young students and researchers as possible 
with financial help.
The purpose of the 55th course is to provide the students with
a) An overview of the current structural and biophysical techniques used in the 
field;
b) The use of informatics tools in drug discovery;
c) The evolving role of chemistry in drug design and biology understanding; and
d)  An introductions to biologics and their applications.
Speakers committed to participate to the school include Tom Blundell (Cambridge 
UK), Charles Lesburg (MSD, Boston, USA), James Fraser (UCSF, S. Francisco, CA, 
USA), Lucia Banci (Florence University, Italy), Ben Davis (Vernalis, Cambdrige, 
UK), Sandra Jacob (Novartis, CH), Georgia McGaughey (Vertex, USA), and Eddy 
Arnold (Rutgers, NJ, USA).

Please see the enclosed poster and visit the school website 
(www.crystalerice.org) for further information.
We are looking forward to welcoming you in Erice

Giovanna


Giovanna Scapin
Sr. principal scientist
Computational and Structural Chemistry
Merck & Co., Inc.
2000 Galloping hill road
Kenilworth, NJ 07033

Notice:  This e-mail message, together with any attachments, contains
information of Merck & Co., Inc. (2000 Galloping Hill Road, Kenilworth,
New Jersey, USA 07033), and/or its affiliates Direct contact information
for affiliates is available at 
http://www.merck.com/contact/contacts.html) that may be confidential,
proprietary copyrighted and/or legally privileged. It is intended solely
for the use of the individual or entity named on this message. If you are
not the intended recipient, and have received this message in error,
please notify us immediately by reply e-mail and then delete it from 
your system.



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Re: [ccp4bb] Dimple anomalous peaks

[Marcin Wojdyr]

Dear Evgenii,

it indeed makes sense to (optionally) use F+/- for refinement, but it
just hasn't been requested before and I didn't think about it myself.
I'm opening a ticket to not forget about it:
https://github.com/ccp4/dimple/issues/13
and I'll get back to it later.

Best wishes,
Marcin


On Tue, 3 Dec 2019 at 13:36, Eugene Osipov  wrote:
>
> Dear Richard,
> yes, it has I(+)/I(-) and corresponding sigmas. I tried the command you've 
> specified - final mtz still contains only "normal" maps but now I see 
> anomalous phases in anode.pha
> In order to get difference anomalous maps I still have to run refmac5 with
> LABIN F+=F(+) SIGF+=SIGF(+) F-=F(-) SIGF-=SIGF(-) FREE=FreeR_flag
> Is it possible to specify in dimple which columns I want it to use during 
> restrained refinement, either F/SIGF or anomalous pairs F+/SIGF+ and F-/SIGF-?
> May be it is possible to modify source code to tell dimple to run refmac5 
> with specified LABINs?
> Kind regards,
> Evgenii
>
>
> вт, 3 дек. 2019 г. в 12:31, Gildea, Richard (DLSLtd,RAL,LSCI) 
> :
>>
>> Dear Evgenii,
>>
>> Does your input mtz file contain I(+)/I(-) and SIGI(+)/SIGI(-) columns? 
>> Dimple runs shelxc to obtain the input reflection file for anode, which 
>> requires anomalous intensities as input.
>>
>> I.e. it essentially runs the following commands:
>>
>> $ mtz2sca AUTOMATIC_DEFAULT_free.mtz anode.sca
>>
>> $ shelxc anode << EOF
>> SAD anode.sca
>> CELL 57.9066 57.9066 150.3051 90.0 90.0 90.0
>> SPAG P 41 21 2
>> EOF
>>
>> $ cp dimple/final.pdb anode.pdb
>>
>> $ anode anode
>>
>> At Diamond we run dimple --anode on the free.mtz file generated by xia2, 
>> which contains the following columns:
>>
>> label#valid  %valid min max type
>> F 32162  99.75%0.01 3130.76 F: amplitude
>> SIGF  32162  99.75%0.01  102.51 Q: standard deviation
>> DANO  31745  98.46% -271.19  227.37 D: anomalous difference
>> SIGDANO   31745  98.46%0.00  124.40 Q: standard deviation
>> F(+)  31777  98.55%0.01 3130.76 G: F(+) or F(-)
>> SIGF(+)   31777  98.55%0.01  102.51 L: standard deviation
>> F(-)  27431  85.08%0.02 2758.00 G: F(+) or F(-)
>> SIGF(-)   27431  85.08%0.01   91.95 L: standard deviation
>> ISYM  32243 100.00%   -1.002.00 Y: M/ISYM, packed partial/reject 
>> flag and symmetry number
>> IMEAN 32162  99.75%   -0.31  780.55 J: intensity
>> SIGIMEAN  32162  99.75%0.00   24.65 Q: standard deviation
>> I(+)  31777  98.55%   -0.48  780.55 K: I(+) or I(-)
>> SIGI(+)   31777  98.55%0.00   24.65 M: standard deviation
>> I(-)  27431  85.08%   -0.44  609.14 K: I(+) or I(-)
>> SIGI(-)   27431  85.08%0.00   16.78 M: standard deviation
>>
>> E.g.:
>>
>> $ dimple AUTOMATIC_DEFAULT_free.mtz 1RQW dimple --anode -fpng
>>
>> Cheers,
>>
>> Richard
>>
>> Dr Richard Gildea
>> Data Analysis Scientist
>> Tel: +441235 77 8078
>>
>> Diamond Light Source Ltd.
>> Diamond House
>> Harwell Science & Innovation Campus
>> Didcot
>> Oxfordshire
>> OX11 0DE
>> 
>> From: CCP4 bulletin board  on behalf of Eugene Osipov 
>> 
>> Sent: 03 December 2019 10:22
>> To: CCP4BB@JISCMAIL.AC.UK 
>> Subject: [ccp4bb] Dimple anomalous peaks
>>
>> Dear CCP4 community,
>> I can't figure out how to tell Dimple to use F(+)/F(-) columns and search 
>> for anomalous peaks.
>> I was trying to run dimple in the next form:
>> dimple -R free.mtz --anode --fcolumn F output.mtz test.pdb dimple_dir
>> In the output mtz  I get only 2Fo-Fc and Fo-Fc maps. When I try to use 
>> --fcolumn F(+) I gen an error.
>> My mtz file contains both averaged F/SIGF, anomalous pairs F(+)/F(-) and 
>> their differences in DANO.
>> Can someone tell how to calculate anomalous difference maps from dimple run?
>> Thanks in advance,
>> --
>> Evgenii Osipov
>> Laboratory for Biocrystallography,
>> Department of Pharmaceutical Sciences,
>> KU Leuven O&N2
>>
>> 
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
>>
>>
>>
>> --
>>
>> This e-mail 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 authorised 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 
>> the e-mail.
>> Any opinions expressed within this e-mail are those of the individual and 
>> not necessarily of Diamond Light Source Ltd.
>> Diamond Light Source Ltd. cannot guarantee that this e-mail 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.
>> Diamond Light Source Limited (company no. 4

Re: [ccp4bb] Dimple anomalous peaks

[Eugene Osipov]

Dear Richard,
yes, it has I(+)/I(-) and corresponding sigmas. I tried the command you've
specified - final mtz still contains only "normal" maps but now I see
anomalous phases in anode.pha
In order to get difference anomalous maps I still have to run refmac5 with
LABIN F+=F(+) SIGF+=SIGF(+) F-=F(-) SIGF-=SIGF(-) FREE=FreeR_flag
Is it possible to specify in dimple which columns I want it to use during
restrained refinement, either F/SIGF or anomalous pairs F+/SIGF+ and
F-/SIGF-?
May be it is possible to modify source code to tell dimple to run refmac5
with specified LABINs?
Kind regards,
Evgenii


вт, 3 дек. 2019 г. в 12:31, Gildea, Richard (DLSLtd,RAL,LSCI) <
richard.gil...@diamond.ac.uk>:

> Dear Evgenii,
>
> Does your input mtz file contain I(+)/I(-) and SIGI(+)/SIGI(-) columns?
> Dimple runs shelxc to obtain the input reflection file for anode, which
> requires anomalous intensities as input.
>
> I.e. it essentially runs the following commands:
>
> $ mtz2sca AUTOMATIC_DEFAULT_free.mtz anode.sca
>
> $ shelxc anode << EOF
> SAD anode.sca
> CELL 57.9066 57.9066 150.3051 90.0 90.0 90.0
> SPAG P 41 21 2
> EOF
>
> $ cp dimple/final.pdb anode.pdb
>
> $ anode anode
>
> At Diamond we run dimple --anode on the free.mtz file generated by xia2,
> which contains the following columns:
>
> label#valid  %valid min max type
> F 32162  99.75%0.01 3130.76 F: amplitude
> SIGF  32162  99.75%0.01  102.51 Q: standard deviation
> DANO  31745  98.46% -271.19  227.37 D: anomalous difference
> SIGDANO   31745  98.46%0.00  124.40 Q: standard deviation
> F(+)  31777  98.55%0.01 3130.76 G: F(+) or F(-)
> SIGF(+)   31777  98.55%0.01  102.51 L: standard deviation
> F(-)  27431  85.08%0.02 2758.00 G: F(+) or F(-)
> SIGF(-)   27431  85.08%0.01   91.95 L: standard deviation
> ISYM  32243 100.00%   -1.002.00 Y: M/ISYM, packed
> partial/reject flag and symmetry number
> IMEAN 32162  99.75%   -0.31  780.55 J: intensity
> SIGIMEAN  32162  99.75%0.00   24.65 Q: standard deviation
> I(+)  31777  98.55%   -0.48  780.55 K: I(+) or I(-)
> SIGI(+)   31777  98.55%0.00   24.65 M: standard deviation
> I(-)  27431  85.08%   -0.44  609.14 K: I(+) or I(-)
> SIGI(-)   27431  85.08%0.00   16.78 M: standard deviation
>
> E.g.:
>
> $ dimple AUTOMATIC_DEFAULT_free.mtz 1RQW dimple --anode -fpng
>
> Cheers,
>
> Richard
>
> Dr Richard Gildea
> Data Analysis Scientist
> Tel: +441235 77 8078
>
> Diamond Light Source Ltd.
> Diamond House
> Harwell Science & Innovation Campus
> Didcot
> Oxfordshire
> OX11 0DE
> --
> *From:* CCP4 bulletin board  on behalf of Eugene
> Osipov 
> *Sent:* 03 December 2019 10:22
> *To:* CCP4BB@JISCMAIL.AC.UK 
> *Subject:* [ccp4bb] Dimple anomalous peaks
>
> Dear CCP4 community,
> I can't figure out how to tell Dimple to use F(+)/F(-) columns and search
> for anomalous peaks.
> I was trying to run dimple in the next form:
> dimple -R free.mtz --anode --fcolumn F output.mtz test.pdb dimple_dir
> In the output mtz  I get only 2Fo-Fc and Fo-Fc maps. When I try to
> use --fcolumn F(+) I gen an error.
> My mtz file contains both averaged F/SIGF, anomalous pairs F(+)/F(-) and
> their differences in DANO.
> Can someone tell how to calculate anomalous difference maps from dimple
> run?
> Thanks in advance,
> --
> Evgenii Osipov
> Laboratory for Biocrystallography,
> Department of Pharmaceutical Sciences,
> KU Leuven O&N2
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
>
>
>
> --
>
> This e-mail 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 authorised 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
> the e-mail.
> Any opinions expressed within this e-mail are those of the individual and
> not necessarily of Diamond Light Source Ltd.
> Diamond Light Source Ltd. cannot guarantee that this e-mail 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.
> Diamond Light Source Limited (company no. 4375679). Registered in England
> and Wales with its registered office at Diamond House, Harwell Science and
> Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
>


-- 
Evgenii Osipov
Laboratory for Biocrystallography,
Department of Pharmaceutical Sciences,
KU Leuven O&N2

##

[ccp4bb] NMR Facility Manager position at King's College London

[caterina alfano]

Hi Everyone,

NMR Facility Manager position will be available at King's College London
from May 2020. Please find details in the attached file.

Kind regards

Caterina



*Caterina Alfano, Ph.D.*



Group Leader

Biophysical Screening and Structural Biology Unit

Fondazione Ri.MED

Via Bandiera, 11

90133, Palermo - Italy

Tel:+39 091 604 / +39 091 23893179

Email: *calf...@fondazionerimed.com *



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Kings_NMR_notice 29.pdf
Description: Adobe PDF document

Re: [ccp4bb] Dimple anomalous peaks

[Gildea, Richard (DLSLtd,RAL,LSCI)]

Dear Evgenii,

Does your input mtz file contain I(+)/I(-) and SIGI(+)/SIGI(-) columns? Dimple 
runs shelxc to obtain the input reflection file for anode, which requires 
anomalous intensities as input.

I.e. it essentially runs the following commands:

$ mtz2sca AUTOMATIC_DEFAULT_free.mtz anode.sca

$ shelxc anode << EOF
SAD anode.sca
CELL 57.9066 57.9066 150.3051 90.0 90.0 90.0
SPAG P 41 21 2
EOF

$ cp dimple/final.pdb anode.pdb

$ anode anode

At Diamond we run dimple --anode on the free.mtz file generated by xia2, which 
contains the following columns:

label#valid  %valid min max type
F 32162  99.75%0.01 3130.76 F: amplitude
SIGF  32162  99.75%0.01  102.51 Q: standard deviation
DANO  31745  98.46% -271.19  227.37 D: anomalous difference
SIGDANO   31745  98.46%0.00  124.40 Q: standard deviation
F(+)  31777  98.55%0.01 3130.76 G: F(+) or F(-)
SIGF(+)   31777  98.55%0.01  102.51 L: standard deviation
F(-)  27431  85.08%0.02 2758.00 G: F(+) or F(-)
SIGF(-)   27431  85.08%0.01   91.95 L: standard deviation
ISYM  32243 100.00%   -1.002.00 Y: M/ISYM, packed partial/reject 
flag and symmetry number
IMEAN 32162  99.75%   -0.31  780.55 J: intensity
SIGIMEAN  32162  99.75%0.00   24.65 Q: standard deviation
I(+)  31777  98.55%   -0.48  780.55 K: I(+) or I(-)
SIGI(+)   31777  98.55%0.00   24.65 M: standard deviation
I(-)  27431  85.08%   -0.44  609.14 K: I(+) or I(-)
SIGI(-)   27431  85.08%0.00   16.78 M: standard deviation

E.g.:

$ dimple AUTOMATIC_DEFAULT_free.mtz 1RQW dimple --anode -fpng

Cheers,

Richard

Dr Richard Gildea
Data Analysis Scientist
Tel: +441235 77 8078

Diamond Light Source Ltd.
Diamond House
Harwell Science & Innovation Campus
Didcot
Oxfordshire
OX11 0DE

From: CCP4 bulletin board  on behalf of Eugene Osipov 

Sent: 03 December 2019 10:22
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] Dimple anomalous peaks

Dear CCP4 community,
I can't figure out how to tell Dimple to use F(+)/F(-) columns and search for 
anomalous peaks.
I was trying to run dimple in the next form:
dimple -R free.mtz --anode --fcolumn F output.mtz test.pdb dimple_dir
In the output mtz  I get only 2Fo-Fc and Fo-Fc maps. When I try to use 
--fcolumn F(+) I gen an error.
My mtz file contains both averaged F/SIGF, anomalous pairs F(+)/F(-) and their 
differences in DANO.
Can someone tell how to calculate anomalous difference maps from dimple run?
Thanks in advance,
--
Evgenii Osipov
Laboratory for Biocrystallography,
Department of Pharmaceutical Sciences,
KU Leuven O&N2



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

-- 
This e-mail 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 authorised 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 the e-mail.
Any opinions expressed within this e-mail are those of the individual and not 
necessarily of Diamond Light Source Ltd. 
Diamond Light Source Ltd. cannot guarantee that this e-mail 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.
Diamond Light Source Limited (company no. 4375679). Registered in England and 
Wales with its registered office at Diamond House, Harwell Science and 
Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom




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Re: [ccp4bb] Powder diffraction database

[Irene Margiolaki]

Regarding X-ray Powder Diffraction software 

http://www.ccp14.ac.uk/ 

Regarding search match procedures and databases there are several 

https://www.ccdc.cam.ac.uk/solutions/csd-system/components/csd/ 

http://www.icdd.com/?gclid=EAIaIQobChMI1NGPpIOZ5gIVhkPTCh3E4gcyEAAYASAAEgIQhPD_BwE


http://www.ba.ic.cnr.it/softwareic/qualxweb/ 

https://www.researchgate.net/post/Are_there_any_freely_available_X-Ray_powder_diffraction_peak_identification_search-match_software_packages


http://cod.iutcaen.unicaen.fr/ 

https://www.malvernpanalytical.com/en/products/category/software/x-ray-diffraction-software/highscore-with-plus-option?creative=338894239672&keyword=highscore%20plus&matchtype=e&network=g&device=c&gclid=EAIaIQobChMIkaLcnISZ5gIVFON3Ch1rvQQIEAAYASAAEgJIRfD_BwE


Regarding protein powder data, unfortunately there is still not a
database available. However, we can help in this matter via our inhouse
databases for anyone who is interested. More info is now available in
the latest volume H of the Int. Tables of Crystallography [1] and our
team's web site [2]. 

I hope this is helpful. 

all the best 

Irene Margiolaki 

Στις 2019-12-02 11:51, Peer Mittl έγραψε:

> Could someone please give me some advice on how to query a publicly available 
> powder diffraction database? Upon (protein) crystallization we always get 
> large spherulites of an inorganic compound and I would like to know what it 
> is. It should be possible to use the scattering angles of these spherulites 
> (its definitely not ice) to query a powder diffraction database. But which 
> database (e.g. CSD) and how?
> 
> All the best,
> Peer
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1

-- 
Irene Margiolaki, PhD
Associate Professor, Department of Biology, Section of Genetics, Cell
Biology and Development, University of Patras, GR-26500, Patras, Greece
Office (Room Number 212) Tel: +302610997408, X-ray Lab (Room Number Y31)
Tel: +302610996773, Crystallization Lab (Room Number 226) Tel.:
+302610997200
Web sites:
http://www.biology.upatras.gr/index.php?option=com_content&view=article&id=652:2012-11-01-08-31-26&catid=48&Itemid=336
https://sites.google.com/view/margiolaki-biology-upat

 

Links:
--
[1]
https://drive.google.com/file/d/1KTnkln0EtWBR95YnxY1JyeDUJdZo7uuQ/view
[2] https://sites.google.com/view/margiolaki-biology-upat/home



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[ccp4bb] Dimple anomalous peaks

[Eugene Osipov]

Dear CCP4 community,
I can't figure out how to tell Dimple to use F(+)/F(-) columns and search
for anomalous peaks.
I was trying to run dimple in the next form:
dimple -R free.mtz --anode --fcolumn F output.mtz test.pdb dimple_dir
In the output mtz  I get only 2Fo-Fc and Fo-Fc maps. When I try to
use --fcolumn F(+) I gen an error.
My mtz file contains both averaged F/SIGF, anomalous pairs F(+)/F(-) and
their differences in DANO.
Can someone tell how to calculate anomalous difference maps from dimple run?
Thanks in advance,
-- 
Evgenii Osipov
Laboratory for Biocrystallography,
Department of Pharmaceutical Sciences,
KU Leuven O&N2



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