Re: [ccp4bb] Problem with ligand identification

[FULVIO SACCOCCIA]

DTT?

Inviato da Outlook per Android

From: CCP4 bulletin board  on behalf of Rafal Dolot 

Sent: Wednesday, November 15, 2023 3:00:50 PM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] Problem with ligand identification

Hello everyone,

I need help identifying the ligand I found on the electron density maps. I have 
soaked ribonuclease A crystals with the phosphorothioate dinucleotide. The 
diffraction experiment was performed on a home source (Cu). When I analysed the 
data, I found both the dinucleotide and this strange object near two 
histidines. Since I did not find anything similar on the list of possibly used 
compounds, it could be a contamination but still unknown to me. I tried 
modelling glycolic acid (GOA) here, but it looks like the electron density 
around the hydroxyl group is greater. Maybe a sulphur containing compound - 
MCR? Do you have any other idea?

Regards
Rafal

--
--
Rafal Dolot, Ph.D.
Polish Academy of Sciences
Centre of Molecular and Macromolecular Studies
Division of Bioorganic Chemistry
Macromolecular Crystallography Laboratory
Sienkiewicza 112
90-363 Lodz, Poland
Phone: +48(42)6803325
Cell:  +48 502897781
--

-
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Re: [ccp4bb] How to make covalent bond for modified nucleic acid

[FULVIO SACCOCCIA]

You May try "Builder" panel embedded in Pymol to make covalent bond.
Best
 Fulvio

Inviato da Outlook per Android


Da: CCP4 bulletin board  per conto di Hsuan-Ai 

Inviato: lunedì, agosto 28, 2023 6:54:01 PM
A: CCP4BB@JISCMAIL.AC.UK 
Oggetto: [ccp4bb] How to make covalent bond for modified nucleic acid

Greeting to all,

I am struggling to place modified nucleotides into an oligonucleotide strand. I 
built the ligand restraint dictionaries both in Acedrg or Elbow; the generated 
liogands look fine, but the covalent bond between the ligand and the 
modification site cannot be generated, also in vain when following the Acedrg 
tutorial (where additional covalent bond restraint was generated). I also tried 
to edit the pdb file directly by specifying which atom links to which. It, 
nevertheless, did mot work as I imagined.

How do you usually make ligand link to protein / nucleic acid via covalent 
bond? Is there some trick to tell the program the existence of covalent bonds? 
Any suggestions are heartily appreciated. Thank you in advanced!

Best regards,
Ai



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[ccp4bb] Citing Combat

[Fulvio Saccoccia]

Dear ccp4i community,

   what is the right way to cite Combat,  is there any paper about it?

Thanks in advance


Fulvio



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[ccp4bb] Post-doc position in Monterotondo (Rome, Italy)

[Fulvio Saccoccia]

Dear ccp4i users,

    a ONE-YEAR POST-DOC POSITION is available at the Institue of  
Biochemistry and Cell Biology (IBBC) of National Research Council  
(CNR) settled in Monterotondo (in the nearby of Rome, Italy), in the  
research group of doct. Giovina Ruberti. The project aims at studying  
the histone deacetylase enzymes belonging to /Schistosoma mansoni/, a  
human parasite, with structural biology and enzymology approaches. The  
candidate will be employed as POST-DOC FELLOW AT SAPIENZA UNIVERSITY  
OF ROME, under the supervision of prof. Andrea Bellelli. 


The announcement is online:  
https://web.uniroma1.it/trasparenza/sites/default/files/BANDO%20A_15%20_2021.pdf


Real deadline is 2022, january 17 (first useful working day after  
reported deadline, january 16) 


For further information, please, contact: andrea.belle...@uniroma1.it

More information on the SCHISTODISCOVERY group and its scopes are  
available  
at _http://www.ibbc.cnr.it/research-applications/poverty-diseases/[1]_


Best wishes

Fulvio



Link:
-
[1] http://www.ibbc.cnr.it



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Re: [ccp4bb] cavities in protein structures

[Fulvio Saccoccia]

You can try VOIDOO as well:

http://xray.bmc.uu.se/usf/voidoo.html

a bit dated but still effective

Cheers, Fulvio


Il 01/02/18 09:54, Claudia Binda ha scritto:

Dear All,

thanks everyone for your help.
Below is a summary of all suggestions for calculating and representing 
cavities of protein structures.

Best
Claudia


Caver (https://www.caver.cz/)

3V (http://3vee.molmovdb.org)

ProFunc (https://www.ebi.ac.uk/thornton-srv/databases/profunc/)

Ghecom (http://strcomp.protein.osaka-u.ac.jp/ghecom/)

using pymol with no other plug-ins required

CastP (http://sts.bioe.uic.edu/castp/index.html)

Metapocket (http://projects.biotec.tu-dresden.de/metapocket/)

Hollow (http://hollow.sourceforge.net/)


2018-01-30 14:55 GMT+01:00 Johannes Cramer >:


Hi Claudia,

another program that I used with success is Hollow
(https://www.ncbi.nlm.nih.gov/pubmed/19014592
).
It is really easy to use. You can get is here
http://hollow.sourceforge.net/ 
It finds pockets in a defined area, fills them with water
molecules and generates a pdb with those waters. You can then
import it into pymol and represent it however you think is fitting.

Cheers,
Johannes

2018-01-30 14:20 GMT+01:00 Vipul Panchal >:

Hi Claudia,
For the identification of cavities and residues linning them,
metapocket is one of the preferred choice as it uses
prediction from various program.
Output of the server is pdb file.

I found caver program represent cavities in a best manner.
There is caver plugin available for pymol. Output is tunnel
like representation with different colours. Interestingly, it
also provides tunnel length, radius and list of residues
linning the bottle-neck of each of the cavity. As a input for
the presentation of cavities, you need to provide list of
residues lining cavities. Identified by other programs.

All the best!


On 30-Jan-2018 6:28 PM, "Boaz Shaanan" > wrote:

Hi Claudia,

Another possibility is CastP:
http://sts.bioe.uic.edu/castp/index.html


They also have a Pymol plugin. I have not used this plugin
since I'm displaying the CastP o/p files in UCSF-chimera
which handles them nicely.


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  Skype: boaz.shaanan
Fax:   972-8-647-2992 or 972-8-646-1710 /
//
//
/

/




*From:* CCP4 bulletin board > on behalf of Claudia Binda
>
*Sent:* Tuesday, January 30, 2018 1:51 PM
*To:* CCP4BB@JISCMAIL.AC.UK 
*Subject:* [ccp4bb] cavities in protein structures
Hi everyone,

I need suggestions to calculate and represent cavities of
protein structures. For years I have been using Voidoo
that produces maps in ezd format which could be converted
in map format (ccp4) using the online server
http://xray.bmc.uu.se/cgi-bin/gerard/mapman_server.pl
.
However, this does not work anymore. Is there another way
to do it? What is the best tool to calculate cavities and
draw them by Pymol or ccp4mg?

Thank you
Claudia







-- 
Claudia Binda

University of Pavia
Dept. Biology and Biotechnology
via Ferrata 1, 27100 Pavia - Italy
Phone: +39-0382-985535 
Fax: +39-0382-528496 
E-mail: claudia.bi...@unipv.it 
Web: http://www.unipv.it/biocr 





--
Claudia Binda
University of Pavia
Dept. Biology and Biotechnology
via Ferrata 1, 27100 Pavia - Italy
Phone: +39-0382-985535
Fax: +39-0382-528496
E-mail: claudia.bi...@unipv.it 
Web: http://www.unipv.it/biocry

[ccp4bb] advances in multisubunit membrane protein

[Fulvio Saccoccia, Sapienza]

Dear ccp4ers,

   I was wondering about most recent advances in production and 
crystallization of complexes of multisubunit membrane proteins, for 
instance succinate dehydrogenase, pyruvate dehydrogenase complex or even 
photosystem complex. As far as I know, many large complexes of membrane 
proteins were produced by tittues extraction rather than by recombinant 
expression but I want to know if there is room to work with these large 
assemblies by using recombinant proteins.


Best wishes


Fulvio

[ccp4bb] Fwd: [ccp4bb] XDS INP

[Fulvio Saccoccia, Sapienza]

Dear Lu
   you can freely download the tutorial from here: 
http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Main_Page 
You can check if your detector is supported here: 
http://xds.mpimf-heidelberg.mpg.de/html_doc/detectors.htm

Best
Fulvio


 Il giorno 07/mag/2015, alle ore 10:33, luzuok luzuo...@126.com ha scritto:
 
 Dear all,
 I'm a XDS beginner and the first problem I encounter was the INP file. 
 The detector type is MX300. Is the detector supported by XDS? How to 
 modified the INP file?
 The sitefile of HKL2000 was attached.
 Can anyone provide some tutorial to use XDS?
 
 Best wishes!
 
 Lu zuokun
 
 
 
 
 
 --
 卢作焜
 南开大学新生物站A202
 
 
 def.site
 

Re: [ccp4bb] how to recover my data

[Fulvio Saccoccia, Sapienza]

Yes, sorry for the mistake;

Smith,
did you try to open your .mtz file with matzdmp from a terminal window? is it 
possible to redirect the output from mtzdmp to a new file, I mean:

mtzdmp corrupted_file.mtz  recovered_file.mtz

???
I don’t know...

Fulvio



Il giorno 05/mar/2015, alle ore 16:18, Harry Powell ha...@mrc-lmb.cam.ac.uk 
ha scritto:

 Hi Fulvio
 
 MTZ files are binary, so I don't think they have line-endings in the sense 
 that text files do.
 
 On 5 Mar 2015, at 15:09, Fulvio Saccoccia, Sapienza wrote:
 
 Sorry, my previous post was not properly attached; I attached my idea:
 
 Dear Smith,
It is curious; I am not sure about what I am going to suggest since I 
 never had that problem but the simplest explanation I found is that you have 
 some Line Endings issues. Windows, Mac and Unix all use different codes to 
 end a line in a text file. A file that is scripted with Windows has Windows 
 line ending (DOS-like) and may not be properly read on Mac or Linux machine. 
 Let me explain: by using WordPad and notepad you might have changed the end 
 line of your PDB/mtz file from UNIX-based (or Mac) line endings to 
 Windows-based Line endings. Line endings cannot be detected by simple 
 inspecting the file, but some programs (in this case Coot) can have problem 
 to open them.
 To be safe, try by opening your files with such a program (TextWrangler for 
 ex. in Mac) and save the file with the correct line ending for your machine 
 (Mac, Linux or Windows). I attached a picture for reference to show you the 
 option you have in TextWrangler when you use Save as… option (other text 
 editors should have similar options)
 sconosciuto.png
 
 Best wishes
 Fulvio
 
 
 Il giorno 05/mar/2015, alle ore 14:51, Robbie Joosten 
 robbie_joos...@hotmail.com ha scritto:
 
 Hi Smith,
 
 If this is really the problem Ian describes, you can try the Linux programs 
 unix2dos and dos2unix the change the line endings. A potential source of 
 the problem might be copying the file with certain (S)FTP clients: in 
 'text-mode' they change the line endings to your OS default to be user 
 friendly.
 
 Cheers,
 Robbie
 
 -Original Message-
 From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
 Ian Tickle
 Sent: Thursday, March 05, 2015 14:04
 To: CCP4BB@JISCMAIL.AC.UK
 Subject: Re: [ccp4bb] how to recover my data
 
 Hi Smith
 
 
 I sympathise with your plight - I have had to do similar things in the 
 past for
 other people!  I think your most fruitful course of action would be to 
 talk to
 the technician who recovered your data because only he knows what he
 actually did to recover it.
 
 
 From your description of your recovery of the PDB file it looks to me like 
 a
 line terminator issue, i.e. was the original file created in Linux, 
 Windows or
 Mac?  This is relevant because the line terminators are different and it
 sounds like the technician didn't simply copy the file, he changed the line
 terminators.  If he did the same with the MTZ file thinking it was a text 
 file
 the additional line terminators would corrupt the binary data making it
 impossible to read with any of the CCP4 MTZ utilities.  If you can 
 understand
 exactly what the technician did you may be able to reverse it and recover 
 the
 binary data.
 
 
 Hope this helps!
 
 
 Cheers
 
 
 -- Ian
 
 
 On 5 March 2015 at 05:36, Smith Lee 0459ef8548d5-dmarc-
 requ...@jiscmail.ac.uk wrote:
 
 
 
Dear All,
 
Recently my computer hardware has been broken and all the data
 has been recovered to movable hardware by technician. However I find the
 recovered PDB file and the MTZcould not be openned by Coot. Then I open
 the revovered PDB file by WordPad, and from WordPad I copied it to
 notepad and save it as pdb file. I find the Coot can open the notepad saved
 pdb file, thus my pdb files can be succesfully recovered from the hardware.
 
But will you please tell me how to have Coot open my mtz file? After
 data recovery by the technicial, the data size of the mtz file did not 
 decrease,
 thus I think there is a way to have it recovered.
 
I have not noticed there were similar or identical posts as mine for
 recovery data before in the CCP4 mail list.
 
Thus I am looking forward to getting a reply from you on how to
 recover my mtz file.
 
 
Smith
 
 
 
 
 Harry
 --
 Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue, 
 Cambridge Biomedical Campus, Cambridge CB2 0QH
 Chairman of International Union of Crystallography Commission on 
 Crystallographic Computing
 Chairman of European Crystallographic Association SIG9 (Crystallographic 
 Computing) 
 
 
 
 
 
 
 
 
 
 

[ccp4bb] Fwd: [ccp4bb] how to recover my data

[Fulvio Saccoccia, Sapienza]

Inizio messaggio inoltrato:

 Da: Fulvio Saccoccia, Sapienza fulvio.saccoc...@uniroma1.it
 Oggetto: Re: [ccp4bb] how to recover my data
 Data: 05 marzo 2015 13:48:34 CET
 A: Smith Lee smith_lee...@yahoo.com
 
 Dear Smith,
It is curious; I am not sure about what I am going to suggest since I 
 never had that problem but the simplest explanation I found is that you have 
 some Line Endings issues. Windows, Mac and Unix all use different codes to 
 end a line in a text file. A file that is scripted with Windows has Windows 
 line ending (DOS-like) and may not be properly read on Mac or Linux machine. 
 Let me explain: by using WordPad and notepad you might have changed the end 
 line of your PDB/mtz file from UNIX-based (or Mac) line endings to 
 Windows-based Line endings. Line endings cannot be detected by simple 
 inspecting the file, but some programs (in this case Coot) can have problem 
 to open them.
 To be safe, try by opening your files with such a program (TextWrangler for 
 ex. in Mac) and save the file with the correct line ending for your machine 
 (Mac, Linux or Windows). I attached a picture for reference to show you the 
 option you have in TextWrangler when you use Save as… option (other text 
 editors should have similar options)
 
 
 Best wishes
 Fulvio
 
 
 
 Il giorno 05/mar/2015, alle ore 06:36, Smith Lee 
 0459ef8548d5-dmarc-requ...@jiscmail.ac.uk ha scritto:
 
 
 
 Dear All,
  
 Recently my computer hardware has been broken and all the data has been 
 recovered to movable hardware by technician. However I find the recovered 
 PDB file and the MTZcould not be openned by Coot. Then I open the revovered 
 PDB file by WordPad, and from WordPad I copied it to notepad and save it as 
 pdb file. I find the Coot can open the notepad saved pdb file, thus my pdb 
 files can be succesfully recovered from the hardware.
  
 But will you please tell me how to have Coot open my mtz file? After data 
 recovery by the technicial, the data size of the mtz file did not decrease, 
 thus I think there is a way to have it recovered.
 
 I have not noticed there were similar or identical posts as mine for 
 recovery data before in the CCP4 mail list.
  
 Thus I am looking forward to getting a reply from you on how to recover my 
 mtz file.
  
 Smith
 

Re: [ccp4bb] how to recover my data

[Fulvio Saccoccia, Sapienza]

Sorry, my previous post was not properly attached; I attached my idea:

Dear Smith,
   It is curious; I am not sure about what I am going to suggest since I never 
had that problem but the simplest explanation I found is that you have some 
Line Endings issues. Windows, Mac and Unix all use different codes to end a 
line in a text file. A file that is scripted with Windows has Windows line 
ending (DOS-like) and may not be properly read on Mac or Linux machine. Let me 
explain: by using WordPad and notepad you might have changed the end line of 
your PDB/mtz file from UNIX-based (or Mac) line endings to Windows-based Line 
endings. Line endings cannot be detected by simple inspecting the file, but 
some programs (in this case Coot) can have problem to open them.
To be safe, try by opening your files with such a program (TextWrangler for ex. 
in Mac) and save the file with the correct line ending for your machine (Mac, 
Linux or Windows). I attached a picture for reference to show you the option 
you have in TextWrangler when you use Save as… option (other text editors 
should have similar options)


Best wishes
Fulvio


Il giorno 05/mar/2015, alle ore 14:51, Robbie Joosten 
robbie_joos...@hotmail.com ha scritto:

 Hi Smith,
 
 If this is really the problem Ian describes, you can try the Linux programs 
 unix2dos and dos2unix the change the line endings. A potential source of the 
 problem might be copying the file with certain (S)FTP clients: in 'text-mode' 
 they change the line endings to your OS default to be user friendly.
 
 Cheers,
 Robbie
 
 -Original Message-
 From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
 Ian Tickle
 Sent: Thursday, March 05, 2015 14:04
 To: CCP4BB@JISCMAIL.AC.UK
 Subject: Re: [ccp4bb] how to recover my data
 
 Hi Smith
 
 
 I sympathise with your plight - I have had to do similar things in the past 
 for
 other people!  I think your most fruitful course of action would be to talk 
 to
 the technician who recovered your data because only he knows what he
 actually did to recover it.
 
 
 From your description of your recovery of the PDB file it looks to me like a
 line terminator issue, i.e. was the original file created in Linux, Windows 
 or
 Mac?  This is relevant because the line terminators are different and it
 sounds like the technician didn't simply copy the file, he changed the line
 terminators.  If he did the same with the MTZ file thinking it was a text 
 file
 the additional line terminators would corrupt the binary data making it
 impossible to read with any of the CCP4 MTZ utilities.  If you can understand
 exactly what the technician did you may be able to reverse it and recover the
 binary data.
 
 
 Hope this helps!
 
 
 Cheers
 
 
 -- Ian
 
 
 On 5 March 2015 at 05:36, Smith Lee 0459ef8548d5-dmarc-
 requ...@jiscmail.ac.uk wrote:
 
 
 
  Dear All,
 
  Recently my computer hardware has been broken and all the data
 has been recovered to movable hardware by technician. However I find the
 recovered PDB file and the MTZcould not be openned by Coot. Then I open
 the revovered PDB file by WordPad, and from WordPad I copied it to
 notepad and save it as pdb file. I find the Coot can open the notepad saved
 pdb file, thus my pdb files can be succesfully recovered from the hardware.
 
  But will you please tell me how to have Coot open my mtz file? After
 data recovery by the technicial, the data size of the mtz file did not 
 decrease,
 thus I think there is a way to have it recovered.
 
  I have not noticed there were similar or identical posts as mine for
 recovery data before in the CCP4 mail list.
 
  Thus I am looking forward to getting a reply from you on how to
 recover my mtz file.
 
 
  Smith
 
 

[ccp4bb] R factor from merged data

[Fulvio Saccoccia]

Dear ccp4 users,
does anyone know if there is a way to (re)calculate the Rmerge from a
deposited .cif file in PDB?
 In this case is an already merged structure factor file.

I know that the EDS from Uppsala makes it, providing the PDB entry, but I
need a procedure in order to do it by myself.
I see that ccp4i utilities only accept unmerged .mtz; have you got any
advice?
Thanks in advance

Fulvio
-- 
Fulvio Saccoccia, PhD
Dept. of Biochemical Sciences
Sapienza University of Rome
00185, Rome (Italy)
Phone: +39 06 4991 0556

Re: [ccp4bb] [ccp4bb] AW: [ccp4bb] uncertainites associated with intensities from twinned crystals; Sorry for HTML.

[Fulvio Saccoccia]

Dear all,
thank you for your reply. I would summarize my concerns and opinions, 
so 
far:

1) for QTLS (non-merohedral twinning - non intersecting lattices) I think one 
should consider the variables as independent and random and it is possible to 
recover the true intensities of a unique lattice from the stronger diffracting 
one (see for example Jenni  Ban, 2009, Acta D65, 101-111). Hence, the 
quadratic formula (reported fomr Jens Kaiser) can be applied;

2) for TLS (merohedral twinning - perfectly overlapping spots) I think one 
should not consider the two variable independent since they are related by 
alpha (see the formulas I reported in my first message). In this case, I think 
the right formula should be that reported by Tim Grune, that as far as I know 
overestimates the true error but in this case the quadratic is not applicable.

Therefore, one would be prone to conclude that the uncertainties associated to 
merohedral-twinned crystals are higher than regular crystals or non-merohedral 
crystals. What's your opinion about? 


In data mercoledì 6 novembre 2013 23:29:01, Jens Kaiser ha scritto:
 Tassos,
   I'm no expert either, and there are caveats for using this formula on
 correlated magnitudes. But I would assume that the intensities of twin
 related reflections should be independent from each other (that's my
 understanding of the sigmoid cumulative intensity distribution of
 twins). Thus, I think the simple Gaussian error propagation should be
 applicable to uncertainty estimates in detwinned intensities.
 
 Cheers,
 
 Jens
 
 On Thu, 2013-11-07 at 08:09 +0100, Anastassis Perrakis wrote:
  Dear Jens,
  
  
  That formula for error propagation is correct for independent
  measurements.
  Does this assumption stand true for Intensities in twinning? I am no
  expert, but I would think not.
  
  
  Tassos
  
  On 7 Nov 2013, at 7:53, Jens Kaiser wrote:
   Fulvio, Tim,
   
 error propagation is correct, but wrongly applied in Tim's
   
   example.
   s_f= \sqrt{ \left(\frac{\partial f}{\partial {x} }\right)^2 s_x^2 +
   \left(\frac{\partial f}{\partial {y} }\right)^2 s_y^2 +
   \left(\frac{\partial f}{\partial {z} }\right)^2 s_z^2 + ...} (see
   http://en.wikipedia.org/wiki/Propagation_of_uncertainty#Simplification)
   The uncertainty in a derived magnitude is always larger than any
   individual uncertainty, so no subtraction, anytime. Furthermore, in
   Tim's example you could end up with negative sigmas..
   
   HTH,
   
   Jens
   
   On Thu, 2013-11-07 at 04:44 +0100, Tim Gruene wrote:
Dear Fulvio,

with simple error propagation, the error would be
sigma(I(h1)) = (1-α)sigma(Iobs(h1))-α*sigma(Iobs(h2))/(1-2α)

would it not?

Although especially for theoretical aspects you should be concerned
about division by zero.

Best,
Tim

On 11/06/2013 05:54 PM, Fulvio Saccoccia wrote:
 Thank you for reply. My question mostly concern a theoretical
 aspect rather than practical one. To be not misunderstood, what is
 the mathematical model that one should apply to be able to deal
 with twinned intensities with their errors? I mean, I+_what? I ask
 this In order to state some general consideration on the accuracy
 about the recovery the true intensities on varying of alpha. Thanks
 
  Fulvio
 
 Fulvio Saccoccia PhD Dept. of Biochemical Sciences Sapienza
 University of Rome 5, Piazzale A. Moro 00185 phone +39 0649910556
 
 Messaggio Originale Da: herman.schreu...@sanofi.com
 Inviato:  06/11/2013, 17:25 A: CCP4BB@JISCMAIL.AC.UK Oggetto:
 [ccp4bb] AW: [ccp4bb] uncertainites associated with intensities
 from twinned crystals
 
 
 Dear Fulvio, you cannot detwin perfectly twinned data with this
 formula. The term (1-2α) becomes zero, so you are dividing by zero.
 With good refinement programs (ShelX, Refmac), refinement is done
 against twinned data, which is better than to detwin the data with
 the formula you mention.
 
 As I understand it, to get map coefficients, the calculated
 contribution of the twin domain (Fcalc’s) is substracted from Fobs
 (with the appropriate weighting factors), so what you see in coot
 is detwinned electron density. In practical terms, the only thing
 you have to do is to specify the TWIN keyword in Refmac.
 
 Best regards, Herman
 
 
 
 Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag
 von Fulvio Saccoccia Gesendet: Mittwoch, 6. November 2013 16:58 An:
 CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] uncertainites associated
 with intensities from twinned crystals
 
 
 Dear ccp4 users
 
 a question about the recovering of true intensities from merohedral
 twinned crystal. Providing alpha and the twin operator one should
 be able to recover the intensities from the formulas:
 
 
 
 I(h1) = (1-α)Iobs(h1

[ccp4bb] uncertainites associated with intensities from twinned crystals

[Fulvio Saccoccia]

Dear ccp4 users
a question about the recovering of true intensities from merohedral 
twinned crystal. Providing alpha and the twin operator one should be able to 
recover the 
intensities from the formulas:

I(h1) = (1-α)Iobs(h1)-αIobs(h2)/(1-2α)
I(h2) = -αIobs(h1)+(1+α)Iobs(h2)/(1-2α)


as stated in many papers and books*.
However I was wondering about the uncertainties associated to these 
measurements, I 
mean: for all physical observable an uncertainty should be given. 
Hence, what is the uncertainty associated to a perfect merohedrally twinned 
crystal 
(alpha=0.5)? It is clear that in this case we drop in a singular value of the 
above 
formulas.
Please, let me know your hints or your concerns on the matter. Probably there 
is 
something that it is not so clear to me.

Thanks in advance

Fulvio


ref. **(C. Giacovazzo, H. L. Monaco, G. Artioli, D. Viterbo, M. Milaneso, G. 
Ferraris, G. 
Gilli, P. Gilli, G. Zanotti and M. Catti. Fundamentals of Crystallography, 3rd 
edition. IUCr 
Texts on Crystallography No. 15, IUCr/Oxford University Press, 2011; Chandra, 
N., 
Acharya, K. R., Moody, P. C. (1999). /Acta Cryst./ *D*55. 1750-1758)
-- 
Fulvio Saccoccia, PhD
Dept. of Biochemical Sciences A. Rossi Fanelli
Sapienza University of Rome
Tel. +39 0649910556

[ccp4bb] R: [ccp4bb] AW: [ccp4bb] uncertainites associated with intensities from twinned crystals

[Fulvio Saccoccia]

Thank you for reply. My question mostly concern a theoretical aspect rather 
than practical one. To be not misunderstood, what is the mathematical model 
that one should apply to be able to deal with twinned intensities with their 
errors? I mean, I+_what? I ask this In order to state some general 
consideration on the accuracy about the recovery the true intensities on 
varying of alpha.
Thanks 
Fulvio

Fulvio Saccoccia PhD
Dept. of Biochemical Sciences
Sapienza University of Rome
5, Piazzale A. Moro 00185
phone +39 0649910556

Messaggio Originale
Da: herman.schreu...@sanofi.com
Inviato:  06/11/2013, 17:25 
A: CCP4BB@JISCMAIL.AC.UK
Oggetto: [ccp4bb] AW: [ccp4bb] uncertainites associated with intensities from 
twinned crystals


Dear Fulvio,
you cannot detwin perfectly twinned data with this formula. The term (1-2α) 
becomes zero, so you are dividing by zero. With good refinement programs 
(ShelX, Refmac), refinement is done against twinned data, which is better than 
to detwin the data with the formula you mention.

As I understand it, to get map coefficients, the calculated contribution of the 
twin domain (Fcalc’s) is substracted from Fobs (with the appropriate weighting 
factors), so what you see in coot is detwinned electron density. In practical 
terms, the only thing you have to do is to specify the TWIN keyword in Refmac.

Best regards,
Herman



Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Fulvio 
Saccoccia
Gesendet: Mittwoch, 6. November 2013 16:58
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] uncertainites associated with intensities from twinned 
crystals


Dear ccp4 users

a question about the recovering of true intensities from merohedral twinned 
crystal. Providing alpha and the twin operator one should be able to recover 
the intensities from the formulas:



I(h1) = (1-α)Iobs(h1)-αIobs(h2)/(1-2α)

I(h2) = -αIobs(h1)+(1+α)Iobs(h2)/(1-2α)

as stated in many papers and books*.

However I was wondering about the uncertainties associated to these 
measurements, I mean: for all physical observable an uncertainty should be 
given.

Hence, what is the uncertainty associated to a perfect merohedrally twinned 
crystal (alpha=0.5)? It is clear that in this case we drop in a singular value 
of the above formulas.

Please, let me know your hints or your concerns on the matter. Probably there 
is something that it is not so clear to me.



Thanks in advance



Fulvio





ref. **(C. Giacovazzo, H. L. Monaco, G. Artioli, D. Viterbo, M. Milaneso, G. 
Ferraris, G. Gilli, P. Gilli, G. Zanotti and M. Catti. Fundamentals of 
Crystallography, 3rd edition. IUCr Texts on Crystallography No. 15, IUCr/Oxford 
University Press, 2011; Chandra, N., Acharya, K. R., Moody, P. C. (1999). Acta 
Cryst. D55. 1750-1758)

--

Fulvio Saccoccia, PhD

Dept. of Biochemical Sciences A. Rossi Fanelli

Sapienza University of Rome

Tel. +39 0649910556

Re: [ccp4bb] XDS not picking spots correctly, please help!

[Fulvio Saccoccia]

Dear Fei,
in addition, take a look here:

https://www.researchgate.net/profile/Fulvio_Saccoccia/contributions/?ev=prf_act 




and download my tutorial on XDS if you want.

Bye


Il 04/07/2013 18:26, Fei Li ha scritto:

Dear all,

I recently collected some 10 degree wedges of data on a very small 
membrane protein. The data processing so far is not working well. XDS 
is the only software that process my data and give a space group and 
cell parameters. However, I ended up with a merged dataset with low 
completeness at low resolution. My data is not overloaded. This is a 
very small protein shot with 5um mini-beam. I checked the FRAME.cbf 
file and looks like XDS is not picking the spots at low resolution 
correctly. It missed a good portion of my low res spots in every 
datasets I checked and picked more at high res, which are weaker. Then 
the indexing step will reject most of my spots for too far away from 
ideal position. imosflm was able to pick the spots correctly, but 
does not index. I can send the FRAME.cbf file and the imosflm picture 
if anyone thinks that will he useful to see. Any suggestion on how to 
make XDS, or imosflm, correctly working for me is greatly appreciated. 
Thanks a lot!


Best regards,

Fei


Fei LI
Graduate Assistant
310 Biochemistry Building
Department of Biochemistry and Molecular Biology
Michigan State University
East Lansing, MI
48824

[ccp4bb] pseudotranslation issues

[Fulvio Saccoccia]

Dear ccp4bb users,
I have a data set collected at 2.2A resolution that I can integrate 
in P4. Aimless, Phaser and Xtriage recognized a pseudotranslation  
(34.6% of origin peak) at fractional coordinates 0.500 0.500 0.479  
(ORTH   46.7   46.7   37.4). However labelit.index run with 
sublattice_allow=true search did not detect the pseudotranslation 
vector. So far, any attempts to phase by molecular replacement was 
unsuccesfull and I suspect that it could be due to incorrect assignement 
of space group:


Now, some questions arise:
1) does the pseudo translation exist or do not?
2) if translational NCS is present, could it mimic a P41/P42/P43 space 
group?
3) in any case, any advices in order to properly deal with tNCS will be 
of great help?


I thank you in advance
Best wishes

--
Fulvio Saccoccia, PhD
Sapienza University of Rome
Dept. of Biochemical Sciences A. Rossi Fanelli
Piazzale Aldo Moro, 5
00185 Rome (Italy)

[ccp4bb] how to deal 3 twin-related domains

[Fulvio Saccoccia]

Dear ccp4 users,
I have a reflections file obtained from a crystal initially scaled 
in H3. All the attempts to phase by Molecular Replacement were not 
successful and I succeeded only in P1. Based on previously solved 
structures from the same protein, I suspected that twinning affected 
crystals; so I used Twin refinement in Refmac. The program gave 
indication of 3 domains:


Twin operator:  H,  K,  L: Fraction = 0.335
Twin operator:  H,  L, -H-K-L: Fraction = 0.332
Twin operator:  H, -H-K-L,  K: Fraction = 0.333

With P1 and twin refinement I obtained a reasonable initial value of FOM 
(0.50) but R/Rfree still remain at very large values (0.46/0.49).
I am not sure about twinning and data handling in presence of 3 twin 
domains and I will appreciate a lot if someone will suggest me how to 
deal out with these data.


Thanks

Fulvio

--
Fulvio Saccoccia, PhD
Sapienza University of Rome
Dept. of Biochemical Sciences A. Rossi Fanelli
Piazzale Aldo Moro, 5
00185 Rome (Italy)

Re: [ccp4bb] Self rotation function interpretation

[Fulvio Saccoccia]

Did you perform Matthews analysis? It should give you some indications 
on the number of monomers in the asymmetric unit. Can you send the list 
of peaks? It should be a file with .tab extension.


Cheers

Fulvio Saccoccia
Dept. of Biochemical Sciences
Sapienza University of Rome

Il 10/02/2013 05:00, Emma Littlejohn ha scritto:


Hi all,

I have generated a self rotation function using MOLREP for a low res 
data set which indexed in space group I222 (attached). I am hoping it 
may provide some information on the oligomeric state of the protein. I 
am new to analysing SF and was wondering if anyone can help with the 
interpretation or has any tips that might be able to help me shed some 
light on what the SF is revealing?


Thanks in advance.
Emma

Re: [ccp4bb] CNS installation

[Fulvio Saccoccia]

Dear ccp4 users,

   I succeeded to install and use CNS 1.3 on 64bit Debain-based Linux distributions. Here my report:

  

  1. install CNS and edit cns_solve_env as described by http://cns-online.org/v1.3/;

  

  2. no other modifications of cns_solve_env or .cns_solve_ens_sh
  were required; use only the first script;

  

  3. in a shell, move to the directory you want to work in and type
  /CNS_intsallation_dir/cns_solve_1.3/cns_solve_env: this will set
  all environment variables for that shell (remember to work only on
  it - csh or tcsh is required, if not present, install one);

  

  4. in the same shell, type cns_solve;

  

  5. the CNS prompt will appear;

  

  6. now, it is possible to run any .inp just typing @command (i.e.
  CNSsolve@cross_rotation.inp).

  

  cns_solve_env and cns_solve_env_sh do not run if I stay in the
  installation directory; that is, running them in
  ~/xtal/CNS/cns_solve_1.3 I still receive the message "Word too
  long". I don't know why

  

  That's all. So far, CNS runs both under Ubuntu 12.04 and Debian
  6.0.4.

  

  Thanks to all for precedent replies.

  

  Best regards

  

      Fulvio Saccoccia

  Dept. of Biochemical Sciences

  Sapienza University of Rome, Italy

  

[ccp4bb] CNS installation

[fulvio saccoccia]

Dear ccp4 users,
I tried to install CNS under Debian 64bit. I followed the installation
giude as reported by CNS developers but  I received the following
message when souurcing cns_solve_env:

bash: setenv: command not found
bash: setenv: command not found
bash: cns_solve_env: line 32: syntax error near unexpected token
`setenv'
bash: cns_solve_env: line 32: `  if ( ! $?CNS_ARCH ) setenv CNS_ARCH `
$CNS_SOLVE/bin/getarch`'

I know that the script would set all variables; it is indicated for csh
(or tcsh) shell. I tried to run the script under a csh shell but I
received a different error:

Word too long

The above statement is also received if a bash-optimized script is run.

Does anyone have experience in CNS installation and environment setting?
Any advice?

Thanks in advance

Fulvio Saccoccia
Dept. of Biochemical Sciences
Sapienza University of Rome, Italy

[ccp4bb] SOMoRe

[fulvio saccoccia]

Dear ccp4 users,
does anyone know where to download SOMoRe for molecular replacement? 

Thanks in advance

Fulvio Saccoccia
PhD student
Dept. of Biochemical Sciences
Sapienza University of Rome
Italy

[ccp4bb] error message in scalepack

[fulvio saccoccia]

Dear ccp4bber,
 I received the following message, during a run with scaling:

forrtl: error (72): floating overflow

does anyone know what does it means and how can I overcome it?

I am trying to scale 900 frames, with data integrated to 3.3 A
resolution.

Thanks in advance

Fulvio Saccoccia, PhD student
Dept. of Biochemical Sciences
Sapienza University of Rome

Re: [ccp4bb] Twinning, Wilson scaling and B factor

[fulvio saccoccia]

Thanks Ian,
I tried to do this:
I took the file containing 
hkl I and sigI 

and generated a new file containing 

hkl I/2 and sigI 

because I know, from the refined structure that the twin fraction is
nearly 0.5. Now, using this new file the wilson plot give me a more
reliable estimated B factor.

Do you think this procedure was correct?

Fulvio

Il giorno gio, 19/05/2011 alle 14.14 +0100, Ian Tickle ha scritto:
 Hi Fulvio
 
 There are 2 different issues here: the Wilson plot scale  B factor on
 the one hand and Wilson statistics on the other.  The first are not
 affected by twinning since they depend only on the intensity averages
 in shells.  The second refers to the distribution of intensities (i.e.
 the proportion of reflections with intensity less than a specified
 value) within a shell, or to the distribution of normalised
 intensities (Z = I/I ignoring symmetry issues for now) over the
 whole dataset.  This distribution is different for a twin because
 averaging the components which contribute to the intensity of a
 twinned reflection tends to shift the distribution towards the mean,
 so you get fewer extreme values.
 
 The Wilson B factor is not a 'statistic' in the strict sense, merely a
 derived parameter.  I suspect the low value you get has more to do
 with the fact that the resolution is only 3 A, than the fact it's
 twinned.
 
 See here for more mathematically-oriented info:
 
 http://www.ccp4.ac.uk/dist/html/pxmaths/bmg10.html
 
 Cheers
 
 -- Ian
 
 On Thu, May 19, 2011 at 1:45 PM, fulvio saccoccia
 fulvio.saccoc...@uniroma1.it wrote:
  Dear ccp4 users,
 I have a data set arising from a nearly-perfect pseudo-merohedrally
  twinned cystal, diffracting up to 3 A. I solved the structure and ready
  for deposition, but there is still a trouble.
  The Wilson scaling from raw data gave a B of 3A^2.
  Initially, I did not seemed too alarming. But I do not know why I have
  these statistics.
 
  Does anyone know why Wilson scaling falls when treating that kind of
  twinned data? I read that twinned data do not obey twe Wilson statistics
  but I don't know why.
  Here the presentation I read:
 
  http://bstr521.biostr.washington.edu/PDF/Twinning_2007.pdf
 
  Do you know any articles, reviews or book in which this particular
  aspect of  of twinned data is treated in depth, possibly in mathematical
  manner?
 
  Thanks to all
 
  Fulvio Saccoccia, PhD student
  Biochemical Sciences Dept.
  Sapienza University of Rome
 

Re: [ccp4bb] Twinning, Wilson scaling and B factor

[fulvio saccoccia]

Ok, so another question in my mind:
the data come from a collection interrupted after the first 200 frames
and restarted after 1 hour to recover the missed 160 frames.
The first and second group of frames, if separately indexed, give cell
parameter values that differ of about 1A for axes and 1 degree in angle.
Can this affect thw wilson plot scaline and as consequence the B
factor? 


Il giorno gio, 19/05/2011 alle 14.14 +0100, Ian Tickle ha scritto:
 Hi Fulvio
 
 There are 2 different issues here: the Wilson plot scale  B factor on
 the one hand and Wilson statistics on the other.  The first are not
 affected by twinning since they depend only on the intensity averages
 in shells.  The second refers to the distribution of intensities (i.e.
 the proportion of reflections with intensity less than a specified
 value) within a shell, or to the distribution of normalised
 intensities (Z = I/I ignoring symmetry issues for now) over the
 whole dataset.  This distribution is different for a twin because
 averaging the components which contribute to the intensity of a
 twinned reflection tends to shift the distribution towards the mean,
 so you get fewer extreme values.
 
 The Wilson B factor is not a 'statistic' in the strict sense, merely a
 derived parameter.  I suspect the low value you get has more to do
 with the fact that the resolution is only 3 A, than the fact it's
 twinned.
 
 See here for more mathematically-oriented info:
 
 http://www.ccp4.ac.uk/dist/html/pxmaths/bmg10.html
 
 Cheers
 
 -- Ian
 
 On Thu, May 19, 2011 at 1:45 PM, fulvio saccoccia
 fulvio.saccoc...@uniroma1.it wrote:
  Dear ccp4 users,
 I have a data set arising from a nearly-perfect pseudo-merohedrally
  twinned cystal, diffracting up to 3 A. I solved the structure and ready
  for deposition, but there is still a trouble.
  The Wilson scaling from raw data gave a B of 3A^2.
  Initially, I did not seemed too alarming. But I do not know why I have
  these statistics.
 
  Does anyone know why Wilson scaling falls when treating that kind of
  twinned data? I read that twinned data do not obey twe Wilson statistics
  but I don't know why.
  Here the presentation I read:
 
  http://bstr521.biostr.washington.edu/PDF/Twinning_2007.pdf
 
  Do you know any articles, reviews or book in which this particular
  aspect of  of twinned data is treated in depth, possibly in mathematical
  manner?
 
  Thanks to all
 
  Fulvio Saccoccia, PhD student
  Biochemical Sciences Dept.
  Sapienza University of Rome
 

[ccp4bb] how convert SF to intensities

[Fulvio Saccoccia]

Dear ccp4 users,	I need to generate intensities from a model (.pdb). That is, I think that a correct procedure could be to convert model to structure factor and then obtain intensities squaring the SF.Does anyone know how can I do?Thanks in advanceFulvio Saccoccia

[ccp4bb] Error in ipmosflm

[fulvio saccoccia]

Dear all,
I received this error message from ipmosflm. I started ipmosflm from
terminal, entered the detector (detector marccd) loaded the image and
then press go. Can anyone help me?

Phi values have not been specified on AUTOINDEX keyword, and
oscillation range from image header is zero. Supply phi values on
AUTOINDEX keyword

Thanks to all in advance

Fulvio Saccoccia

[ccp4bb] Is the Rmerge invalidate by twinned data?

[fulvio saccoccia]

Dear all,
I have a data set collected at 3A resolution. I processed the data but I 
had to cut the resolution at 3.6A for the high value of Rmerge (at 3.6A 
it is 0.18). After scaling and MR I realized that my data were twinned. 
This is my question: can I  reprocess all the data set using all the 
reflections up to 3A resolution even if the Rmerge is very high, knowing 
that data are twinned? and also, is the Rmerge invalidate by the twinning?