date:20220531

[ccp4bb] Regarding R factor value

2022-05-31 Thread Abhilasha Thakur

Hello!!

I have 1500 processed PDB files and I need the R factor value for each pdb
files. How I get this R factor value, because it's there initially but,
after processing, some data from PDB is deleted. Manually to get R factor
is not possible.

Please suggest me, how to get this R factor value for the entire PDB ids.



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[ccp4bb] Eiger images and XDS

2022-05-31 Thread Patrick Loll

Hi all,

Apologies for the non-CCP4 question: 

I’m attempting to use XDS to process some data from the Eiger detector at the 
AMX beamline (NSLS-2 17-ID-1). 

To read in the Neggia library, my XDS.INP contains the line 
“LIB=/…path.../dectris-neggia-mac.so"

I’ve successfully used the same dectris-neggia-mac.so library file for years, 
but now I obtain an error message (see error message #1 below), which suggests 
that the library file is now problematic.

For this reason, I grabbed a copy of dectris-neggia.so from 
https://strucbio.biologie.uni-konstanz.de/pub/mac_bin/ (thank you!). Alas, this 
file also gives a similar, but non-identical error (error message #2 below).

In both cases, the error appears to involve an inability to open the neggia 
library. I’ve double-checked that the library files are indeed present, and 
that I’m specifying the correct path.

This error seems to be associated with the current version of XDS, since a data 
set that I could process last year without problem is now giving an error (same 
data, same computer—Intel Mac running OSX 10.14.6).

I’m not sure how to proceed. Any suggestions welcome.

Thanks,

Pat Loll

---
Patrick J. Loll, Ph. D.  (he, him, his)
Professor of Biochemistry & Molecular Biology
Drexel University College of Medicine
Room 10-102 New College Building
245 N. 15th St., Mailstop 497
Philadelphia, PA  19102  USA

(215) 762-7706
pjl...@gmail.com
pj...@drexel.edu



_ERROR MESSAGE #1

master_file=../G7_558_master.h5
 [generic_data_plugin] - INFO - generic_open
   + library  = 
   + template_name= <../G7_558_master.h5>
   + dll_filename = 
   + image_data_filename   = <../G7_558_master.h5>
 [generic_data_plugin] - ERROR - Cannot open Handle: dlopen(/sw/share/xtal/XDS/d
 ectris-neggia-mac.so, 258): no suitable image found.  Did find:
/sw/share/xtal
 /XDS/dectris-neggia-mac.so: file too short
/sw/share/xtal/XDS/dectris-neggia-m
 ac.so: file too short
 generic_getfrm: could not open /sw/share/xtal/XDS/dectris-neggia-mac.so ier=
  -2
 [generic_data_plugin] - INFO - generic_get_header
 [generic_data_plugin] - ERROR - Cannot open Handle
 ?
 generic_getfrm: could not get header from ../G7_558_master.h5 ier=  -1
INFO(1:5)=vendor/major version/minor version/patch/timestamp=   1   0   0   
0
 generic_getfrm: data are from Dectris
 generic_getfrm: expected info_array(2)=0 but got   123456789

 !!! ERROR !!! Unknown image format: ../G7_558_01.h5



_ERROR MESSAGE #2

master_file=../G7_558_master.h5
 [generic_data_plugin] - INFO - generic_open
   + library  = <~/Desktop/dectris-neggia.so>
   + template_name= <../G7_558_master.h5>
   + dll_filename = <~/Desktop/dectris-neggia.so>
   + image_data_filename   = <../G7_558_master.h5>
 [generic_data_plugin] - ERROR - Cannot open Handle: dlopen(~/Desktop/dectris-ne
 ggia.so, 258): image not found
 generic_getfrm: could not open ~/Desktop/dectris-neggia.so ier=  -2
 [generic_data_plugin] - INFO - generic_get_header
 [generic_data_plugin] - ERROR - Cannot open Handle
 ?
 generic_getfrm: could not get header from ../G7_558_master.h5 ier=  -1
INFO(1:5)=vendor/major version/minor version/patch/timestamp=   1   0   0   
0
 generic_getfrm: data are from Dectris
 generic_getfrm: expected info_array(2)=0 but got   123456789

 !!! ERROR !!! Unknown image format: ../G7_558_01.h5


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[ccp4bb] Notebooks for CryoEM and Crystallography

2022-05-31 Thread Andrea Felnolvi

Dear Community,


I published some notebooks in order to help students, PhDs, and all
colleagues to better organize CryoEM and Crystallography data!

After discussing this with colleagues and friends, I found that it is
difficult to get reproducibility of results due to a lack of the right
information, so I propose to you these notebooks to better manage grids
freezing, crystals growth, data collections, processing... (list of
notebooks below!)


I hope these Notebooks will benefit your research and projects as much as
they are already benefiting our Team!

Follow me on my new Twitter profile: *@felnolvi*



*Notebooks for CryoEM:*


Notebook for Freezing Grids: Cryo-EM https://amzn.to/38AOUyY via @amazon

Notebook for Screening Grids: Cryo-Em https://amzn.to/3xgDbxV via @amazon

Notebook for Data Collection: Cryo-EM https://amzn.to/3GtWYOx via @amazon

Notebook for Data Processing: Cryo-EM https://amzn.to/3GDHBmz via @amazon




*Notebooks for Crystallography: *


Notebook for Crystal Growth Evaluation: 24-well Plates X-ray
Crystallography https://amzn.to/3GxWUNF via @amazon

Notebook for Crystal Growth Evaluation: 48-well Plates X-ray
Crystallography https://amzn.to/3t4oFrB via @amazon

Notebook for Freezing Crystals: X-ray Crystallography
https://amzn.to/3PSGRhK via @amazon

Notebook for Data Collection: X-ray Crystallography https://amzn.to/38uvvPY
via @amazon

Notebook for Data Processing: X-ray Crystallography https://amzn.to/3GuokEb
via @amazon



Best regards,

Andrea Felnolvi

Researcher Protein Sciences

Università di Roma



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Re: [ccp4bb] displaying residues (as a surface perhaps) for one component of a p-p-i

2022-05-31 Thread Oganesyan, Vaheh

So does PISA with great detailed info on interface residues available.

VO

From: CCP4 bulletin board  On Behalf Of Jan Dohnalek
Sent: Tuesday, May 31, 2022 2:48 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] displaying residues (as a surface perhaps) for one 
component of a p-p-i

Dear Fred,
CCP4MG has this capability of automated interface display.
When opening a structure you can select from many predefined styles of display. 
My favourite is
Interfaces, then "residues", the surface can be displayed when you ask for PISA 
analysis within CCP4MG and then select a particular interface and display it.
I hope it works for you,

Jan

On Tue, May 31, 2022 at 8:12 AM Fred Vellieux 
mailto:frederic.velli...@lf1.cuni.cz>> wrote:
Dear bb members,

I am quite certain that someone must have needed to do this already. I
looked at publications but no details were given concerning how figures
were prepared.

So here is the problem:

Given a protein protein interface (with the 3D structure of the complex
available) I am looking for a method allowing me to identify and display
the interface forming residues of one of the protein components. Plus a
surface representation of that part, for the 3D structure.

Thanks in advance for any tips.

Regards,

Fred. Vellieux

--
MedChem, 1st F. Medicine, Charles University
BIOCEV, Vestec, Czech Republic

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--
Jan Dohnalek, Ph.D
Institute of Biotechnology
Academy of Sciences of the Czech Republic
Biocev
Prumyslova 595
252 50 Vestec near Prague
Czech Republic
Tel. +420 325 873 758

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Re: [ccp4bb] displaying residues (as a surface perhaps) for one component of a p-p-i

2022-05-31 Thread Jan Dohnalek

Dear Fred,
CCP4MG has this capability of automated interface display.
When opening a structure you can select from many predefined styles of
display. My favourite is
Interfaces, then "residues", the surface can be displayed when you ask for
PISA analysis within CCP4MG and then select a particular interface and
display it.
I hope it works for you,

Jan




On Tue, May 31, 2022 at 8:12 AM Fred Vellieux 
wrote:

> Dear bb members,
>
> I am quite certain that someone must have needed to do this already. I
> looked at publications but no details were given concerning how figures
> were prepared.
>
> So here is the problem:
>
> Given a protein protein interface (with the 3D structure of the complex
> available) I am looking for a method allowing me to identify and display
> the interface forming residues of one of the protein components. Plus a
> surface representation of that part, for the 3D structure.
>
> Thanks in advance for any tips.
>
> Regards,
>
> Fred. Vellieux
>
> --
> MedChem, 1st F. Medicine, Charles University
> BIOCEV, Vestec, Czech Republic
>
> 
>
> 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/
>


-- 
Jan Dohnalek, Ph.D
Institute of Biotechnology
Academy of Sciences of the Czech Republic
Biocev
Prumyslova 595
252 50 Vestec near Prague
Czech Republic

Tel. +420 325 873 758



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[ccp4bb] displaying residues (as a surface perhaps) for one component of a p-p-i

2022-05-31 Thread Fred Vellieux


Dear bb members,

I am quite certain that someone must have needed to do this already. I 
looked at publications but no details were given concerning how figures 
were prepared.


So here is the problem:

Given a protein protein interface (with the 3D structure of the complex 
available) I am looking for a method allowing me to identify and display 
the interface forming residues of one of the protein components. Plus a 
surface representation of that part, for the 3D structure.


Thanks in advance for any tips.

Regards,

Fred. Vellieux

--
MedChem, 1st F. Medicine, Charles University
BIOCEV, Vestec, Czech Republic



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[ccp4bb] Regarding R factor value

[ccp4bb] Eiger images and XDS

[ccp4bb] Notebooks for CryoEM and Crystallography

Re: [ccp4bb] displaying residues (as a surface perhaps) for one component of a p-p-i

Re: [ccp4bb] displaying residues (as a surface perhaps) for one component of a p-p-i

[ccp4bb] displaying residues (as a surface perhaps) for one component of a p-p-i

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