Re: [ccp4bb] Problem with ligand identification

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

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

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] Citing Combat

Dear ccp4i community, what is the right way to cite Combat, is there any paper about it? Thanks in advance Fulvio To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-

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

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 t

Re: [ccp4bb] cavities in protein structures

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

[ccp4bb] E.coli strain, knock-out for SDH/FR

question is off-topic but I am confident about your kindness. Cheers Fulvio -- Fulvio Saccoccia, PhD Institute of Cell Biology and Neurobiology (IBCN) Consiglio Nazionale delle Ricerche Via E. Ramarini, 32 - 00015 Monterotondo Scalo Roma (RM) tel.+390690091244

[ccp4bb] advances in multisubunit membrane protein

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 pr

[ccp4bb] Fwd: [ccp4bb] XDS INP

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, luzu

Re: [ccp4bb] how to recover my data

ore 16:18, Harry Powell 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 att

Re: [ccp4bb] how to recover my data

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 differe

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

Inizio messaggio inoltrato: > Da: "Fulvio Saccoccia, Sapienza" > Oggetto: Re: [ccp4bb] how to recover my data > Data: 05 marzo 2015 13:48:34 CET > A: Smith Lee > > Dear Smith, >It is curious; I am not sure about what I am going to suggest since I &

[ccp4bb] R factor from merged data

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.

> > > > > > > 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 asp

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

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

[ccp4bb] uncertainites associated with intensities from twinned crystals

. 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

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

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 sm

[ccp4bb] pseudotranslation issues

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 Fa

[ccp4bb] how to deal 3 twin-related domains

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

Re: [ccp4bb] Self rotation function interpretation

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

Re: [ccp4bb] CNS installation

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

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

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] Rif: [ccp4bb] indexing(?) question in P21

Dear Wolfram, your a and c axes are very similar; and your beta is near 120°: It sounds me a twinned crystal. Did you perform a twinning analysis in P21 space group? Can you post any refined parametrs (R, Rfree, Resolution, Wilson ADP)?-CCP4 bulletin board ha scritto: -Per: CCP4BB@JISCM

Re: [ccp4bb] error message in scalepack

Solved. I run scalepack under C shell (csh) and seems it works fine. Fulvio Il giorno mar, 18/10/2011 alle 12.18 +0200, fulvio saccoccia ha scritto: > Dear ccp4bber, > I received the following message, during a run with scaling: > > forrtl: error (72): floating overflow > >

[ccp4bb] error message in scalepack

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

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

atically-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 > wrote: > > Dear ccp4 users, > >I have a data set arising from a nearly-perfect pseudo-merohedrall

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

> 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 > wrote: > > Dear ccp4 users, > >I have a data set arising

[ccp4bb] Twinning, Wilson scaling and B factor

u/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

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

Re: [ccp4bb] GLRF and TF under Ubuntu: not part of ccp4 package

F and TF program under Ubuntu (10.04 and 10.10) but it > > did not run. I received the following message: permission denied. So I > > changed the permissions to glrf and received: invalid exec format Wrong > > Architecture. > > > > Does anyone know what to do? > > > > Thanks in advance > > > > Fulvio Saccoccia > >

[ccp4bb] Error in ipmosflm

upply phi values on AUTOINDEX keyword" Thanks to all in advance Fulvio Saccoccia

[ccp4bb] Is the Rmerge invalidate by twinned data?

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