[ccp4bb] A little diversion: New Article On Ethics and Evolution in Science and Life

, Dr. Arka Chakraborty 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

[ccp4bb] Inputs required

Dear Structural Biology community, I am again seeking guidance on a matter. What precedence do we have for cases of academic misconduct where 1. Research belonging to another researcher is misappropriated by another researcher and used for obtaining funding in a local setup (the idea here is no

[ccp4bb] Bringing Up The Next Pivotal Change in Training and Supporting x-ray/cry-oem scientists

useful. Great science requires great environment. Best wishes, Arka Dr. Arka Chakraborty, PhD Senior Scientist To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe

Re: [ccp4bb] AW: [ccp4bb] Lattice Translocation Disorder Correction

, which may be easier to handle. Good luck! Herman *Von:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *Im Auftrag von *Arka Chakraborty *Gesendet:* Mittwoch, 27. August 2014 20:12 *An:* CCP4BB@JISCMAIL.AC.UK *Betreff:* [ccp4bb] Lattice Translocation Disorder Correction Dear

[ccp4bb] Lattice Translocation Disorder Correction

Dear CCPers, Is there an existing script or program for implementing the intensity corrections for trans-located lattices in macromolecular crystals as described in Wang et al (2004)?. Any input or sharing will be immensely helpful. Thanks a lot, Arko -- *Arka Chakraborty* *ibmb (Institut

[ccp4bb] SCRIPT FOR RUNNING MULTIPLE RUNS OF SHELX C DE FOR RIP

solving structures with RIP in low symmetry sg, eg. P1211 at ~2.9 ang resolution (according to I/sigmaI =1.9 in the highest shell, CC half around 0.85) and would kindly share it that will be great. Thanks a lot, Best Regards, Arka Chakraborty -- *Arka Chakraborty* *ibmb (Institut de Biologia

Re: [ccp4bb] SCRIPT FOR RUNNING MULTIPLE RUNS OF SHELX C DE FOR RIP

Dear Dr. Tim Gruene, Thanks a lot for helping me out. My limited knowledge of shell scripting failed me. I will try it out. Best Regards, Arko On Mon, Jul 28, 2014 at 1:49 PM, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: Dear Arka Chakraborty, such a task is best done with shell tools

Re: [ccp4bb] Intergrown crystals

cents, cheers! Arka Chakraborty On Wed, Jan 22, 2014 at 4:57 PM, Enrico Stura est...@cea.fr wrote: Klaus, You say that crystallises readily So you have solved your own problem. You need to control the rate at which the crystals grow. Among all the things you have tried already, you

[ccp4bb] SISA Script Problem

Regards, -- *Arka Chakraborty* *ibmb (Institut de Biologia Molecular de Barcelona)* *BARCELONA, SPAIN*

Re: [ccp4bb] crystals with large solvent content -dehydratation

in the central portions that might have occurred during crystal growth or vitrification.) My humble two cents, Best, Arka Chakraborty On Tue, Oct 29, 2013 at 5:17 PM, Danilo Belviso danilo.belv...@ic.cnr.itwrote: Dear Andre, you could try with the protocol described in the following paper Acta

Re: [ccp4bb] Resolution, R factors and data quality

Diederich and Karplus will be the best persons to comment on that ( as they have already done in the paper :) ) best, Arka Chakraborty p.s. Aimless seems to suggest a resolution limit bases on CC1/2=0.5 criterion ( which I guess is done to be on the safe side- Dr. Phil Evans can explain

Re: [ccp4bb] Resolution, R factors and data quality

Hi all, does this not again bring up the still prevailing adherence to R factors and not a shift to correlation coefficients ( CC1/2 and CC*) ? (as Dr. Phil Evans has indicated).? The way we look at data quality ( by we I mean the end users ) needs to be altered, I guess. best, Arka Chakraborty

Re: [ccp4bb] DNA geometry

Macromolécules Biologiques (UMR7257) CNRS, Aix-Marseille Université Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France Tel: +33(0) 491 82 55 93 Fax: +33(0) 491 26 67 20 mailto:miguel.ortiz-lombar...@afmb.univ-mrs.fr http://w2.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia -- *Arka Chakraborty

Re: [ccp4bb] hi all

, review articles, advices,lectures, power point presentation but more simple . thanks a lot for reading yours Amr -- Oh, suddenly throwing a giraffe into a volcano to make water is crazy? Julian, King of Lemurs -- *ARKA CHAKRABORTY

[ccp4bb]

. getting its crystal is important for my thesis. so need help. -- *ARKA CHAKRABORTY* *CAS in Crystallography and Biophysics* *University of Madras* *Chennai,India*

Re: [ccp4bb] high temp factor in coot!

] *On Behalf Of *Arka Chakraborty *Sent:* Saturday, April 21, 2012 11:14 AM *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* [ccp4bb] high temp factor in coot! ** ** Hi all, I have solved the structure of a decamer dna oligonucleotide. Analysis in CCP4 using baverage shows acceptable(30) avg b factors

[ccp4bb] high temp factor in coot!

like to ask how should this be interpreted? What exactly does the bfactor plot in coot signify? Thanks in advance, ARKO -- *ARKA CHAKRABORTY* *CAS in Crystallography and Biophysics* *University of Madras* *Chennai,India*

Re: [ccp4bb] setting occupancy for disordered water

that the water is not near a symmetry axis - there are often artefact of density near symmetry elements. Tim On 03/07/2012 02:20 PM, arka chakraborty wrote: Hi all, I am having a structure where there is a disordered water .I have fixed one water into the density, yet

[ccp4bb] setting occupancy for disordered water

would like to know how to modify the pdb so that phenix.refine accepts it. Thanks in advance, Regards, ARKO -- *ARKA CHAKRABORTY* *CAS in Crystallography and Biophysics* *University of Madras* *Chennai,India*

Re: [ccp4bb] twin refinement in refmac

was stuck 30% when I used the initial job's output MTZ. Many thanks in advance for your helpful comments. Wolfram Tempel -- *ARKA CHAKRABORTY* *CAS in Crystallography and Biophysics* *University of Madras* *Chennai,India*

Re: [ccp4bb] twin refinement in refmac

Hi all, Thanks for the express replies. Your insights along with the article by Prof. Garib pointed to by Prof. Pavel completes the story for me. Regards, ARKO On Fri, Mar 2, 2012 at 3:09 PM, Steiner, Roberto roberto.stei...@kcl.ac.ukwrote: On 2 Mar 2012, at 08:01, arka chakraborty wrote

Re: [ccp4bb] R-mergd-F

Hi all, Thanks for providing the solution. Regards, ARKO On Wed, Feb 22, 2012 at 10:14 AM, arka chakraborty arko.chakrabort...@gmail.com wrote: Hi all , I will like to know which program we can use to calculate R-mergd-F( not Rmerge) between two data sets, or more generally R factor

[ccp4bb] R-mergd-F

Hi all , I will like to know which program we can use to calculate R-mergd-F( not Rmerge) between two data sets, or more generally R factor between two data sets. Thanks in advance, Regards, ARKO -- *ARKA CHAKRABORTY* *CAS in Crystallography and Biophysics* *University of Madras* *Chennai

Re: [ccp4bb] Best method for weighted averaging of Friedel pairs?

://enigmail.mozdev.org/ iD8DBQFPOUi5UxlJ7aRr7hoRArTUAJ**4uF/sx2CcdWeETz1G+**r19vi7W6SQCgzlAp nSEYj5gbOlOvZ1+KBYRUrdM= =qg83 -END PGP SIGNATURE- -- *ARKA CHAKRABORTY* *CAS in Crystallography and Biophysics* *University of Madras* *Chennai,India*

[ccp4bb] Evidence for hydrogen bonds between adjacent residues

such experimental evidence? I could'nt find any reference. Thanks in advance, Regards, ARKO -- *ARKA CHAKRABORTY* *CAS in Crystallography and Biophysics* *University of Madras* *Chennai,India*

Re: [ccp4bb] Reasoning for Rmeas or Rpim as Cutoff

-- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu *** -- *ARKA CHAKRABORTY* *CAS in Crystallography and Biophysics* *University of Madras* *Chennai,India*

Re: [ccp4bb] Merging data collected at two different wavelength

will help others suggest a suitable phasing scenario. F On Jan 19, 2012, at 12:39 PM, arka chakraborty wrote: Hi all, Thanks a lot for the valuable suggestions.I have tried detwinning it but the detwinning program in CCP4 takes care of only merohedral data( if I am not wrong

Re: [ccp4bb] Merging data collected at two different wavelength

your system. -- *ARKA CHAKRABORTY* *CAS in Crystallography and Biophysics* *University of Madras* *Chennai,India*

Re: [ccp4bb] Merging data collected at two different wavelength

Scientist On 1/19/2012 8:20 AM, arka chakraborty wrote: Hi all, Thanks for providing multiple solutions to my problem. Prof . Tim Gruene and Prof. James Holton provided some nice solutions. However since the data are collected from different crystals, I am not sure whether I can do MAD

[ccp4bb] Merging data collected at two different wavelength

Hi all, I have two datasets, both CO SAD data, one collected at CO anomalous wavelength at synchroton and the other at home source. I wish to combine these two data-sets and use for SAD phasing. Can anyone suggest how this can be done? Regards, ARKO -- *ARKA CHAKRABORTY* *CAS

Re: [ccp4bb] Molecular Transform Superimposed on a Dataset

!!! -- *ARKA CHAKRABORTY* *CAS in Crystallography and Biophysics* *University of Madras* *Chennai,India*

[ccp4bb] MERGING THREE DATASETS

Hi all, I have three datasets with same space-group and identical cell dimensions which I want to merge together. I remember that this was discussed in the blog some time back. Nevertheless, I can use some help! Thanks in advance, ARKO -- *ARKA CHAKRABORTY* *CAS in Crystallography

Re: [ccp4bb] MERGING THREE DATASETS

:15 AM, arka chakraborty wrote: Hi all, I have three datasets with same space-group and identical cell dimensions which I want to merge together. I remember that this was discussed in the blog some time back. Nevertheless, I can use some help! Thanks in advance, ARKO Harry -- Dr

Re: [ccp4bb] MERGING THREE DATASETS

Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH -- *ARKA CHAKRABORTY* *CAS in Crystallography and Biophysics* *University of Madras* *Chennai,India* -- *ARKA CHAKRABORTY* *CAS in Crystallography and Biophysics* *University of Madras* *Chennai,India*

Re: [ccp4bb] Failure in Phaser EP

script reads LABIN F+ = F(+) SIGF+ = SIGF(+) F- = F(-) SIGF- = SIGF(-) Try and replace SIGF+ with either SIG+ or SIGF(+); same for SIGF-. Tim On 12/10/2011 09:33 AM, arka chakraborty wrote: Hi CCPers! I have a strange problem..I am trying to obtain phases for a dna decamer

[ccp4bb] Failure in Phaser EP-and a new problem!

script reads LABIN F+ = F(+) SIGF+ = SIGF(+) F- = F(-) SIGF- = SIGF(-) Try and replace SIGF+ with either SIG+ or SIGF(+); same for SIGF-. Tim On 12/10/2011 09:33 AM, arka chakraborty wrote: Hi CCPers! I have a strange problem..I am trying to obtain phases for a dna decamer

[ccp4bb] Failure in Phaser EP

hrs 0 mins 0.00 secs (0.00 secs) Finished: Sat Dec 10 13:45:46 2011 /pre /html #CCP4I TERMINATION STATUS 1 #CCP4I TERMINATION TIME 10 Dec 2011 13:45:46 #CCP4I MESSAGE Task completed successfully -- *ARKA CHAKRABORTY* *CAS in Crystallography and Biophysics* *University of Madras* *Chennai