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

sincerely, 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&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP

[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 one

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

suggestions will be very 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.

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

tted hkl file, 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@JIS

[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

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

use for example > tcsh handles jobs differently. > See both scripts enclosed, at least for inspiring. > > Best regards > > Jan > > -- Původní zpráva -- > Od: Arka Chakraborty > Komu: CCP4BB@JISCMAIL.AC.UK > Datum: 28. 7. 2014 14:19:08 > Předmět: Re:

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 wrote: > Dear Arka Chakraborty, > > such a task is best done with shell tools. Assuming y

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

experience 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 d

Re: [ccp4bb] Intergrown crystals

y two cents, cheers! Arka Chakraborty On Wed, Jan 22, 2014 at 4:57 PM, Enrico Stura 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 th

[ccp4bb] SISA Script Problem

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

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

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 wrote: > Dear Andre, > > you could try with the protocol described in the following paper > > Acta Cry

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

ways, Dr 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 explai

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

not as good and I'm not sure if I can justify cutting data. > > > > So my question is, should I cut the data to 1Angstrom or should I keep > the data I have? > > > > Also, taking geometric restraints off during refinement the Rfactors > improve marginally, am

Re: [ccp4bb] DNA geometry

miny, 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* *ibmb (Institut de Biologia Molecular de Barcelona)** **BARCELONA, SPAIN** *

Re: [ccp4bb] hi all

nly throwing a giraffe into a volcano to make water is crazy? > Julian, King of Lemurs > > -- *ARKA CHAKRABORTY* *CAS in Crystallography and Biophysics* *University of Madras* *Chennai,India*

[ccp4bb]

in doesnt aggregate..doesnt loose activity even after boiling at > 80C. > > 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!

> > *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *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

[ccp4bb] high temp factor in coot!

uld 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

nates from 'B' to the second peak. > > Make sure 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

[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

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 wrote: > On 2 Mar 2012, at 08:01, arka chakraborty wrote: > > Hi all, &

Re: [ccp4bb] twin refinement in refmac

stablish twinning versus underestimated symmetry? And what do > I need to know about my free-R? Did refmac assign a new flag? Whereas the > output file's flags are all 1s and 0s, the input file had 0 ... 19. During > the first run, Rfree dropped to <28%. But on a subsequent run, Rfree 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] 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, o

[ccp4bb] Evidence for hydrogen bonds between adjacent residues

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] Best method for weighted averaging of Friedel pairs?

valent_obs(): >>>> >>>> same as methods 2, except that >>>> >>>> sigImean is the larger of either >>>> a) sigImean = 1 / sqrt(w+ + w-) >>>> or >>>> b) sigImean = sqrt( wvariance ) >>>> >>>> where wvariance = >>>> (w+ + w-) / [ (w+ + w-)^2 - (w+^2 + w-^2) ] * >>>> [ w+*(F+ - Imean)^2 + w-*(F- - Imean)^2 ] >>>> >>>> What are the advantages and disadvantages of each method? Should method >>>> 1 be used at all? >>>> >>>> Some example from my dataset: >>>> Reflection (1, 1, 0), space group P3 2 1 >>>> >>>> I+: 23841.50 sigI+: 634.01 I-: 9628.57, sigI-: 264.75 >>>> Method 1: Imean=13815.32, sigImean=186.76 >>>> Method 2: Imean=11738.95, sigIMean=244.31 >>>> Method 3: Imean=11738.95, sigIMean=7106.47 >>>> >>>> Thanks a lot! >>>> >>>> Cheers, >>>> Markus >>>> >>> >>> >> - -- >> - -- >> Dr Tim Gruene >> Institut fuer anorganische Chemie >> Tammannstr. 4 >> D-37077 Goettingen >> >> GPG Key ID = A46BEE1A >> >> -BEGIN PGP SIGNATURE- >> Version: GnuPG v1.4.10 (GNU/Linux) >> Comment: Using GnuPG with Mozilla - http://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] 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] Reasoning for Rmeas or Rpim as Cutoff

e cut-off surface of significance in reciprocal > > space should perhaps be an ellipsoid, not a sphere. I know there are > > several programs for anisotropic scaling, but I'm not aware of any > > that apply anisotropic resolution cutoffs (or even whether this would > > be advisable). > > > > Cheers

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

ng > a little bit more about your system 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

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

have available for any given hkl > index. > > -James Holton > MAD 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 so

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

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

[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 in

Re: [ccp4bb] Molecular Transform Superimposed on a Dataset

> >> > >>> > >>> JPK > >>> > >>> On Fri, Jan 13, 2012 at 11:41 AM, Yuri Pompeu > wrote: > >>>> to echo Tim's question: > >>>> If by pattern you mean the position of the spots on the film, I dont > think they would change based on the complexity of the macromolecule being > studied. As far I know it, the position of the spots are dictated by the > reciprocal lattice points > >>>> (therefore the real crystal lattice) (no?) > >>>> The intensity will, obviously, vary dramatically... > >>>> ps. Very interesting (cool) images James!!! > >>> > >>> > >>> > > > > > > > -- *ARKA CHAKRABORTY* *CAS in Crystallography and Biophysics* *University of Madras* *Chennai,India*

Re: [ccp4bb] MERGING THREE DATASETS

u still have the unmerged files? >>>> In that case just feed them to pointless and redo scala/etc.. >>>> >>>> If you only 3 merged data sets, you will have to use combat to convert >>>> the mtz files into an fake "unmerged" format then put the

Re: [ccp4bb] MERGING THREE DATASETS

If you only 3 merged data sets, you will have to use combat to convert >>> the mtz files into an fake "unmerged" format then put them through >>> pointless/scala to get relative scales and merge them.. >>> >>> Eleanor >>> >>> On 12/21/2

[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 and

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

December 2011 15:40, Tim Gruene wrote: > >> -BEGIN PGP SIGNED MESSAGE- >> Hash: SHA1 >> >> Dear Arko, >> >> your input script reads >> LABIN F+ = F(+) SIGF+ = SIGF(+) F- = F(-) SIGF- = SIGF(-) >> >> Try and replace SIGF+ with

Re: [ccp4bb] Failure in Phaser EP

December 2011 15:40, Tim Gruene wrote: > >> -BEGIN PGP SIGNED MESSAGE- >> Hash: SHA1 >> >> Dear Arko, >> >> your input script reads >> LABIN F+ = F(+) SIGF+ = SIGF(+) F- = F(-) SIGF- = SIGF(-) >> >> Try and replace SIGF+ with

[ccp4bb] Failure in Phaser EP

SIGF(+) or SIG+ -- EXIT STATUS: FAILURE CPU Time: 0 days 0 hrs 0 mins 0.00 secs (0.00 secs) Finished: Sat Dec 10 13:45:46 2011 #CCP4I TERMINATION STATUS 1 #CCP4I TERMINATION TIME 10 Dec 2011 13:45:46 #CCP4I MESSAGE Task completed