Re: [ccp4bb] how to get protein crystal

Hi Amala, In addition to Limbini´s suggestions. 1. You can always do MALS, SLS, Native Page or cross linking experiments to check whether your protein is monodisperse in the solution or not. This is very important step. 2. When you set up crystallization and if you have 40-50% drops precipit

Re: [ccp4bb] R-merge is too high !!

I totally agree with Berry. Please consider Rpim, CC1/2 and I/sigI for cutting the data. Rmerge is old approach as it is data redundancy dependent. Thank you Rajesh ---x With regards Rajesh K. Harijan, Ph.D. Schramm Laboratory Albert Einstein College of Medicine 1300 Morris Park Ave., Bro

Re: [ccp4bb] Open SESAME & Instruct-ERIC Workshop on Remote X-ray Data Collection from European Synchrotrons at the Weizmann Institute of Science on 14-18 May 2018

Dear Rik and Joel, Thank you very much for organizing this great workshop for students. I followed it online from New York. It was nice to see some familiar faces as the speaker. Hoping to see you all in coming future. regards, Rajesh ---x With regards Rajesh K. Harijan, Ph.D. Schramm

Re: [ccp4bb] Open SESAME & Instruct-ERIC Workshop on Remote X-ray Data Collection from European Synchrotrons at the Weizmann Institute of Science on 14-18 May 2018

Dear Rik and Joel, This is really great. Thank you very much. I will follow it from New York. Have a great workshop. regards, Rajesh ---x With regards Rajesh K. Harijan, Ph.D. Schramm Laboratory Albert Einstein College of Medicine 1300 Morris Park Ave., Bronx, NY 10461 Tel: 718.430.2777

Re: [ccp4bb] Unknown density

gt; > > With best regards, > Ivan Shabalin, Ph.D. > Research Scientist, > Department of Molecular Physiology and Biological Physics, > University of Virginia, > 1340 Jefferson Park Avenue > <https://maps.google.com/?q=1340+Jefferson+Park+Avenue&entry=gmail&s

Re: [ccp4bb] Unknown density

d be > cacodylate? Or water, am not sure. > > Cheers, > Hussain > > > On 7 Mar 2018, at 9:19 am, Rajesh Kumar wrote: > > > > Dear All, > > > > Have you had experience with this kind of density? I am wandering what > this could be? > > > > Thank you very much for the help. > > > > -Rajesh > > > > > > > > >

Re: [ccp4bb] COOT problem

Dear Paul, It seems that XQuartz 2.7.7 is working in my macbook and I can run COOT a bit faster. Thank you for the help. -Rajesh On Wed, Feb 28, 2018 at 5:42 AM, Paul Emsley wrote: > On 27/02/2018 21:11, Rajesh Kumar wrote: > >> >> I just had installed new SSD and latest

Re: [ccp4bb] COOT problem

Dear Paul, Thank you very much. Only COOT is giving problem. Other programs work very well. I will change XQuartz to 2.7.8 and see if COOT works. regards, Rajesh On Wed, Feb 28, 2018 at 5:42 AM, Paul Emsley wrote: > On 27/02/2018 21:11, Rajesh Kumar wrote: > >> >> I just

[ccp4bb] COOT problem

Dear All, I just had installed new SSD and latest macOS High Sierra 10.13.3 into my macbook pro. It seems my macbook is much faster but running COOT is a bit problem. When I open COOT, screen becomes gray for a second and then it opens. When I try to move from one residue to next, it does not mo

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Re: [ccp4bb] weird diffraction pattern

Hi Chenjun, Few suggestions from my side. Process the data with XDS and look into acentric intensity distribution (it indicates any twinning possibility). Run XTRIAGE and SFCHECK to understand any twinning or pseudo translation possibilities. Twinning can confuse the program and suggest you smalle

Re: [ccp4bb] Ramachandran oultliers increase upon restrained refinement

Dear Meytal, PHENIX-REFINE has an option for Ramachandran outlier refine. If you check this on, it will do the work. But after this refinement, you must check every residues to make sure residues are in the density. Thank you Rajesh ---x With regards Rajesh K. Harijan, Ph.D. Schramm La

Re: [ccp4bb] R/Rfree values

Dear Rohit, Try to run sfcheck or XTRIAGE and check, if your data is fine. Check for twinning or pseudo-translation. You can send your processed mtz to me and I would be more than happy to help you. You can look into cumulative intensity distribution (if you processed with XDS, it will be in CORR

Re: [ccp4bb] CNS installation

Hello Ben, Thanks a lot. After your mail, I looked up your suggestions in old thread on cnsbb. Installed gfortran and built as you suggested. It worked very well. Thanks Yogi > Date: Sat, 28 Jul 2012 17:18:09 -0400 > From: b...@hkl.hms.harvard.edu > Subject: Re: [ccp4bb] CNS installation >

Re: [ccp4bb] CNS installation

Hello Ed, I have is 32 bit pc, do I still need ia32-libs. When I searched "synaptic package manager" for ia32-libs I dont see any thing to install. Date: Sat, 28 Jul 2012 16:39:07 -0400 From: epozh...@umaryland.edu Subject: Re: [ccp4bb] CNS installation To: CCP4BB@JISCMAIL.AC.UK Rajesh, this

Re: [ccp4bb] CNS installation

cns_solve_env'. The source command has to be run every time a new terminal window is opened to set the paths to the executables. Cheers, Roger Rowlett On 07/28/2012 12:40 PM, Rajesh Kumar wrote: Dear

[ccp4bb] CNS installation

Dear All, I am trying to install CNS in ubuntu 10.04 LTS. Even after reading all the advice on CNS installation on CCP4bb, I have failed to get it working. Both in bash and tcsh, cns_web works but cns_solve gives error "command not found". yogesha@yogesha-laptop:~/work$ echo $CNS_SOLVE /hom

[ccp4bb] linking PLP-Lys

Dear All, My friend needs a help.What is the best way to connect Lys to PLP with covalent bond.I am sure there are many ways do it. My friend would appreciate if you could simplify and explain this so that he could learn it without difficulties. Also I could learn I appreciate your time and hel

Re: [ccp4bb] Improvement of diffraction quality

Pradeep, I have similar problem-needles. Seeding/MMS is one method most would suggest. I got good crystals but they appeared fast and they never diffracted (not a single spot while needle diffract 4.5A but hard to pick them as they are very thin) but it might work for you. You could try diff

Re: [ccp4bb] zinc with HEPES/seeding

Thanks. I will try. Rajesh Date: Fri, 11 May 2012 12:38:20 -0500 From: j-kell...@fsm.northwestern.edu Subject: Re: [ccp4bb] zinc with HEPES/seeding To: CCP4BB@JISCMAIL.AC.UK mitegen loops might help, particularly micromesh... JPK On Fri, May 11, 2012 at 12:35 PM, Rajesh Kumar wrote: Dear

Re: [ccp4bb] zinc with HEPES/seeding

o: ccp4...@hotmail.com > > Rajesh, > 10mM zinc seems a bit too high. I normally used it at <50uM conc. > ray > > On Fri, May 11, 2012 at 12:26 PM, Rajesh Kumar wrote: > > Dear All, > > > > This question sounds simple but I dont know the answer. > >

Re: [ccp4bb] zinc with HEPES

> > Rajesh, > 10mM zinc seems a bit too high. I normally used it at <50uM conc. > ray > > On Fri, May 11, 2012 at 12:26 PM, Rajesh Kumar wrote: > > Dear All, > > > > This question sounds simple but I dont know the answer. > > I was preparing a 24 well crys

Re: [ccp4bb] zinc with HEPES

If there is no cure , then fine.pH may not be the answer as it doesn't Happen with TRIS buffer pH 7.6.Thanks to every oneRajesh Date: Fri, 11 May 2012 12:35:45 -0400 From: dj...@cornell.edu Subject: Re: [ccp4bb] zinc with HEPES To: CCP4BB@JISCMAIL.AC.UK There is no cu

Re: [ccp4bb] zinc with HEPES

concentrated HEPES. Also it depends what else is in your cocktail. JPK On Fri, May 11, 2012 at 11:26 AM, Rajesh Kumar wrote: Dear All, This question sounds simple but I dont know the answer.I was preparing a 24 well crystal screen. When I try to use 10 mM ZnSO4 with HEPES (pH 7.6) buffer it

[ccp4bb] zinc with HEPES

Dear All, This question sounds simple but I dont know the answer.I was preparing a 24 well crystal screen. When I try to use 10 mM ZnSO4 with HEPES (pH 7.6) buffer it precipitates. I tried both ZnCl2 and Zn acetate the effect is same. I dont know why this Zn in not compatible with HEPES.Could

Re: [ccp4bb] NCS on ligands

question is whether they should? Can't you try both options to see which one works best in your specific case? Pavel On Sat, May 5, 2012 at 6:02 AM, Rajesh Kumar wrote: Dear all, Is ligands and metals could also be NCS restrained during the refinement. I have Na+ and SO4 in my model

[ccp4bb] NCS on ligands

Dear all, Is ligands and metals could also be NCS restrained during the refinement. I have Na+ and SO4 in my model which are NCS related. Thanks for the help Warm regards Rajesh Sent from my iPhone

Re: [ccp4bb] effective iodide conc. for SAD data

t; derivatization time <10 min. >> >> Good luck, >> >> Florian >> >> >> >> >> Am 03.05.12 15:51, schrieb Rajesh Kumar: >>> Dear All, >>> >>> I have very thin crystals but diffracting

[ccp4bb] effective iodide conc. for SAD data

Dear All, I have very thin crystals but diffracting. I was not able to handle them easily for iodide soak. I always lost the crystals during manipulation and other big crystals obtained after seeding doesn't even give any diffraction. I tried for co-crystallizing with NaI. The crystals appear o

Re: [ccp4bb] finding NCS in water

for information about which waters obey NCS although the output is not standard nomenclature.. Alternately just use the coot facility to fit chain A over chain B and see which waters overlap each other in the Copy and original..(Remember to turn symmetry ON) Eleanor On 22 April 2012 16:33, Rajesh

[ccp4bb] finding NCS in water

Dear All, I would like to learn how to relate water molecules by NCS and refine them. When I googled, CCP4 utilities sortwater and watncs showed up. I also found "Applying NCS to a high resolution structure , including water molecules in NCS restraints" on autobuster examples. Some how I got er

Re: [ccp4bb] zinc fingre

Dear All, Thanks everyone for the suggestions. I did go to library to look up some chapters in books which gave me lot of information about conserved zinc finger domain. My protein has Cx4C and Cx3C and with very large spacing, so I suspect it could be zinc finger like protein (though no softw

Re: [ccp4bb] zinc fingre

Of Rajesh kumar Sent: Tuesday, April 03, 2012 10:07 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] zinc fingre Dear All, I am trying to crystallize a protein, so far I got no diffraction though I have large crystals. It has few cystines and a histidine near by at N-terminal. I dont

[ccp4bb] zinc fingre

Dear All, I am trying to crystallize a protein, so far I got no diffraction though I have large crystals.It has few cystines and a histidine near by at N-terminal. I dont have much literature on biochemistry of this protein available in pubmed (5 papers only).Is there a way if I could check usi

Re: [ccp4bb] refining phosphorylated residues

Otago Pouaka Poutapeta 56 Otepoti 9054 Aotearoa Ph / Waea +64 3 4797293 Fax / Waeawhakaahua +64 3 4797034 From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Rajesh kumar Sent: Thursday, 22 March 2012 12:00 p.m. To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] ref

Re: [ccp4bb] refining phosphorylated residues

www.researcherid.com/rid/C-2803-2008 > Pukeka Matua > Te Kura Taiwhanga Putaiao > Te Whare Wananga o Otago > Pouaka Poutapeta 56 Otepoti 9054 > Aotearoa > > Ph / Waea +64 3 4797293 > Fax / Waeawhakaahua +64 3 4797034 > > From: CCP4 bulletin board [

[ccp4bb] refining phosphorylated residues

Dear All, I have a structure of a protein and peptide complex, in which peptide has modified residues ( phosphoserine and phosphothreonine). During refinement these both gets disconnected with adjacent residues and its hard to connect them.Could you please suggest me some options. ThanksRajesh

[ccp4bb] microseeding

Dear All, I have few papers in hand which explain me about microseeding, matrix microseeding, and cross seeding.I have also read few earlier threads and some more literature in google.Using Phoenix robot, I did a matrix micro-seeding and matrix cross seeding. I have few hits with this.In 96 we

Re: [ccp4bb] MTZ file

This sentence in my previous posting may or may not be correct technically- May be make sure about this as it says reindex because only you need to rescale it like in HKL2000. It its wrong I am Sorry in advance. Date: Wed, 14 Mar 2012 07:43:15 -0500 From: ccp4...@hotmail.com Subject: Re: [ccp4

Re: [ccp4bb] MTZ file

Mahesh, You should always use output_1.mtz for refinement. Dont use output_2. mtz for further refinement instead use some ccp4 utilities to change output_1.mtz (C222) to say output1_mod.mtz (C2221). This will become your master file for all further refinement. What ever remaining 2.mtz, 3.mt

Re: [ccp4bb] recombinant enterokinase

http://www.neb.com/nebecomm/products/productP8070.asp Date: Mon, 12 Mar 2012 09:38:22 -0400 From: elias.fernan...@utk.edu Subject: [ccp4bb] recombinant enterokinase To: CCP4BB@JISCMAIL.AC.UK Dear all,Would anyone know of a source for recombinant enterokinase? Best,Elias

Re: [ccp4bb] sudden drop in R/Rfree

Dear All, Thanks for all the suggestion. Data is anisotropic. Since anisotropic correction with the UCLA server didnt give any good Molprobity scores and didnt reduce the R/Rfree at 2.1A, I am using ~3.3A data for further refinement. Using Tom's suggestion of target restrains reduced the gap b

Re: [ccp4bb] sudden drop in R/Rfree

Womack (Global Phasing) HTH, Regina From: Rajesh kumar To: CCP4BB@JISCMAIL.AC.UK Sent: Friday, March 2, 2012 10:54 AM Subject: [ccp4bb] sudden drop in R/Rfree Dear All, I have a 3.3 A data for a protein whose SG is P6522. Model used was wild type structure of same protein

[ccp4bb] sudden drop in R/Rfree

Dear All, I have a 3.3 A data for a protein whose SG is P6522. Model used was wild type structure of same protein at 2.3 A. After molecular replacement, first three rounds of refinement the R/Rf was 26/32.8, 27.1/31.72 % and 7.35/30.88 % respectively.In the fourth round I refined with TLS a

Re: [ccp4bb] coot with probe and reduce

Dear B,Yes its working. Thanks for your help. ThanksYogi > Date: Sun, 26 Feb 2012 22:49:08 +0100 > From: bernh...@chem.gla.ac.uk > Subject: Re: [ccp4bb] coot with probe and reduce > To: CCP4BB@JISCMAIL.AC.UK > > Dear Raj, > > please follow exactly what is written in the FAQ > http://www.ysbl.

[ccp4bb] coot with probe and reduce

Dear All, I am trying to use probe and reduce with coot new version. I tried as suggested in coot FAQ page- 1. renamed probe.exe and reduce.exe were put in C:\WinCoot\bin- didnt show validate/probe clashes as active n coot 2. made changes to group settings.py in wincoot/share/coot/python folder

Re: [ccp4bb] His Purification

May be this one helps " The current study presents the design, engineering, and characterization of two E. coli BL21(DE3) derivatives, NiCo21(DE3) and NiCo22(DE3), which express the endogenous proteins SlyD, Can, ArnA, and (optionally) AceE fused at their C terminus to a chitin binding dom

Re: [ccp4bb] bias removal server

building pretty much the same can be achieved nowadays (pus benefit of a model), the ARP/wARP server in Hamburg is a well-working and up-to-date alternative. BR From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Rajesh kumar Sent: Tuesday, December 20, 2011 10:19 AM To: CCP4BB

[ccp4bb] bias removal server

Dear All, Any of you know if the Bias removal server at http://tuna.tamu.edu/ works?My friend says that 'may be the server doesn't exist' as he never heard back from them about login info. ThanksRajesh

Re: [ccp4bb] adxv-SOLVED WITH FONTS

Dear Ian, I installed the fonts from the link http://www.scripps.edu/~arvai/adxv.html.Everything works now on my linux system.There was no need of extra fonts on my xming (I had already installed extra fonts from the link you have suggested) and it works just fine. Thanks to your time to help.

Re: [ccp4bb] adxv

x-machine. > > Cheers, > Tim > > On 11/22/2011 02:27 PM, Rajesh kumar wrote: > > > > I don't know if I need that installed on my windows computer terminal.On > > the server also I could run adxv. Thought of using other ccp4 utilities. > > Thanks for

Re: [ccp4bb] help with the structures

w resolution and > anisotropic. Maybe this is the best you can do.. > > I think I would make sure the apo structure is as good as it can be, > then fit that to the 3.3A data set, and only use that 3.3A data to > deduce whatever features differ from the APO structure. > >

Re: [ccp4bb] adxv

t: Re: [ccp4bb] adxv > To: CCP4BB@JISCMAIL.AC.UK > > yum install lesstif ? > > but wouldn't the motif stuff be required for the X-server, i.e. your > terminal, not for the > server running adxv? > > Rajesh kumar wrote: > > Dear Mark, > > > >

Re: [ccp4bb] adxv

> ftp://ftp.parallelgeo.com/SPW_Products/Linux/Current_Release/ReadMe_for_recent_Linux_distributions.txt > [2] http://sbgrid.org/news/newsletters/2009/06 (search for the string "adxv") > > > On 20 November 2011 19:45, Rajesh kumar wrote: > > > > Dear Tim, > > Thanks. Your suggestion

Re: [ccp4bb] adxv

ectory' is not part of your bash's PATH variable. As you login, type > export PATH=$PATH:/full/path/to/your/work/adxv > then run adxv. > > I am not sure whether this will prevent the last error to occur, but > since you can run other graphical programs there is a fai

[ccp4bb] adxv

Dear All, I have connected to unix server of the lab through ssh/xming/x11. I can run open phenix and CCP4 GUI. I am trying to adxv to see images but I am unable to do so. I have got two files adxv and adxv.i686FC2 sitting in my work/adxv/. when i run adxv in bash bash: adxv: command not f

[ccp4bb] help with the structures

Dear All, We have an anisotropic dataset of 3.3 A and it was solved (not by me) with P6522 with R/freeR 29.1/37.3. I got the corrected mtz file by plugging in the .HKL (P6122) file to anisotropy diffraction server at 2.04 A. I reindexed this p6122 to p6522 and extended the resolution a

Re: [ccp4bb] pointless error-summary

Thanks to Harry Powell, Phil Evans, De-Feng Li for suggestions and special thanks to Charles Ballard looking in to my data. The summary is Harry Powell and Phil Evans-Pointless needs update as newer version is up to version 1.6.8 - the latest copy is at ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/po

[ccp4bb] pointless error

Dear all, mtzdump shows my space group as 'C 2 2 21' (number 20) pointless gives error "Space group is not in library". part of the log file is following. I appreciate all the help. Thanks Raj ** *

Re: [ccp4bb] Installation of CCP4 under Windows 7

I have slightly different problem. I have windows 7 Enterprise. I don't get any shortcuts on my desktop after installation.I work with admin account. If I try to execute /ccp4-6.2.0/ccp4i/bin/ccp4i.tcl I get the following error. please see attachment.I installed " ActiveTcl8.4.19.5.294332-win32

Re: [ccp4bb] changing names of many files

760D6a0***.img do mv $i ${i%760D6a0***}760D6a0_${i#760D6a0} done Rajesh On Wednesday 12 March 2008 02:32, Raja Dey wrote: > CCP4BB@jiscmail.ac.uk -- Rajesh Kumar Singh, PhD Institut fur Biochemie Universitat Greifswald Fe

[ccp4bb] Open position at the Institute for Biochemistry (Advt. Nr. 07/B51)

/wissenschaftliches-personal/institut-fuer-biochemie-nr-07b51.html As mentioned in the advertisment, the deadline for applications is 15.10.2007. With best regards Rajesh Kumar Singh -- Rajesh Kumar Singh, PhD Institut fur Biochemie Universitat Greifswald Felix-Hausdorff-Str. 4 D-17489 Greifswald

Re: [ccp4bb] "B" in B-factor

yeah, atomic displacement parameter is abbreviated as ADP. I wanted to know if there is some specific term for "B" in B factor as "R" refers to Reliability in R-factor. Rajesh On Wednesday 24 January 2007 14:52, evrard wrote: > Rajesh Kumar Singh wrote: > > M

[ccp4bb] "B" in B-factor

May be too trivial, I was just wondering what "B" stands for in the term "B-factor". Thanks Rajesh -- Rajesh Kumar Singh Institut fur Biochemie Universitat Greifswald Felix-Hausdorff-Str. 4 D-17489 Greifswald Germany E.Mail: [EMAIL PROTECTED] Phone: +49-3834- 86 4392