Re: [ccp4bb] Unidentified density

2012-02-09 Thread Vandana Kukshal
ral Biology Laboratory > SLS, JNU, > New Delhi-110067 > -- Vandana kukshal

Re: [ccp4bb] Dye for protein affinity measurement

2012-02-08 Thread Vandana Kukshal
t; > > > > > -- > patr...@douglas.co.ukDouglas Instruments Ltd. > Douglas House, East Garston, Hungerford, Berkshire, RG17 7HD, UK > Directors: Peter Baldock, Patrick Shaw Stewart > > http://www.douglas.co.uk > Tel: 44 (0) 148-864-9090US toll-free 1-877-225-2034 > Regd. England 2177994, VAT Reg. GB 480 7371 36 > > -- Vandana kukshal

Re: [ccp4bb] How to add add atoms by Coot

2012-01-03 Thread Vandana Kukshal
reenshot? > > I am looking forward to getting your reply. > > Cheers, > > Dialing > -- Vandana kukshal

Re: [ccp4bb] a PDB tool

2012-01-03 Thread Vandana Kukshal
troduce me a server so that I can convert it to another PDB file starting > from 200 to 300? > > Cheers, > > Dialing > -- Vandana kukshal

Re: [ccp4bb] Hydrophobic interactions

2011-12-15 Thread Vandana Kukshal
n? > > ** ** > > Thanks in advance**** > > ** ** > > Amit > -- Vandana kukshal

Re: [ccp4bb] How can improve diffraction quality

2011-10-18 Thread vandana kukshal
CP4BB@JISCMAIL.AC.UK > Subject: [ccp4bb] How can improve diffraction quality > > Dear ccp4 user > > I am facing one crucial problem regarding diffraction. Actually the size of > my crystal is good enough 0.5mm but it was diffracted only 4 A. > > The conditions of crystallization recipes are 4.5% PEG 1000, 0.1M Tris and > 25mM Na citrate. I really need your suggestions regarding how can i > improve my diffraction quality? > > Your support is highly appreciable. > > Best Regards > > AFSHAN > -- Vandana kukshal

Re: [ccp4bb] data processing problem with ice rings

2011-10-14 Thread vandana kukshal
.7% -15% 0.435 119774 > > Note that I/SIGMA of each resolution shell is <2.5, so how should I do to > process the dataset properly? Any suggestion about this super ice rings? > Thanks! > > Tiantian > > -- > Shanghai Institute of Materia Medica, Chinese Academy of Sciences > Address: Room 101, 646 Songtao Road, Zhangjiang Hi-Tech Park, > Shanghai, 201203 > -- Vandana kukshal

[ccp4bb] mising atoms

2011-08-04 Thread vandana kukshal
chain atom is this wil be correct way to do these calculation. welcome ur valuable sugessions . -- Vandana Kukshal Postdoc Fellow structure biology group international Center For Genetic Engineering and Biotechnolgy India

Re: [ccp4bb] stoichiometry of complex and incubator

2011-08-03 Thread vandana kukshal
t; > -- > Konstantin Korotkov, Ph.D. > > Research Scientist > University of Washington > Department of Biochemistry > Box 357742 > Seattle, WA 98195-7742 > > (206)616-4512 > k...@u.washington.edu > -- -- Vandana Kukshal Postdoc Fellow structure biology group international Center For Genetic Engineering and Biotechnolgy India

Re: [ccp4bb] Influence of symmetry related molecules on a protomer conformation in crystal structures

2011-07-14 Thread vandana kukshal
molecules for a given crystal structure. But I'm looking for some > program/software (for batch) by which I can find out the number > of symmetry related molecules (distance cutoff <= 5A) interacting with > a given chain in a crystal structure. > > Thanking you, > suku >

Re: [ccp4bb] crystallization of a weird protein

2011-05-22 Thread vandana kukshal
t;> The solution is getting clear in the room temperature within 5 mins when I >> set up the trays. >> >> I would like to take any advice. I would appreciate your input. >> >> Best >> >> Min >> > > -- Vandana Kukshal Postdoc Fellow structure biology group international Center For Genetic Engineering and Biotechnolgy India

Re: [ccp4bb] B factor

2011-05-12 Thread vandana kukshal
mit Luthra, Ph.D. > Post-Doctoral Fellow > The Radolf Laboratory > Department of Medicine > University of Connecticut Health Center > [w] http://spirocheteresearch.uchc.edu > -- Vandana Kukshal Postdoc Fellow structure biology group international Center For Genetic Engineering and Biotechnolgy India

Re: [ccp4bb] about the "working solution"

2011-04-25 Thread vandana kukshal
better shape, did I got the point? > > Best wishes > > Xinghua Qin > > -- > Xinghua Qin > Room 4022, Center for Life Sciences, > China Agricultural University, > No.2, Yuan Ming Yuan West Road, Haidian District, > Beijing,China,100193 > Tel: +86-10-62732672 > >

Re: [ccp4bb] how to Collecting Data from Long Unit Cell Axes ?

2011-04-05 Thread vandana kukshal
hello if u are getting merged spot then try to increase detector distance it may work . instead of this u try to reduce delta phi (gonimeter phi angle per frame) default it is 1 degree u can try 0.5, 0.25 degree.

Re: [ccp4bb] metal binds?

2011-03-25 Thread vandana kukshal
I take it to synchrotron which is far away? > > thanks > Careina > > -- Vandana Kukshal Postdoc Fellow structure biology group international Center For Genetic Engineering and Biotechnolgy Aruna Asaf Ali Marg 110 067 New Delhi INDIA

Re: [ccp4bb] determining the domain for overexpression and crystallization

2011-03-17 Thread vandana kukshal
> > to have an idea of the intrinsically disordered regions in the protein, >> transmemebrane regions and disulfide bonds that would certainly help you in >> initiating in the right direction. >> > >> > Best wishes >> > Gauri >> > >>

[ccp4bb] Fwd: [ccp4bb] use of beta-mercaptoethanol in crystallization

2011-03-15 Thread vandana kukshal
d TCEP in ur buffer instead of Beta mercaptoethanol. for one of my crystallization experiment i used 1- 10 mM of Beta mercaptoethanol. -- vandana kukshal CSIR-senior research fellow X ray lab ,MSB division central drug research institute lucknow -- Vandana Kukshal Postdoc Fellow structure b

[ccp4bb]

2010-07-28 Thread Vandana Kukshal
hello sir , recently i have collected one data of 3.0 A of a protein having no sequence homology with any known PDB . but while fold prediction i got 100 %  identical fold with some of the protein . space group of my protein is P622 and showing 6 molecule in a assymetric unit. the homologous

[ccp4bb] covalent bond

2010-07-14 Thread Vandana Kukshal
how to make covalent bond between ligand and protein residue by using CCp4 package

[ccp4bb]

2009-12-09 Thread Vandana Kukshal
i have one Query . after using phenix auto build for building model R factor and R free reduced but B factor is increesed for all the atom .what next i should do to decrease the B factor of atoms.

[ccp4bb]

2009-11-26 Thread Vandana Kukshal
hello  this is not a new question i was searching this in archives but i did'nt get . just send me link for this . i want to link AMP covalently with lysine in my structure (phosphoamide bond)how i will do this  in coot and refmac . in turbo there is option make bond but in this n

[ccp4bb] multi domain protein

2009-10-26 Thread Vandana Kukshal
i have one query. that if we have a multi domain protein structure to solve ,and we know about only one small domain of the protein for MR . other domain structure is not known then how we can proceed. is there any procedure to utilize  phase from the solution with known domain .

[ccp4bb] multi domain protein

2009-10-21 Thread Vandana Kukshal
hello     i  have 3.25 A data of multidomain protein with 4 individual domain .one domains structure is already known . and for others domain 40 % simmilar structure is known . when i am running phaser with one known domain i am getting the solution but after getting solution i am

Re: [ccp4bb] Reducing Agent Tips?

2009-10-09 Thread Vandana Kukshal
you can try glutathione and cysteine  as reducing agent with conc 0.01-0.001M or higher

[ccp4bb]

2009-10-09 Thread Vandana Kukshal
total number of atoms are 5113

[ccp4bb]

2009-10-09 Thread Vandana Kukshal
i am using restrain refmac for refine ment and coot for fiting its resolution range is 116.248 -3.00 number of used reflections 20215 the R factor is 27.7 and R free is 27.0 and if i am doing further restrain refinement with 0.03 geometry weight  R factor is going down to 25.5 but R f

[ccp4bb]

2009-10-09 Thread Vandana Kukshal
hi i am solving one structure in which after refinement i got R factor=27 and R free =27.7 i want to know that is it correct or i did some over refinment the Resolution is 3.0 A