Re: [ccp4bb] CCP4i Reflection DataUtilities: Convert to/modify/extend MTZ does not work

I face exactly the same problem. any advice in this regard would be greatful. S.Jayashankar Research Student Institute for Biophysical Chemistry Hannover Medical School Germany. On Wed, Feb 29, 2012 at 2:58 AM, Dialing Pretty wrote: > > Dear All, > > I want to use "CCP4i Reflection DataUtiliti

[ccp4bb] Clustal omega

Dear All, A bit offtopic question, Does any body know how can I get the PIR output of the aligned sequence from clustal omega. I have a full length protein solved, to give weightage during comparitive modelling, I use domains of the same/similar protein solved before. I expect an alignment someth

Re: [ccp4bb] Clustal omega

, Tim Gruene wrote: > -BEGIN PGP SIGNED MESSAGE- > Hash: SHA1 > > Dear S. Jayashankar, > > have you tried the clustalw options '-convert -output=PIR'? This should > result in a pir-formatted output file. > > Tim > > On 03/27/12 10:18, Jayashankar

Re: [ccp4bb] Clustal omega

t; > Dear Jayashankar, > > sorry, you did explain this in your model and I flipped clustalo with > clustalw. Even though when I used the option '-convert', clustalw does > not re-align the input but simply converts it, so in case it can read > the clustalo output, this should d

Re: [ccp4bb] salt or protein...

s! > > Best, > Herman > > -- > *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of * > Jayashankar > *Sent:* Sunday, May 29, 2011 11:18 PM > *To:* CCP4BB@JISCMAIL.AC.UK > *Subject:* [ccp4bb] salt or protein... > > Dear Friends , > > I need to kn

[ccp4bb] citric acid + 40%MPD (pHI -H1 condition)

Dear friends, Should I be happy if i get my crystals with one of the condition with a commercial kit containing citric acid and 40%MPD+ protein in(hepes+MgCl2)+ADP+VO3 any insights ... S.Jayashankar Research Student Institute for Biophysical Chemistry Hannover Medical School Germany.

Re: [ccp4bb] problem with ARP/wARP module in CCP4

Dear Victor, I faced the same problem and got the same error for arpwarp solvent module, and I have even communicated you through my system admin for arp warp classic module giving some trouble. sincerely S.Jayashankar Research Student Institute for Biophysical Chemistry Hannover Medical School

Re: [ccp4bb] Biobar 2.0.1

Very much appreciable. thanks S.Jayashankar Research Student Institute for Biophysical Chemistry Hannover Medical School Germany. On Fri, Apr 23, 2010 at 4:50 PM, Jawahar Swaminathan wrote: > Biobar version 2.0.1 is now available. > > Biobar is a powerful browsing and searching toolbar develop

[ccp4bb] spring constant

Dear members, What is the maximum spring constant a protein can have as such. Is it possible to calculate how stiff a protein molecule is. What is the correlation between the diffusion coefficient of a protein and its surface tension during protein-protein interactions? -- S.Jayashankar Researc

[ccp4bb] CCP4i and modeller integration

Dear friends and scientists, I want to ask about for an integration of modeller in the ccp4i interface. The interface in ccp4i is designed for modeller Version 6.2, we have by now modeller 9.2 , which is a lot different. Nevertheless I tried to enter the necessary data in ccp4i. I could not try

Re: [ccp4bb] B-factors, H/D exchange and protein flexibility

Dear Brad, the flexibility, that is how far a protein is stabilized with cold and heat denaturation of a protein, this inturn depends on 1.solvation enthalpy of nonpolar moieties(need more energy,so there needs to be some randomness) 2.shift in temparature due to the enthalpy associated with tra

Re: [ccp4bb] Optimization of needle crystals?

hi Ngo, Reduce such showering by increasing the reservoir volume, or by increasing the protein concentration. On Wed, Apr 16, 2008 at 4:08 PM, Van Den Berg, Bert < [EMAIL PROTECTED]> wrote: > Hi Ngo, > > your needles actually look like very thin plates. They seem promising to > me. From appeara

[ccp4bb] problem in coot

Dear ccp4bb and Paul emsley, I have a problem in coot, I could clearly see the density for some small molecule that was present in the sample buffer. when I generate .cif from monomer sketch library from ccp4 and use same .cif in coot for real space refinement, the small molecule goes back and si

[ccp4bb] Right terminal residues for constructs.

Dear friends and scientists, (A pre-Structural biological question.) I Have a multidomain protein , I know the domain boundaries, But am still not that rational to what residues a construct should start or end? But I have learned from people that changing one residue changes the fate of the cons

[ccp4bb] Fwd: Right terminal residues for constructs.

-- Forwarded message -- From: Jayashankar <[EMAIL PROTECTED]> Date: Tue, May 20, 2008 at 7:34 PM Subject: Right terminal residues for constructs. To: CCP4BB@jiscmail.ac.uk Dear friends and scientists, (A pre-Structural biological question.) I Have a multidomain protein ,

[ccp4bb] Article needed

*Dear Friends,* I am a research student , looking for an article mentioned below. I kindly request for the reprint or online copy of, * * *J. Appl. Cryst.* (1971). *4*, 333[ doi:10.1107/S0021889871007131] Apparatus for growth of crystals for X-ra

Re: [ccp4bb] Article needed

I have received the article, thanks for all. On Wed, Jun 11, 2008 at 3:11 PM, bharath SR <[EMAIL PROTECTED]> wrote: > attached ,... > > > > On Wed, Jun 11, 2008 at 4:48 PM, Jayashankar <[EMAIL PROTECTED]> > wrote: > >> *Dear Friends,* >> >&g

[ccp4bb] need test data set

Dear scientists and friends, I am much interested to learn things by my own. There are many guys out there as me. To fulfill the thirst and quest for more crystallographic practical knowledge, I need test data set for SAD,MAD,SIR,MIR,SIRAS,MIRAS. And I want to remind kevin and Martyn that they t

[ccp4bb] is it Ok to freeze

Dear Scientists and Friends, I am not sure, whether organic crystals need to be in cryo stream necessarily during data collection from an in house xray machine . How most of the organic crystals have been solved mostly? -- S.Jayashankar (A bit confused new generation researcher). Research

Re: [ccp4bb] Off-topic: Headhunters

Dear Bill, A person started his career as a Laboratory Technician and raised to a level of Associate Professor(and still dont know the next highest level) , this transitions in Sanskrit called as avatars (every state serve its purpose of its existence) , there is always good reasons for an indiv

[ccp4bb] Parameter MAXSAVE exceeded

Dear scientists and friends, When I try to convert a .cv file to .mtz by f2mtz I got the following error,what it means ans what should I do to get rid of it. ''Parameter MAXSAVE exceeded'' -- S.Jayashankar Research Student Institute for Biophysical Chemistry Hannover Medical School Germany

Re: [ccp4bb] Parameter MAXSAVE exceeded

oard [mailto:[EMAIL PROTECTED] On Behalf Of Ezra > Peisach > Sent: Thursday, July 03, 2008 11:28 AM > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] Parameter MAXSAVE exceeded > > I do not know off hand what a .cv file is - unless it is a cns/xplor > reflection file. Instead

Re: [ccp4bb] Using the BB for file sharing

Dear All, Scott has good point.And the requesting party should reply to these kind mails very quickly ,so as to avoid of receiving huge number of same paper from different persons,(such a basic sense is important to avoid of wasting others time.) thanks. (still am confused about how far or how m

Re: [ccp4bb] creat 3D small molecules

DearAriel, http://davapc1.bioch.dundee.ac.uk/prodrg/ try this and see, On Tue, Jul 22, 2008 at 9:42 PM, Ariel Talavera <[EMAIL PROTECTED]> wrote: > > Hi all, > > I need to create the coordinates of a small molecule with no structure yet. > Could any one tell me what program can I use to build

[ccp4bb] comparing interfaces

Dear Friends and scientists, I know An inhibitor(Say A) that acts as an anti destabilizing agent for a homotetrameric protein. that is the disturbance in the tetramer leads to aggregation of the protein ,this inhibitor A stabilizes this disturbancethis is one story. the other, recently we wer

[ccp4bb] jokes out of science for science community

Dear Scientists, Sorry if the mail intervene you scientific thinkings. Can anybody Share a wonderful site to share jokes on science. moreover it would be nice if we have a tool to create such jokes. (And is there any ready made photoshop kind of thing to create a cartoon character for the jokes)

[ccp4bb] fink problem

Dear Computational crystallographers and developers, I still struggle with my mac book pro, to install crystallographic softwares, The fink list has cctbx, I want to know whether this cums in unstable or stable branch of fink distribution. And i have hard time in updating my fink with fink selfup

[ccp4bb] Crystallogrphy today

Dear friends and crystallographers, During One of my lab meeting , I told twinning in crystals are ok, because ccp4's recent releases just need the keyword TWIN to solve them, As a new generation research student, I am now confused, is that I need to learn and understand all programs(so many...b

Re: [ccp4bb] Crystallogrphy today

Dear Jacob, You are absolutely right, I was very much excited and clear when I read Randy J.Read 's paper Improved Fourier coefficients for maps using phases from partial structures with errors. its a must read paper for all students like me. thanks S.Jayashankar Research Student Institute for

Re: [ccp4bb] Definition of salt bridge

Dear Fransico, *Salt bridges are close range electrostatic interaction which depend on conformer population. *S.Jayashankar Research Student Institute for Biophysical Chemistry Hannover Medical School Germany. On Thu, Oct 16, 2008 at 8:21 AM, Chavas Leo <[EMAIL PROTECTED]> wrote: > Dear Franci

Re: [ccp4bb] Definition of salt bridge

(or ion pairs) can be long-range (up to 7-8 Ang). They obey > > Coulomb's law. > > In contrast, H-bonds are short-range and are further anisotropic. > > > > For those with general interest in electrostatics, I suggest to go back > > to the > > 1978 paper of

[ccp4bb] terminal window

Dear Friends, I recently followed William Scott page and followed his advice to install fink and crystallographic softwares... But out of my curiosity i once tried to install arpwarp as per the instructions and it was done successfully, no problem, but whenever i open a new terminal window,i see

[ccp4bb] is it possible or is it existing ?

Dear ccp4bb caretakers, I am very young for the ccp4bb thread(2007 jan-my thread date of birth). Is is possible to compile very important issues in a hyperlinked style of the important problems,discussions and queries with in ccp4 threads. for example when am reading a query of 2006 regarding so

[ccp4bb] fink:coot problem

t code 1 Failed: can't install package dbus-1.2.3-6 jayashankar-selvadurais-macbook-pro-2:~ Jai$ kindly help me in this regard thanks S.Jayashankar Research Student Institute for Biophysical Chemistry Hannover Medical School Germany.

Re: [ccp4bb] [SPAM:#] [ccp4bb] O/T: can a protein which dimerizes in solution crystallize as a monomer?

Here we are dealing with two different state of chemistry, solid state and solution state, If one of the minima in solid state resembles the biological state minimum, then there is a possiblw way to clearly define the biology and its significant interaction of that particular 'mer' of a protein, o

Re: [ccp4bb] COOT Problem

since its a same coot problem, i have one more, i am using mac 10.5 leopord osx the thing is, i dont get any pop upped table even after i do a translate and do a real space refinement . is it a bug or is it a problem in setups of other supportive libraries S.Jayashankar Research Student I

Re: [ccp4bb] COOT Problem

Yes CCP4I, works better, S.Jayashankar Research Student Institute for Biophysical Chemistry Hannover Medical School Germany. On Sat, Dec 13, 2008 at 6:43 AM, William Scott wrote: > Does ccp4i work? > > > > On Thu, December 11, 2008 8:06 pm, Jayashankar wrote: > > since it

Re: [ccp4bb] COOT Problem

Paul and William, since we are end users, we have to depend on big heads like you. and i believe that things will be bug free and efficient soon. If it is a trivial problem, then please do update the FAQs so as to make our ccp4bb not just to bug with these type of questions . should i uninstall

Re: [ccp4bb] iMosflm in 6.1 under OS X

Yes, William I do agree with you, and in the same line of doubt, I have one more thing to ask you. Where is this .cvspass resides. I have problem in updating my fink , with fink selfupdate-cvs. thanks S.Jayashankar Research Student Institute for Biophysical Chemistry Hannover Medical School Ger

Re: [ccp4bb] unknown density for a small molecule

Hi, If you could send in stereo mode of the density you want to get suggestion, it will be convenient for the well trained eyes. S.Jayashankar Research Student Institute for Biophysical Chemistry Hannover Medical School Germany. On Tue, Feb 10, 2009 at 3:16 PM, wrote: > Hi, > > It could be a

[ccp4bb] PDB protein strucutrues as screen saver

Dear Scientists, It may be too much... But as a biophysics student I would like to appreciate and feel happy to have pdb structures as my computers screen savers than to have some funny and fancy stuffs. And it may help me as a motivator to solve my own structures in future I want to ask is

Re: [ccp4bb] PDB protein strucutrues as screen saver

t;>> >>> >>> For mac, a screen saver (structure) is already available. moreover it's >>> free and displays couple of structural information exactly the way >>> Jayashankar wants. >>> >>> http://www.sourcecod.com/structure/ >>>

[ccp4bb] protein folds

Dear Folks, The last novel proteins fold were from the yr 2007(pdb statistics), >From 2007 to till date no novel fold has been identified, this mean the present 1283 fold are the final or should I wait, if so , with what criteria do I expect for a new fold..or what are the expectations ... If we

Re: [ccp4bb] protein folds

, Paul Emsley wrote: > Jayashankar wrote: > >> Dear Folks, >> > > Dear gmail-user, > > >> The last novel proteins fold were from the yr 2007(pdb statistics), >> From 2007 to till date no novel fold has been identified, this mean the >> present 1283 fold

[ccp4bb] What can a learning student should post in our forum- are any restrictions for discussing science[what is science?] with intellectuals :)

Dear scientists I have asked a question in previous discussions regarding cryo conditions for collecting data of a crystal. What is the cryo condition followed in a small molecule data collection in olden days. I got wonderfull answers.i am very happy for that. Is any one confused in this issue li

Re: [ccp4bb] Design Constructs

Hi Hari, Right terminal residues for constructs. some time back there was some discussion with this subject. you can check that threads also. S.Jayashankar Research Student Institute for Biophysical Chemistry Hannover Medical School Germany. On Tue, Mar 31, 2009 at 5:10 AM, Ho-Leung Ng wrote:

[ccp4bb] Multiple active or allosteric pocket allignment

Dear friends, Is it possible to allign structure of proteins of same class or family just based on acive site residues or defined by its volume of cavity with preferred deviation. any suggestions could possibly help me. sincerely S.Jayashankar Research Student Institute for Biophysical Chemis

Re: [ccp4bb] Multiple active or allosteric pocket allignment

specify the residues involved in the > actal alignment, and the residues to calculate the RMS on > > Miri > > > On Tue, 16 Jun 2009, Jayashankar wrote: > > Dear friends, >> >> Is it possible to allign structure of proteins of same class or family >> just &g

Re: [ccp4bb] unknown density

Hi, Did you check for the 2N,2O coordination. Does your protein has copper ion as cofactor, whats the pH of the buffer. And if pH below 6 we can partially eliminate the speculation of copper ion. S.Jayashankar Research Student Institute for Biophysical Chemistry Hannover Medical School Germ

Re: [ccp4bb] Gridzilla - A graphical tool to calculate crystal optimization screening grids

Dear Hari, In the first hand , i thank you for this handy tool. But, I am so curious to know how can i rectify the following error. selva...@pc3241769:~/Desktop/tools/GridZilla_0.1beta_binary> ./GridZilla Traceback (most recent call last): File "/usr/lib/python2.5/site-packages/cx_Freeze/inits

Re: [ccp4bb] Warren DeLano

Let his soul rest in peace,In our Life we just pass many people and some sits in our memory because of their deeds and contribution to the world. with heavy heart A humble student and a Fan of PyMol. S.Jayashankar Research Student Institute for Biophysical Chemistry Hannover Medical School Germa

[ccp4bb] ccp4i to shelxcde path error

:/CCP4/6.3/bin/ ; and open the windows batch file ccp4i.bat , now after the gui pops-up now the module shelxcde opens with no complains from the program list. the problem is similar with when i try jligand. Thanks (Jay) Dr. Jayashankar Selvadurai Hannover Germany

Re: [ccp4bb] ccp4i to shelxcde path error

Dear Edward, Thanks for your help. Dr. Jayashankar Selvadurai Hannover Germany On Fri, Jul 5, 2013 at 6:48 PM, Edward A. Berry wrote: > Right-click on the shortcut on your desktop, select "properties", and see > what folder > it has for "start in". Try changing

[ccp4bb] Stout and Jensen

Dear All, I would like to buy the book '' X-ray structure determination'' by George.H.Stout and Lyle.H.Jensen. If in any case , somebody has shelved it and want to give away for reasonable price. I would buy it. sincerely Dr. Jayashankar Selvadurai (Jay) Hannover Germany

Re: [ccp4bb] Stout and Jensen

Thanks for the links and suggestions, actually the second edition is expensive and the prices are comparable to that of amazon. sincerely Dr. Jayashankar Selvadurai Hannover Germany On Mon, Oct 22, 2012 at 8:50 PM, Frances C. Bernstein < f...@bernstein-plus-sons.com> wrote: > T

Re: [ccp4bb] alpha Lactose LTB molecule from Coot Library

Dear Rex Palmer, Get monomer--->LBT->Save coordinate HTH Dr. Jayashankar Selvadurai Hannover Germany On Tue, Oct 23, 2012 at 3:17 PM, Rex Palmer wrote: > Does anyone know if the alpha lactose molecule LBT coordinates are in the > Coot library. If so how can they be accesse

Re: [ccp4bb] need some suggestions for crystallization

Dear Powell, Isn't it there a way to data mine the PDB or the other repository source for the time/duration/days of the crystals obtained. Dr. Jayashankar Selvadurai Hannover Germany On Mon, Feb 4, 2013 at 5:10 PM, Harry Powell wrote: > Hi David > > try going back to the one t