Re: [ccp4bb] Refmac buccaneer combination

map that you are providing? It might help if you provide it with a starting model to build from, e.g. a molecular replacement solution. Otherwise try ARP/wARP wit the same data. Best wishes, Ronan   On 18/03/14 21:41, Debajyot

[ccp4bb] Refmac buccaneer combination

Hi all, I am running autobuild and refinement in buccaneer/refmac pipeline. Does anybody have any idea about the following error . Refmac_5.8.0069: Check input coordinates Traceback (most recent call last): File "/Applications/ccp4-6.4.0/bin/buccaneer_pipeline", line 199, in control.run

[ccp4bb] twist angle bwtween monomers

Hi all, Does anybody know of any software to calculate the twist angle between two monomers in a dimeric assembly. Or calculate manually. Thank you in advance. Sincerely Debajyoti

[ccp4bb] Hydrophobic protein surface and SDS page

Dear All, Sorry for the off topic question. I am purifying one protein which is showing increased molecular weight +5kDa (more than adding up the Hexa His and cloning artifact) in normal 12% SDS PAGE. The DNA sequence is as it is. The gel runs without blurring the lanes and without any difficu

Re: [ccp4bb] data processing deviations chisq

Hi all, Thank you all how have replied for their kind suggestions and diagnosis of collected data. sincerely Debajyoti On Sat, 26 Mar 2011 04:44:42 +0530 wrote > > Hi all, > > I have collected one iodine soaked data in our home source, and processing the data using HKL2000. Exposure tim

[ccp4bb] data processing deviations chisq

Hi all, I have collected one iodine soaked data in our home source, and processing the data using HKL2000. Exposure time per frame is 5min/1 degree. While processing I have noticed that the Chisq values, cell parameters and rotation change Vs frame are deviating like anything. Please find the p

[ccp4bb] Changing cell constants

Hi all, I have been processing data using XDS which results in the cell constants 179.1  55.21  149.5    90  124.3 90. and the space group is C2. Checking systematic absences have shown that the screw axis is not present. Again I was checking the space group using POINTLESS. It was re

[ccp4bb] Heavy atom salt at low pH

Hi All, Sorry for a non CCP4 question. I have been trying to phase a protein structure using different heavy atom derivatives. The problem is the crystallization pH is very low (from 2.8 to 3.5). I will be highly benefited if anybody kindly suggests me the possible heavy atom salts to try sincer

[ccp4bb] crystals of 1D

Hi All, I am dealing with a protein that crystallizes in 1D. The broom stick crystals does not yield with any improvement w.r.t their dimension. I have tried using different concentration of salt, ppt and pH around the parent condition, even tried seeding and temperature changing. However, any

Re: [ccp4bb] how to improve resolution

Hi, The situation is somewhat like my case. Have you checked the purity level of the protein in SDS PAGE. In that case you may try to introduce another purification step. regards Debajyoti On Fri, 05 Feb 2010 10:05:23 +0530 wrote >Hi, All, We are trying to crystallize a protein

[ccp4bb] I apologize

Hi everybody, I really apologize to every members of CCP4BB for not to give attention to my addressing phrase. It is truly misleading. I swear not to make such bad mistake in future. I am really ashamed for such a deed. Sincerely Debajyoti Dutta On Fri, 21 Aug 2009 21:29:23

[ccp4bb] I apologize

Hi everybody, I really apologize to every members of CCP4BB for not to give attention to my addressing phrase. It is truly misleading. I swear not to make such bad mistake in future. I am really ashamed for such a deed. Sincerely Debajyoti Dutta On Fri, 21 Aug 2009 21:29:23

Re: [ccp4bb] cyseteine modification

Dear Sir, Thank you all who have replied. I jast want to enquire that if there is any option in coot to introduce the OH bond with Cys residue as well as to introduce the secondary peptide like bond between carboxylic carbon with amino group of lys. Sincerely Debajyoti Dutta On Wed

[ccp4bb] cyseteine modification

looks as if it can accomodate only one oxygen atom and not more. Thank you for reply in advance. Sincerely Debajyoti Dutta

[ccp4bb] refinement with REFMAC5

Debajyoti Dutta

[ccp4bb] Fw: Re: [ccp4bb] Phantom Crystals

Note: Forwarded message attached -- Original Message -- From: "Debajyoti Dutta" debajyoti_dutt...@rediffmail.com To: deti...@hwi.buffalo.edu Subject: Re: [ccp4bb] Phantom Crystals--- Begin Message --- There may be a chance of getting crystal like formations. This I presum

Re: [ccp4bb] Hanging vs. Sitting

Hi, >From the experiance of mine I can tell you that the crystal size sometimes >matters between these two methods. Hanging drop may yield bigger crystals than >sitting drop, that may be due to the evaporation rate(surface area). Hanging >drop allow us to set different protocols also like f

[ccp4bb] Confusing Diff Map peaks

is surface region, though there B factors are not high (around 25). Thank you for your suggestions and help. Sincerely Debajyoti Dutta

[ccp4bb] Liquid liquid phase separation

  Hi, Sorry for posting a non CCP4 query. I am wondering about liquid-liquid phase separation in crystallization outcomes. So far I gain my knowledge about it that it is due to microgravity. It makes the protein to concentrate at a certain place. However phase separation may or may not yield

Re: [ccp4bb] R pim and Rmeans

Email: [EMAIL PROTECTED] * >* GERMANY Web: www.embl-hamburg.de/~msweiss/ * >* * >**** > > >On Sat, 6 Dec 2008, Debajyoti Dutta wrote: > > > >Dear members, > >I have a little query hare about Rpim and Rmeans. How these are used to mark >data quality, and how can one calculate it. > >Thak you for your reply in advance. > >Sincerely >Deb

[ccp4bb] R pim and Rmeans

  Dear members, I have a little query hare about Rpim and Rmeans. How these are used to mark data quality, and how can one calculate it. Thak you for your reply in advance. Sincerely Deb

Re: [ccp4bb] getting weak diffracting crystals

uL of >the well solution to see their effect. > >good luck, >Mathews > > > > > From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Debajyoti > Dutta >Sent: Thursday, December 04, 2008 9:04 PM >To: CCP4BB@JISCMAIL.AC.UK

Re: [ccp4bb] getting weak diffracting crystals

  Hi again, Thank you for your reply. I know that the loop regions are notorious for crystallization however in this case it is yielding the crystals but with lower quality. Does it not due to the quick crystallization, the lattice has no time to form up. That’s why it is happening. Can I n

[ccp4bb] getting weak diffracting crystals

  Dear Members, I am getting crystals of my protein. The secondary structure prediction implies that it has N-terminal with high degree of loop regions. I also get some mountable crystals yielding weak diffraction pattern(10 A). The quality of the crystals can also be assumed from its texture

Re: [ccp4bb] protein degradation

ird chemistry involving the >imidazole ring at high temp. no doubt). > > > >Artem > > _ > > From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of >Debajyoti Dutta >Sent: Sunday, August 24, 2008 3:21 AM >To: CCP4BB@JISCMAIL.AC.UK >Subject:

Re: [ccp4bb] protein degradation

protein cannot sustain low salt and get ppt during dialysis. Sincerely Debajyoti Dutta On Sat, 23 Aug 2008 Artem Evdokimov wrote : >Hi, > > > >If you are plagued by 'generic' proteolysis, it is not likely that changing >buffers from TRIS to phosphate will help reduce the

[ccp4bb] protein degradation

a DNA binding (pI~ 10) and Tris-Hcl buffer is used with 10% glycerol and 300mM NaCl. for purification. Does Phosphate buffer do any help in stopping the degradation. All suggestions are welcome. Thank you for your reply in advance. Sincerely Debajyoti Dutta

Re: [ccp4bb] MR problem --molrep

Hi, I dare to say about the possible way to do molrep from my recent experience. You can choose "rotation and translation function" job at first and do the self rotation fuction (for multimer) after that.Each of these run will generate two different outputs *_rf.molrep_rf ans *_srf.molrep_rf

Re: [ccp4bb] From the CNS1.2 trnaslation error

using CNS MR module. Thank you all of you Sincerely Yours Debajyoti Dutta On Fri, 11 Jul 2008 Ed Pozharski wrote : >There is only one map format in CNS, and mapman should open it. Then >you can convert it to all other formats. Does mapman report some error? > >You can rota

[ccp4bb] From the CNS1.2 trnaslation error

ATOM 5109 CB ALA 1 32.637 74.346 146.854 1.00 20.00 C etc.. (Omitted the total chain: all are taking a reasonable values) Will you please help me with these problems. Thank you very much for your attention and suggestions in advance. Your Sincerely Debajyoti Dutta

Re: [ccp4bb] Binding to Nickel in the presence of SDS or arginine

Hi, Does high salt concentration(around 0.7M Nacl) in NiNTA elution do better. And what about the purification of high positively charged protein (like PI 10) in NiNTA. Thanks Debajyoti Dutta On Sat, 28 Jun 2008 Artem Evdokimov wrote : >Ni salt of dodecyl sulphate is not solu

Re: [ccp4bb] B-factor problem

Hi, What is the lower limit of the weighting term one can use. If the data is around 2A can one use 0.04 or less and which type of refinement is more useful when one is doing the initial refinement (isotropic, aisotropic, overall or mixed). sincerely Debajyoti On Tue, 17 Jun 2008 Roger R

[ccp4bb] tri and tetra problem

space group. I am confused with the results. But the tetramer is yielding a good decrement of R free and R factor. Thank you for your attention and suggestion in advance. Yours sincerely Debajyoti Dutta

[ccp4bb] Free_R, Nmol/asymm and libcheck

Dear Sir/Madam I have some questions from different parts of CCP4 suite regarding refinement with Refmac and ArpwARP, Cell content analysis and libcheck. 1. After initial refinement I am giving the sequence to the ArpwArp expert system. It seems it is excluding R free and incorporate model b