Re: [ccp4bb] phaser

Hello Aaron, this usually means that you have a second version of phaser installed, e.g. from the phenix package. To find out, go to a terminal from which you would start ccp4i and type 'which phaser'. My guess is that the answer to that command does not show phaser in the ccp4-directory. To

Re: [ccp4bb] Offtopic: Alscript question

Dear Andy, This is not exactly an answer to your question, but depending on the exact result you want from ALSCRIPT you might consider trying out our GUI-based program ALINE: http://crystal.bcs.uwa.edu.au/px/charlie/software/aline/ Bond, C.S. and Schüttelkopf, A.W. (2009), "An Extensible WYSIW

[ccp4bb] Re :Re: [ccp4bb] MAD phasing

hello peteri tried phenix.autosol. It gave me following results.  but the data analyses says that my data pseudo translational symmetry, I have pasted it. Do phenix handle pseudotranslation. Need suggestion on thisSolution # 1  BAYES-CC: 15.3 +/- 27.3 Dataset #1   SG: "P 61 2 2"   FOM: 0.4Score

[ccp4bb] Re :Re: [ccp4bb] MAD phasing

hi BertThank you for your reply. Your are right about the values for your Pattersons and NatFourier, but the systematic absences and pointless suggested me to be P6122 and according to mathews coeff i get   1 molecule with Vm=  2.06 solvent=  40.42. My protein has two SeMet sites so i searched

[ccp4bb] MAD phasing

helloI am have a MAD dataset collected upto 2.3A but anomalous signal is upto 3.5A. The dataset is in P6 and based on pointless and absences it is P6122. Overall Rlin/rsym is (0.07/ 0.06). the overall redundancy is 10. I have two Se peaks, i used solve/resolve to find those peaks. I used dataset

[ccp4bb] issues with TLS refinement

The issue is: While running tls and restrained refinement, the program doesn't perform the given no. of tls refinements. For e.g., if you ask it to perform 10 TLS and 5 restrained refinement rounds, it'll run may be 2 or 3 rounds of TLS and then jump to restrained refinement rounds and fi

Re: [ccp4bb] Problem with Rfree and Rfac

Dear Sravanti, Did you checked your data for twinning as It may be a case of pseudomerohedral twinning because the beta angle is near 90 degrees. > > Space group- P1 21 1 > Resolution- 3A > Solvent content- 39% > unit cell parameters- 63.3, 90.72 , 86.11, angles- 90, 91.5 , 90 > > > -- Tara

Re: [ccp4bb] [ccp4-dev]: sfall atmmap resolution

Paul Emsley wrote: GRID r*a*3 r *b*4 r*c*3 r=resolution(in Angstroms) Ooops - I mean: GRID a*3/r b*3/r c*3/r (plus rounding up of course) Paul.

Re: [ccp4bb] [ccp4-dev]: sfall atmmap resolution

Zhong Ren wrote: *** For details on how to be removed from this list visit the *** ***CCP4 home page http://www.dl.ac.uk/CCP/CCP4/main.html*** Hi, I found the message below asking whether RESOLUTION keyword is affecting atmmap, but I found no answer. I copy that message in 2004 to th

Re: [ccp4bb] CD spectroscopy sensitivity

Dear Francisco, Dear All I got recently a comment on a paper review suggesting me to perform CD spectroscopy to determine the alpha-helical content of a mutant protein involved in a human disease. The diferences between the wild type and the mutant protein are just 17 aminoacids. My question

[ccp4bb] CD spectroscopy sensitivity

Dear All I got recently a comment on a paper review suggesting me to perform CD spectroscopy to determine the alpha-helical content of a mutant protein involved in a human disease. The diferences between the wild type and the mutant protein are just 17 aminoacids. My question is if CD spectro

Re: [ccp4bb] Problem with Rfree and Rfac

A very relevant article: G.J. Kleywegt and T.A. Jones, Model-building and refinement practice, Methods in Enzymology, 277, 208-230 (1997), . Sincerely, Navdeep

Re: [ccp4bb] TLSANL gives zero off-diagonal ANISOU matrix in CCP4 6.1

Apologies, this was a bug introduced by a recent change. It is fixed and will be in 6.1.2 Martyn -Original Message- From: CCP4 bulletin board on behalf of Alejandro Buschiazzo Sent: Thu 5/21/2009 6:26 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] TLSANL gives zero off-diagonal ANISOU ma

[ccp4bb] TLSANL gives zero off-diagonal ANISOU matrix in CCP4 6.1

Dear all, I have observed a strange behavior when using TLSANL (v. 3.8) under CCP4 6.1.0 : using identical input (only coordinates have changed a bit after some TLS+restrained refinement) what used to work perfectly well before (under CCP4 6.0), now gives an evidently wrong calculation, result

Re: [ccp4bb] issues with TLS refinement

Not sure if this is your problem, but I had a different issue with using this version of refmac5 from the OSX binaries off the CCP4 website. I upgraded to the latest version off of Garbs website and everything seems to be back normal or a least consistent across various platforms. Leona

Re: [ccp4bb] pH sensitive fluorescent dye

Looks like one option is BCECF/AM--from a paper I was reading recently (Cell Physiol Biochem. 2008;22(1-4):15-30. Epub 2008 Jul 25.) However, you would probably want to use the non-permeable variant, if you want to monitor the endocytosed vesicles. Jacob "Cells were loaded with BCECF/AM (Molec

[ccp4bb] phaser

Dear all, When running phaser with ccp4i the program exits with a message saying that the program had a fatal runtime error and that it could not open the mtz file. All other programs I use with ccp4i manage to run without problems. Any ideas? Thank's for any input. Aaron

[ccp4bb] pH sensitive fluorescent dye

Hi, Sorry for the off-CCP4 question. Crystallographers are now doing everything... We are looking for a fluorescent dye that will be turned on, or increase signal, when pH goes from neutral to acidic. More specifically, we would like to monitor the internalization of a protein into the ac

[ccp4bb] Problem with Rfree and Rfac

Hello CCP4i GURUs, I am working on a 3A resolution structure and I recently got a solution from Phaser. I have just started building and refining the structure. I started with Rfree-43 , R-41.7 and the first round of building and refining gave me Rfree- 40 and Rfac- 35.5. The Rfree and R do not de

[ccp4bb] Offtopic: Alscript question

To the CCP4bb, I have an off-topic request regarding Alscript, a program used to make postscript images from sequence alignments. Does anyone have an Alscript script file (.als) that successfully implements the "RELATIVE_TO" and "mask ILLEGAL" commands that I could look at? I haven't been

Re: [ccp4bb] Isomer images

Haitao, The journal Biochemistry (and others no doubt) specifies that the two images should be separated by 5.5 - 6.5 cm as measured between similar points (e.g. the same atom in either image). -Andy === Andrew T. Torelli Ph.D. Postdoctoral Associate

[ccp4bb] Complex degradation

Dear members, I am trying to crystallize a complex of two proteins prepared in Tris, NaCl and DTT. The problem is one of the proteins degrades over time and allows only the second protein to crystallize. While addition of protease inhibitors such as EDTA is one of the ways to go, I would like to kn

Re: [ccp4bb] issues with TLS refinement

I might be wrong but it seems Garib has implemented some sort of line minimization for the tls part which causes the observed behavior. Garib? Roberto On 21 May 2009, at 00:39, Dima Klenchin wrote: The issue is: While running tls and restrained refinement, the program doesn't perform