Re: [ccp4bb] backbone b-factor

Hi Mohd: The script below should also be able to edit the PDB file according to both of your needs. Think it is also easily modified to use for other similar PDB file editing needs. Best wishes, Navdeep # #! /usr/bin/gawk -f # # bf

[ccp4bb] cryosolvent

Hi, All, What's the general rules for selecting cryosolvent?I got crystals in 30% PEG4000/PEG3350, 0.2M AS and 0.1M NaAC,how should I choose cryosolvent? Thanks. Rui

Re: [ccp4bb] Tcl error - Snow Leopard OSX

Dear Jose: Please try putting this into /sw64/fink/dists/unstable/main/finkinfo/x11 it contains what is hopefully a fix to blt. blt-x86_64.info Description: Binary data Thanks. Bill On Sep 15, 2009, at 4:43 PM, José Trincão wrote: Hello all, I upgraded my Macbook Pro to snow leopard

Re: [ccp4bb] In PYMOL looks different from that in O

Hi Raja, On Wed, 16 Sep 2009 16:57:18 -0700, Raja Dey wrote: > Hi, > I am getting a problem to prepare a figure in PYMOL. I have 4 nearly > identical monomers in the AU sitting at the corners of a rectangle. The 2 > front monomers almost perfectly superimpose on the back 2 when I am looking

Re: [ccp4bb] In PYMOL looks different from that in O

> On Wed, 16 Sep 2009 16:57:18 -0700, Raja Dey said: > Hi, I am getting a problem to prepare a figure in PYMOL. I have 4 > nearly identical monomers in the AU sitting at the corners of a > rectangle. The 2 front monomers almost perfectly superimpose on > the back 2 when I am l

[ccp4bb] In PYMOL looks different from that in O

Hi, I am getting a problem to prepare a figure in PYMOL. I have 4 nearly identical monomers in the AU sitting at the corners of a rectangle. The 2 front monomers almost perfectly superimpose on the back 2 when I am looking along the plane. I can see this view in O program. For some reason I

[ccp4bb] CryoEM Postdoc positions available

POSTDOCTORAL FELLOW POSITIONS UNIVERSITY OF PITTSBURGH We are looking for research associates/postdoctoral fellows to work on structures of macromolecular complexes and assemblies involved in HIV-1 biology and bacterial chemotaxis using cryo-EM methods. Motivated candidates with research expe

Re: [ccp4bb] bond lengthening in atomic resolution structure

Hi Ivan- Since you most likely have the data to back it up and I assume you have the computational firepower to do it, why don't you run a full matrix refinement in SHELX to get estimates of bond lengths and their deviations? It's worked for me in calculating carboxylate C=O bond lengths to determi

Re: [ccp4bb] bond lengthening in atomic resolution structure

To judge the significance of the value of a bond length, you cannot rely on global measures of precision. You need the standard uncertainty of this particular distance in this particular crystal. Refmac will not perform this calculation for you. Shelxl will. It is certainly more cumbersome t

Re: [ccp4bb] bond lengthening in atomic resolution structure

On Wednesday 16 September 2009 11:19:11 Ivan Shabalin wrote: > Dear all, > > I have an atomic resolution (1.1Å) structure of enzyme with the bound > cofactor NAD. During the analysis of the refined structure I found that > important double C=O bond of the cofactor in the active site was slightly >

[ccp4bb] bond lengthening in atomic resolution structure

Dear all, I have an atomic resolution (1.1Å) structure of enzyme with the bound cofactor NAD. During the analysis of the refined structure I found that important double C=O bond of the cofactor in the active site was slightly lengthened from standard 1.22Å to 1.26Å. Then I increased the sigma's o

Re: [ccp4bb] Regarding CCP4 on mac

Hi Mohinder, Are you having problems because the CCP4I_TCLTK environment variable is not set correctly? From the shell, you can check ~$ echo $CCP4I_TCLTK /usr/local/bin ...so you should have a tclsh binary there: /usr/local/bin/tclsh Otherwise, check the troubleshooting pa

Re: [ccp4bb] backbone b-factor

Many thanks to all of you who replied, many great suggestions and I'll try to utilize some of your ideas very soon. Thanks, Mohd Mohd A. Salameh, Ph.D. Mayo Clinic Cancer Center Griffin Cancer Research Building 4500 San Pablo Road Jacksonville

Re: [ccp4bb] off topic; alignment keeping upper and lower case

Charlie Bond's ALINE program (http://crystal.bcs.uwa.edu.au/px/charlie/software/aline/) can handle upper/lower case sequences. In the menu bar: Tools > Alignment > Align All Sequences does the job (using clustalw as a back-end IIRC) without changing cases. Best, Stephen 2009/9/16 MARTYN SYMMONS

Re: [ccp4bb] off topic; alignment keeping upper and lower case

Dear All - I am looking for a multiple alignment program that will work with upper and lower case letters in the sequences and preserve them through to the output. I used to use PILEUP but that is no longer supported here. Any suggestions much appreciated. regards

[ccp4bb] Regarding CCP4 on mac

Dear ccp4bb, I have just installed ccp4 6.1.2 with ccp4i 1.4.2 on a MacBook Pro running OSX 10.5.8. When I try to run Refmac5 (or phaser) I get the status "starting" in the GUI but the program fails to run and no log file is generated. I source: /usr/local/ccp4-6.1.2/bin/ccp4.setup-sh befor

Re: [ccp4bb] attachments

Hi Ian, > I think the fundamental problem is that some people are still very much > attached (pun not intended) And none taken .-) > to their text-based e-mail client (Pine, Pico or whatever), and I > completely agree that on this BB we have to cater for the lowest common > denominator. If

Re: [ccp4bb] Summary for "Anisotropic Diffraction In Refinement" question

Just to add my two ha'porth. I discussed this some years ago with Garib, just after I'd added the anisotropic cutoff to the resolution limits in Mosflm (mentioned by Andrew below); as I remember (and this is an invitation to Garib to contribute and correct me here!), the answer went along t

Re: [ccp4bb] Summary for "Anisotropic Diffraction In Refinement" question

Hi Everyone, I echo Andrew's thanks for the summary offered by Justin. I would like to mention another way to trim anisotropic diffraction patterns of the weak patches 'at source', as it were, in MOSFLM, by specifying a sigma cut off applied to each image. from the manual: RESOLUTION [ ] < hi

[ccp4bb] Off topic: Course in protein crystallisation at the University of Helsinki Institute of Biotechnology

The protein crystallisation facility at the Institute of Biotechnology will organise a three-day practical course on protein crystallisation techniques. The course is aimed at graduate students and post docs with interest in structural characterisation of proteins. The course will include lectu

Re: [ccp4bb] Summary for "Anisotropic Diffraction In Refinement" question

I would like to have some comments on whether the maps before or after truncation are better . (obviously the Rfactors will be lower for the truncated data ..) I suspect it iwill be completely anecdotal - but I confess to a gut unhappiness about throwing out measurements.. eleanor Pavel Afon

Re: [ccp4bb] backbone b-factor

Choose another graph from the loggraph - it also gives the main chain alone and the side chains alone (not so useful!) Eleanor Salameh, Mohd A., Ph.D. wrote: Dear All, I would like to prepare a plot showing the b-factor of only the alpha carbon and/or the backbone atoms and I wonder if somebod

Re: [ccp4bb] Summary for "Anisotropic Diffraction In Refinement" question

I would like to thank Justin for his summary of this topic, which I'm sure many people found of interest, and is very much in the spirit of the bulletin board. I would just like to correct one factual error, in that it has been possible to specify anisotropic resolution limits to MOSFLM for