Re: [ccp4bb] Patterson Map missing a peak?

2009-09-15 Thread Nicholas M Glykos
Hi Engin, Two thoughts: * Is the Patterson map consistent ? (with different resolution ranges, exclusions, ...). You could possibly give 'GraphEnt' a try [assuming it still works with current generation mtz files]. * The number of heavy atoms may be much larger and may deviate from the

[ccp4bb] attachments

2009-09-15 Thread Stein, Norman (STFC,DL,CSE)
In the past month there have been several postings to the BB with large (100kB or more) attachments. Can I remind subscribers that it is our policy to discourage attachments as, amongst other things, they can cause mailboxes to fill at an alarming rate. A link to a website carrying the data which

Re: [ccp4bb] attachments

2009-09-15 Thread Phil Evans
while we're on this topic, it would be nice also if messages were sent in plain text, not as html (like yours, Norman :-)), particularly as these ones generally come out in a tiny font in my (Apple) mail reader, for some reason Phil On 15 Sep 2009, at 09:45, Stein, Norman (STFC,DL,CSE)

Re: [ccp4bb] attachments

2009-09-15 Thread Ian Tickle
Phil I had this same problem a while ago, if you recall. Modern e-mail clients sending a message in HTML format will almost certainly send it in 2 parts, the first a version converted to plain text and the second the original HTML version (and possibly other versions of the same message). This

Re: [ccp4bb] attachments

2009-09-15 Thread Phil Evans
There are two problems, I think 1. Sending a simple mail like this in anything other than plain text is wasteful, and also enforces the sender's way of displaying it on the reader, rather than following the reader's preference. (That may of course be appropriate in some cases where

Re: [ccp4bb] attachments

2009-09-15 Thread Joachim Reichelt
=3D is the escaped = =xx were is the hex code of any 8bit char Am 15.09.2009 11:46, schrieb Phil Evans: There are two problems, I think 1. Sending a simple mail like this in anything other than plain text is wasteful, and also enforces the sender's way of displaying it on the reader, rather

Re: [ccp4bb] attachments

2009-09-15 Thread Ian Tickle
Phil Nothing at all wrong with plain text for simple messages as you say, but if you want to communicate a complicated equation (particularly one containing a lot of Greek letters and math symbols not in the standard ASCII set!) the HTML version is much cleaner and easier to understand. Obviously

Re: [ccp4bb] attachments

2009-09-15 Thread Harry Powell
Hi Apple mail (which is what I think Phil uses) is a bit of a nuisance - there is no menu option to display plain text by default, apparently (IMWBW) - you have the option to view the current message in plain text, but you have to do this on a message-by-message basis. There is a

Re: [ccp4bb] attachments

2009-09-15 Thread Phil Evans
Thanks for that - it works! Phil On 15 Sep 2009, at 11:43, Harry Powell wrote: Hi Apple mail (which is what I think Phil uses) is a bit of a nuisance - there is no menu option to display plain text by default, apparently (IMWBW) - you have the option to view the current message in

Re: [ccp4bb] attachments

2009-09-15 Thread Phil Evans
On 15 Sep 2009, at 11:24, Ian Tickle wrote: Phil Nothing at all wrong with plain text for simple messages as you say, but if you want to communicate a complicated equation (particularly one containing a lot of Greek letters and math symbols not in the standard ASCII set!) the HTML version

Re: [ccp4bb] attachments

2009-09-15 Thread Ian Tickle
Yes, obviously it doesn't provide full equation formatting capabilities, as in LaTeX for example, but at least one can type or paste in equations containing for example the Greek 'sigma' character (upper or lower case of course) or the 'square root' symbol instead of having to spell them all out!

Re: [ccp4bb] attachments

2009-09-15 Thread Ian Tickle
I suppose I also don't understand why people composing html messages would select a tiny font size, or is that a function of the Mail reader rather than the writer (which would seem to defeat the purpose of the writer formatting the message)? Assuming your mail reader has correctly

Re: [ccp4bb] Preparation of seed-stocks without seed-beads

2009-09-15 Thread Hargreaves, David
Take two siliconised glass cover slips. Place 2-5ul of mother liquor on one and transfer a single crystal to this solution. Place the other cover slip on top and press down. The two optically flat surfaces crush the crystal (best observed using a microscope). Slide the two cover slips apart and

Re: [ccp4bb] attachments

2009-09-15 Thread William G. Scott
On Sep 15, 2009, at 3:43 AM, Harry Powell wrote: I googled and found something about editing ~/Library/Preferences/ com.apple.mail.plist (double click on the icon, don't try with emacs or vi...)and adding the following to the start of the first dictionary:- keyPreferPlainText/key true/

Re: [ccp4bb] attachments

2009-09-15 Thread William G. Scott
On Sep 15, 2009, at 5:07 AM, Ian Tickle wrote: it doesn't provide full equation formatting capabilities, as in LaTeX for example, but at least one can type or paste in equations jsMath provides a convenient and easy-to-use way to embed and render LaTeX in HTML:

Re: [ccp4bb] attachments

2009-09-15 Thread Ethan Merritt
On Tuesday 15 September 2009, Ian Tickle wrote: Yes, obviously it doesn't provide full equation formatting capabilities, as in LaTeX for example, but at least one can type or paste in equations containing for example the Greek 'sigma' character (upper or lower case of course) or the 'square

Re: [ccp4bb] attachments

2009-09-15 Thread Ian Tickle
Why do you say that? Typing non-ascii text is the same process whether it's wrapped in HTML or not. Here's your sigma: ∑ My e-mail client only allows me to insert non-ASCII characters into HTML (or RTF), not plain text: the option to insert symbols is greyed out in plain text mode. If I

Re: [ccp4bb] Preparation of seed-stocks without seed-beads

2009-09-15 Thread Magnus Alphey
You can always make your own 'seed-bead' using a French Press nylon ball (1/8) and an eppendorf. Or in the absence of French Press consumables suppliers, just find your local industrial gadget supplier (I found Dejay Distribution Ltd in the UK via google). They quoted me £4.45 for 100 x 1/8 nylon

Re: [ccp4bb] attachments

2009-09-15 Thread Ian Tickle
-Original Message- From: owner-ccp...@jiscmail.ac.uk [mailto:owner-ccp...@jiscmail.ac.uk] On Behalf Of William G. Scott Sent: 15 September 2009 15:15 To: Ian Tickle Cc: CCP4BB@jiscmail.ac.uk Subject: Re: [ccp4bb] attachments jsMath provides a convenient and easy-to-use way to

Re: [ccp4bb] Peg3350 model

2009-09-15 Thread Dalibor Milic
Hi! On Pet, rujan 11, 2009 15:37, sajid akthar wrote: I have some density and I can fit a peg molecule in their. I am confused and when I search database for peg3350, I have no hit. How can I build a model for Peg 3350. I found some PDB's with peg; but they they have used peg400; Is there any

[ccp4bb] backbone b-factor

2009-09-15 Thread Salameh, Mohd A., Ph.D.
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 somebody knows a module or software that I can use, I tried the structure analysis/Temperature factor analysis module in CCP4 but it plots the average b-factor of all

Re: [ccp4bb] backbone B-factor

2009-09-15 Thread Palm
Dear Mohd, to plot the B-factors, I would read the pdb file in Excel (or similar). Take care that 5.45 is read as a number and not as a string, which happens at least in German versions because of the . instead of the German,. Specify the decimal separator. The sort by Atmon name to get all

Re: [ccp4bb] backbone b-factor

2009-09-15 Thread Pavel Afonine
Hi Mohd, here is how using PHENIX tools: Step 1: phenix.pdbtools model.pdb keep=backbone Step 2: phenix.pdbtools model_backbone_only.pdb --show-adp-statistics Please let me know if you have questions about the above tools. Pavel. On 9/15/09 9:37 AM, Salameh, Mohd A., Ph.D. wrote: Dear

[ccp4bb] Assistant Professor Position Available in Structural Biology

2009-09-15 Thread Smith Steven
FACULTY POSITION Structural Biology and Biochemistry Stony Brook University invites applications for a tenure-track position as Assistant Professor in the Department of Biochemistry and Cell Biology in the area of structural biology/biochemistry starting Fall 2010. Stony Brook's proximity and

[ccp4bb] Meeting Announcement for the 5th International Conference on Structural Analysis of Supramolecular Assemblies by Hybrid Methods

2009-09-15 Thread Wes Sundquist
Dear Colleagues: We are delighted to announce that the 5th International Conference on Structural Analysis of Supramolecular Assemblies by Hybrid Methods will be held from March 10-14, 2010 in Lake Tahoe, California at the Granlibakken Conference Center. We invite you to visit our Symposium

[ccp4bb] Summary for Anisotropic Diffraction In Refinement question

2009-09-15 Thread Justin Hall
Dear All; In response to my Anisotropic Diffraction In Refinement, which asked for suggestions for how best to proceed with refinement with an anisotropic data set, I received a large number of responses which overwhelmingly suggested using the UCLA Anisotropy Server

[ccp4bb] Tcl error - Snow Leopard OSX

2009-09-15 Thread José Trincão
Hello all, I upgraded my Macbook Pro to snow leopard and followed William G. Scotts Crystallography on OSX wiki to install CCP4 using Fink. I used the 64bit install with full compilation, not the pre-compiled binaries. When I start ccp4i I get a warning: Application initialization failed:

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

2009-09-15 Thread Peter Zwart
Application of a elliptical resolution boundary is justified because the resolution boundary from common integration programs (Denzo and Mosflm for example) is spherical where diffraction for anisotropic data is ellipsoidal. A spherical boundary would result in the inclusion of numerous poorly

[ccp4bb] Seeding and protease questions

2009-09-15 Thread Joseph Brock
Hi everyone, I have two conditions that I want to try and improve by microseeding. I have been reading the literature on the subject and am a bit confused as to what exactly is the stabilizing mother liquor that is used in the serial dilution of the seed stock. Is this just purified protein

Re: [ccp4bb] backbone b-factor

2009-09-15 Thread Charlie Bond
Hi Salameh, Not sure if you mean a graph of B-factor vs sequence, or a 3D structure plot. Either way you can get such a plot using aline http://crystal.bcs.uwa.edu.au/px/charlie/software/aline/ which can produce a sequence alignment (or single sequence) coloured by B-factor (CA, Main, Side

Re: [ccp4bb] Seeding and protease questions

2009-09-15 Thread Artem Evdokimov
Stabilizing mother liquor is anything that (hopefully) will keep your seeds 'competent' (capable of nucleating single crystals). This may be anything but typically what people start with is something on the lines of the well solution supplemented perhaps with a bit extra precipitant. As to

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

2009-09-15 Thread Pavel Afonine
This is why phenix.refine by default outputs both maps: 2mFo-DFc filled and not filled, and it is the best to look at both keeping in mind all pros and cons of each of them. Pavel. On 9/15/09 5:22 PM, Peter Zwart wrote: Application of a elliptical resolution boundary is justified because

Re: [ccp4bb] Tcl error - Snow Leopard OSX

2009-09-15 Thread William G. Scott
On Sep 15, 2009, at 4:43 PM, José Trincão wrote: Hello all, I upgraded my Macbook Pro to snow leopard and followed William G. Scotts Crystallography on OSX wiki to install CCP4 using Fink. I used the 64bit install with full compilation, not the pre-compiled binaries. When I start ccp4i I

Re: [ccp4bb] Tcl error - Snow Leopard OSX

2009-09-15 Thread William G. Scott
On Sep 15, 2009, at 4:43 PM, José Trincão wrote: Hello all, I upgraded my Macbook Pro to snow leopard and followed William G. Scotts Crystallography on OSX wiki to install CCP4 using Fink. I used the 64bit install with full compilation, not the pre-compiled binaries. When I start ccp4i I