Re: [ccp4bb] If it is a new structure?

2010-12-20 Thread Vellieux Frederic
Hi, Last couple of times I asked myself the same question (what does it look like?) I used ssm (or PDBeFold as seems to be called now). http://www.ebi.ac.uk/msd-srv/ssm/ HTH, Fred. Liu Zhao wrote: The structure of my protein is as shown as the purple one. Another one ,as shown as

Re: [ccp4bb] If it is a new structure?

2010-12-20 Thread Andreas Förster
You're welcome! Next time, irrespective of whether your structure is a new one or not, please upload your images to picasa, flickr, your university's file sharing server or some such thing and include the link in your email. Don't flood several thousand inboxes with megabytes of pixels. And

[ccp4bb] Postdoc position at IBS Grenoble, France

2010-12-20 Thread Stéphanie Ravaud
A post-doctoral position is available to join the group of Pr. E. Pebay-Peyroula at IBS (Institut de Biologie Structurale, Grenoble, http://www.ibs.fr). The group explores functional and structural aspects of membrane proteins mainly focussing on the mitochondrial carriers family. The

[ccp4bb] off topic: young scientists linkedin group

2010-12-20 Thread Jamaine SC Davis
Dear CCP4 users: This email is to encourage you to join the Young Scientist Special Interest Linkedin Group, as part of the American Crystallographic Association. Anyone with an interest in promoting the professional development of young scientists in the field of crystallography is encouraged

Re: [ccp4bb] If it is a new structure?

2010-12-20 Thread Justin Hall
Hi Liu, If I understand your question correctly, youre asking how different do two structures need to be for one to be new'. If by new you mean a new fold, then the answer is NO. Your structure and the homolog have the same fold. However, if your structure is the first structure of a

Re: [ccp4bb] If it is a new structure?

2010-12-20 Thread David Schuller
On 12/20/10 05:49, Liu Zhao wrote: The structure of my protein is as shown as the purple one. Another one ,as shown as green,is homologous .But the structure of my protein can't be obtained by using molecular replacement. And both structures have much different, especially in B chain. If my

Re: [ccp4bb] REFMAC 5.2.0019 question

2010-12-20 Thread Ed Pozharski
On Sun, 2010-12-19 at 18:58 -0500, Hailiang Zhang wrote: (1). CTLS=a, CC=b (2). CTLS=a, CC=0; followed by: CTLS=0, CC=b In (2), you are doing two separate runs, with the second not using TLS. If you want to combine TLS and positional refinement, you must have them included in the same refmac

Re: [ccp4bb] REFMAC 5.2.0019 question

2010-12-20 Thread Ian Tickle
I would try it with the latest version (5.6.x) in case there's a bug. That's a very old version you're still using! -- Ian On Sun, Dec 19, 2010 at 11:58 PM, Hailiang Zhang zhan...@umbc.edu wrote: Hi, I am using REFMAC 5.2.0019 to run the following script: *** refmac5 hklin a

Re: [ccp4bb] REFMAC 5.2.0019 question

2010-12-20 Thread Ian Tickle
PS one other thought: in your run 2b you are not reading in (as TLSIN) the TLSOUT file produced by run 2a. So run 2b is not starting from the same point that it would have done as in run 1. I. On Sun, Dec 19, 2010 at 11:58 PM, Hailiang Zhang zhan...@umbc.edu wrote: Hi, I am using REFMAC

[ccp4bb] Bfactor is zero?

2010-12-20 Thread Zhibing Lu
Hi All, Recently I solved a structure in which some water molecules have Bfactors at 0 and overall wilson Bfactor is 0.654 based on PHENIX refinement. Is it possible? Bill Lu

Re: [ccp4bb] Bfactor is zero?

2010-12-20 Thread Nat Echols
On Mon, Dec 20, 2010 at 7:34 AM, Zhibing Lu billz...@gmail.com wrote: Recently I solved a structure in which some water molecules have Bfactors at 0 and overall wilson Bfactor is 0.654 based on PHENIX refinement. Is it possible? Very unlikely - it might be worth trying the latest nightly

Re: [ccp4bb] REFMAC 5.2.0019 question

2010-12-20 Thread Robbie Joosten
Dear Hailiang, I regularly separate TLS refinement from restraint refinement to spead things up when I try to optimise the restraint weights. Using Refmac 5.6, I do the following: - Do TLS Refinement in refmac - Use TLSanl to change the total B-factors to residual B-factors. - Load the output

Re: [ccp4bb] REFMAC 5.2.0019 question

2010-12-20 Thread Hailiang Zhang
Thanks Ian, but I was using the output from 2a for 2b running. Results are still different between 2 and 1. More curious is more second question, the region with identical ADPs still ended up with identical ADPs (although different from before running) after 1, and that's why I also tried 2.

Re: [ccp4bb] Bfactor is zero?

2010-12-20 Thread Ralf W. Grosse-Kunstleve
some water molecules have Bfactors at 0 B-factors refining towards zero may be an indication of heavier molecules, e.g. SO4. You have to model them manually. Ralf

Re: [ccp4bb] REFMAC 5.2.0019 question

2010-12-20 Thread Ed Pozharski
On Mon, 2010-12-20 at 13:11 -0500, Hailiang Zhang wrote: Thanks Ian, but I was using the output from 2a for 2b running. It's not enough to use the pdb output - you have to make the proper tls input file for refmac to incorporate the tls correction -- I'd jump in myself, if I weren't so good at

Re: [ccp4bb] If it is a new structure?

2010-12-20 Thread Clayton, Gina Martyn
Hi Liu Looks like (on the images you show) that you have a nice conformational difference for some of the helices between the 2 structures... Happy Hols Gina -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Justin Hall Sent: Monday, December 20,

Re: [ccp4bb] Mg2+ or water

2010-12-20 Thread Phil Evans
Mg2+ is (almost) aways octahedrally coordinated, usually by oxygen atoms, with distances of ~2A. Phil On 20 Dec 2010, at 21:16, jlliu liu wrote: Hi All, I am refining a structure and encountered a problem of modeling a difference density as water or Mg2+, and would like to hear opinions

Re: [ccp4bb] Mg2+ or water

2010-12-20 Thread Jacob Keller
what is the .odp file extension? JPK On Mon, Dec 20, 2010 at 3:48 PM, Robbie Joosten robbie_joos...@hotmail.com wrote: Dear jlliu liu, Also note that Mg2+ is significantly smaller than water. It fits in places where water cannot go. This doesn't look like a magnesium site on first glance.

Re: [ccp4bb] Mg2+ or water

2010-12-20 Thread Francis E Reyes
If it's more than likely Mg and it's easy to grow crystals, try soaking/cogrowing BaCl2/BaOAc. At least in the RNA world, Mg sites can easily be displaced by Ba. The latter of course has anomalous signal on the home sources. Place your divalents using the anomalous diff map. Have no clue

Re: [ccp4bb] Mg2+ or water

2010-12-20 Thread Paul Emsley
On 20/12/10 21:48, Robbie Joosten wrote: Also note that Mg2+ is significantly smaller than water. It fits in places where water cannot go. This doesn't look like a magnesium site on first glance. I tend to agree with Robbie. I wonder what WASP would say... (if you use Coot, you can try

Re: [ccp4bb] Mg2+ or water

2010-12-20 Thread Dima Klenchin
Sorry, the attachment is in here. Doesn't look like Mg2+ at all. Distances are too long, Mg is never coordinated by amides and if it were Mg you would have seen waters around it. Looks like tightly bound water to me. - Dima On Mon, Dec 20, 2010 at 4:16 PM, jlliu liu

Re: [ccp4bb] Bfactor is zero?

2010-12-20 Thread Ezra's gmail
On 12/20/2010 10:34 AM, Zhibing Lu wrote: Hi All, Recently I solved a structure in which some water molecules have Bfactors at 0 and overall wilson Bfactor is 0.654 based on PHENIX refinement. Is it possible? Bill Lu Hi Bill, What resolution are you working with here? An overall Wilson B

Re: [ccp4bb] Bfactor is zero?

2010-12-20 Thread Pavel Afonine
Hi Bill, if you put a water oxygen in place where a heavier atom is, then water oxygen's B-factor will refine to a value close to zero. This is the feature that we currently use as one of many criteria to develop automatic identification and building of metals. Overall Wilson B-factor of 0.6A**2