[ccp4bb] few questions about resolving new structure through MR

2013-11-07 Thread Zhihong Yu
Hi, all I'm a rookie in resolving a brand new structure. I have some questions for my current case and look forward to some suggestions. Now I’m working on a protein like this: N-ter(55aa)—domainA(110aa)—linker(30aa)—domainB(150aa)—C-ter(20aa), I got a diffraction data just to 3.5Å, and there is

Re: [ccp4bb] few questions about resolving new structure through MR

2013-11-07 Thread Roger Rowlett
Count yourself lucky that you may have a partial solution for your structure with only 30% identity. The question now is: can you see any reasonable, traceable electron density for domain A? Cheers, ___ Roger S. Rowlett Gordon Dorothy Kline Professor

Re: [ccp4bb] few questions about resolving new structure through MR

2013-11-07 Thread Greg Costakes
- Original Message - From: Zhihong Yu nkyuz...@gmail.com To: CCP4BB@JISCMAIL.AC.UK Sent: Thursday, November 7, 2013 11:36:51 AM Subject: [ccp4bb] few questions about resolving new structure through MR Hi, all I'm a rookie in resolving a brand new structure. I have some questions for my

Re: [ccp4bb] few questions about resolving new structure through MR

2013-11-07 Thread Zhihong Yu
, November 7, 2013 11:36:51 AM *Subject: *[ccp4bb] few questions about resolving new structure through MR Hi, all I'm a rookie in resolving a brand new structure. I have some questions for my current case and look forward to some suggestions. Now I’m working on a protein like this: N-ter(55aa

Re: [ccp4bb] few questions about resolving new structure through MR

2013-11-07 Thread Tim Gruene
- -- *From: *Zhihong Yu nkyuz...@gmail.com *To: *CCP4BB@JISCMAIL.AC.UK *Sent: *Thursday, November 7, 2013 11:36:51 AM *Subject: *[ccp4bb] few questions about resolving new structure through MR Hi, all I'm a rookie in resolving a brand new structure. I have some

Re: [ccp4bb] few questions about resolving new structure through MR

2013-11-07 Thread Francis Reyes
Do you expect more than one molecule in the asymmetric unit? Determined from the Matthews Coefficient (poor), size exclusion column (better), or self RF (best) ? On Nov 7, 2013, at 8:36 AM, Zhihong Yu nkyuz...@gmail.com wrote: Hi, all I'm a rookie in resolving a brand new structure. I

Re: [ccp4bb] few questions about resolving new structure through MR

2013-11-07 Thread Zhihong Yu
Thanks Francis, No, only one molecule in the asu. The Matthews Coefficient is 3.3, corresponding solvent content is 62.6%, maybe that's why this crystal show such weak diffraction? Zhihong On Thu, Nov 7, 2013 at 5:37 PM, Francis Reyes francis.re...@colorado.eduwrote: Do you expect more than

Re: [ccp4bb] few questions about resolving new structure through MR

2013-11-07 Thread Zhihong Yu
-optimal cases Best, Debanu. From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of Zhihong Yu [nkyuz...@gmail.com] Sent: Thursday, November 07, 2013 2:53 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] few questions about resolving new

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

2010-12-21 Thread Sergii Buth
Dear CCP4 users, I would like to draw your attention to the topic If it is a new structure?, which is one more case, when new community members were welcomed, and were gently explained about the rules of files sharing, as it is an evidence, that the rules about files sharing are not well

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

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] If it is a new structure?

2010-12-20 Thread Clayton, Gina Martyn
, 2010 8:57 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] If it is a new structure? 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