[ccp4bb] How to reduce R factor

Dear Crystallographers, Can anybody guide me how to reduce R-factor, means which are the basic parameters I have to look for to reduce the R-factor during refinement. I am newly learning the refinement. After running molrep R-factor is around 53% (100% identity), after rigid body refinement

Re: [ccp4bb] mammalian expression vector

Hi Jerry, You may find that pcDNA3.1 won't give you the protein yields needed for crystallization. Have a look at PMID: 17001101 for an alternative. Your Kozak sequence looks good, radu -- A. Radu Aricescu, PhD University Research Lecturer MRC Career

Re: [ccp4bb] How to reduce R factor

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Dipankar, if you refine your model straight after molecular replacement you risk to further strengthen model bias which could result in hovering out features in your data which otherwise help you improve your model. Look at the model and the

Re: [ccp4bb] How to reduce R factor

Hi Dipankar If you've been reading the ccp4bb for more than a couple of weeks, you should have realised that reducing your R-factor is *not* the goal of refinement - having a low R-factor is one of the consequences of having built your model well and of having performed a good

Re: [ccp4bb] How to reduce R factor

Dear Dipankar, Molrep Rfactors around 50% with a model with 100% identity means that something went wrong and you did not find the solution. To find the problem, I would proceed as follows: 1) check the processing of the data and the space group: Are the statistics of the processing ok? Did you

Re: [ccp4bb] How to reduce R factor

Dear Dipankar, It just occurred to me that your high Rfactors may also be due to a large conformational change of your protein. In that case you have to split your search model in separate pdb files for the separate domains and rund Molrep with these separate domains. Best, Herman

Re: [ccp4bb] MTZ file

Dear crystallographers, According *UMA RATU*'s mtz labellings, *Vellieux Frederic *sir answered, output of the scalepack2mtz is used as master mtz for all refining (refmac5) input(if i am wrong, sorry ). am confused when Eleanor sir answered... here my labellings !!! scalepack2mtz

Re: [ccp4bb] MTZ file

Sorry my answers were confusing.. There are two problems. 1) When you finish data processing you should have the correct point group, but you may not have the correct spacegroup (SG). You will get an mtz file after processing, but may have to correct the SG later. Eg an orthorhombic point

Re: [ccp4bb] MTZ file

Mahesh, You should always use output_1.mtz for refinement. Dont use output_2. mtz for further refinement instead use some ccp4 utilities to change output_1.mtz (C222) to say output1_mod.mtz (C2221). This will become your master file for all further refinement. What ever remaining 2.mtz,

Re: [ccp4bb] MTZ file

This sentence in my previous posting may or may not be correct technically- May be make sure about this as it says reindex because only you need to rescale it like in HKL2000. It its wrong I am Sorry in advance. Date: Wed, 14 Mar 2012 07:43:15 -0500 From: ccp4...@hotmail.com Subject: Re:

Re: [ccp4bb] How to reduce R factor

On Wed, 2012-03-14 at 09:26 +, Dipankar Manna wrote: After running molrep R-factor is around 53% (100% identity), after rigid body refinement its showing around 49% and after restrained refinement its showing around 47%. Sounds like you didn't get a solution. With 100% identity MR in

Re: [ccp4bb] How to reduce R factor

Dipankar, An MR R-factor of 53% is close to what you get with a random, incorrect solution. Even for challenging MR cases, your MR R-factor should normally be under 50% before rigid-body refinement of the MR solution. As others have mentioned, you should not proceed directly to refinement

[ccp4bb] CrystFEL: Software for FEL crystallography

Hi all, This is just to draw the attention, of anyone who might find it interesting, to the availability of the first public version of CrystFEL: a new software suite for analysis of serial femtosecond crystallography data acquired using free-electron laser sources such as the Linac Coherent

[ccp4bb] March 15, 2012 deadline- User proposal submission for Collaborative Crystallography at BCSB

Dear Users, The deadline for May/June 2012 Collaborative Crystallography proposals will be *Mar 15, 2012. * Through the Collaborative Crystallography Program (CC) at the Advanced Light Source (ALS), scientists can send

[ccp4bb] Postdoctoral research associate in fragment-based inhibitor design

We are seeking to appoint a Research Associate in the group of Dr Marko Hyvonen to develop chemical tools against signalling proteins using fragment-based drug discovery methods. The post is part of a Wellcome Trust funded, multi-disciplinary programme between Departments of Biochemistry (Prof

Re: [ccp4bb] Help! weird thing

Dear all, Thank you very much for all the great suggestions on my case. Yes, I run the latest version of Phaser in Phenix. The analysis showed that there is one non-origin distinct peak more than 15 angstroms from the origin. 44.1% origin:FRAC 0.000 0.042 0.500 (ORTH -15.72.8 103.5)