[ccp4bb] Is it possible to install stereo view in labtop or desktop?

Dear Everyone, I have to work at home because of the budget cut. However, I still want to do some research at this difficult time. I have been used to viewing the crystal structures with stereo view with program O. I want to find out is it possible to install the stereo option in my labtop.

Re: [ccp4bb] Why NCS doesn't help?

From: Eleanor Dodson c...@ysbl.york.ac.uk To: Sun Tang suntang2...@yahoo.com Cc: CCP4BB@jiscmail.ac.uk Sent: Wednesday, July 8, 2009 10:06:41 AM Subject: Re: [ccp4bb] Why NCS doesn't help? There are many reasons why this could have ocurred. One is that your NCS operator is very close to being

[ccp4bb] Why NCS doesn't help?

with the refinement? Thank you very much for your suggestions? Best wishes, Sun Tang

Re: [ccp4bb] How to refine a solution obtained by molecular replacement

Dear All, Thank you very much for all your suggestions. They are very helpful in my further refinements. I am adding some more information about the problem: 1) The Z-score is 11.2 and LLG is 125. 2) The model has 390 aa while my structure has about 440 aa.  Please let me know of any further

Re: [ccp4bb] question about getting rid of model bias in refinement

getting rid of model bias in refinement To: [EMAIL PROTECTED] Date: Thursday, July 31, 2008, 11:41 AM Sun Tang wrote: Hello Everyone, I have a question about getting rid of model bias in refinement with refmac. I solved the structure with molecular replacement. After final refinement

Re: [ccp4bb] question about getting rid of model bias in refinement

also allows you to make a composite-omit map.  I haven't seen that in phenix yet but presumably it is doable. Bill William G. Scott Contact info: http://chemistry.ucsc.edu/~wgscott/ On Jul 25, 2008, at 10:53 PM, Sun Tang wrote: Hello Everyone, I have a question about getting rid

[ccp4bb] question about getting rid of model bias in refinement

Hello Everyone,   I have a question about getting rid of model bias in refinement with refmac. I solved the structure with molecular replacement. After final refinement of the structure, I found out some key amino acids in the structure and wanted to make sure their conformations are correct. I

[ccp4bb] How to generate two molecules of proteins and two chains of RNA in CNS 1.2

downloaded the input files from the CNS website and I tried true and false for the renaming segid but all did not work. Thank you very much! Best, Sun Tang - Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now.

[ccp4bb] anomalous signal of Mn and Ca ions

to maximize the anomalous signal from Mn or Ca? Any ideas and suggestions are greatly appreciated! Sun Tang - Never miss a thing. Make Yahoo your homepage.

[ccp4bb] Check the conformation of one important amino acid

for your suggestions! Best wishes, Sun Tang - Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now.

Re: [ccp4bb] an over refined structure

ID = A46BEE1A On Mon, 4 Feb 2008, Sun Tang wrote: Hello All, I refined a structure with Refmac in CCP4i and the R/Rfree is 0.215/0.277. The difference between R and Rfree is too much even though I used 0.01 for weighting term in the refinement (the default value is 0.3). The RMSD

[ccp4bb] an over refined structure

. What may be wrong with the over-refined structure? What is the reason for leading to an over-refined structure? How to avoid it? Best wishes, Sun Tang - Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now.

Re: [ccp4bb] an over refined structure

and 0.186/0.267 (FOM=0.807) for wa=0.2, respectively. It seemed that increase in wa decreases both R and Rfree with R more than Rfree. Which wa value is the best one in this case? Thank you very much for your valuable help. Best, Sun Ian Tickle [EMAIL PROTECTED] wrote: Hi Sun Tang

Re: [ccp4bb] an over refined structure

Hi Anastassis, Thank you very much for your suggestions. I answered the questions as follows. I used NCS before rigid body refinement. After that I did not put NCS restraints in the restrained refinement and TLS+restrained refinement because it raised the R/Rfree quite a lot. The resolution is

Re: [ccp4bb] Why there are difference density when occupancy is 1.00

Hi James, I did check teh B-factors and they are similar to the flanking regions (about 40). The difference density appeared at the later stage of refinement (TLS and restrained in CCP4i). What do you think and how to do it? Best, Sun Tang James Irving [EMAIL PROTECTED] wrote: Hi Sun, I

[ccp4bb] Why there are difference density when occupancy is 1.00

occupancy for those residues? Thank you very much for your opinions and suggestions! Best wishes, Sun Tang - Never miss a thing. Make Yahoo your homepage.

[ccp4bb] How to refine a structure with ATP and AMP and pyrophosphate sharing the same density in CCP4i?

the TLS and restrained refinement in CCP4i. It is hard to tell from the R-factor because they are only a very small part of the whole structure. Can anyone tell whether it is the correct way to do? Any suggestions are greatly appreciated. Thank you very much! Sincerely, Sun

[ccp4bb] How to improve the density of another molecule in Asymmetric unit

, but for the second one, the density is much worse than the first one. Are there any ways to improve the density of the second molecule, such as some kinds of averaging? Why that happens? Thank you very much for your help! Sincerely, Sun Tang [EMAIL PROTECTED