Re: [ccp4bb] ionic interaction inside a protein

2013-03-24 Thread Seema Nath
The link is fine. If you still get the 'error message', then google "PIC webserver" , fullform of PIC - protein interactions calculator. Seema Nath

Re: [ccp4bb] How to convert file format from CNS to CCP4

2013-03-24 Thread Tommi Kajander
Ok. you filled my mailbox the second time today - please do stop sending junk to the list. -tommi On Mar 23, 2013, at 3:59 PM, Wei Feng wrote: > Dear Steffi, > Thank you very much for you patient reply! > I have tried to use your script to convert the map format, but no > ***omit_map.coeff c

Re: [ccp4bb] Isothermal titration calorimetry

2013-03-24 Thread Bosch, Juergen
Hi George, this is probably a very stupid suggestion and you likely have tried it, but I'll suggest the obvious nevertheless. What happens to your .nitc file when you rename it to .itc can you read it in Origin then ? Jürgen On Mar 24, 2013, at 6:39 AM, George Kontopidis wrote: Chris, indeed

Re: [ccp4bb] molecular replacement problem.

2013-03-24 Thread Appu kumar
Sorry for the misconception. Yes i am expanding the space group from merged mtz file. Actually i have enough number of images collected. when i indexed, integrate, and scale the data in either C2221 or P 21, it fetches the overall 98% completeness. But when i am trying to reindex the data from C2

Re: [ccp4bb] molecular replacement problem.

2013-03-24 Thread Raji Edayathumangalam
Dear Appu, You want to be sure you have good reason to drop the space group from C222(1) to P2(1). There may be many reasons why your Rfree may not drop following refinement, especially if you only have one domain in your protein located and just in case there are more molecules to locate in the M

[ccp4bb] How to add base-pair restraint between DNA strands?

2013-03-24 Thread 李翔
Hi guys, I need to manually build a model in Coot without a map. I want to link to 2 loops from 2 DNA strands together by base-pairings while keep the rest part as freezing as possible. The sequences of the loops are complimentary but the current orientations of the loops is not correct. Is there

Re: [ccp4bb] molecular replacement problem.

2013-03-24 Thread vellieux
Hello, Here we deal with symmetry and the unique part of reciprocal space (the reciprocal space "asymmetric unit" so to speak). C222(1) has eight asymmetric units (international tables, space group 20); P2(1) only has two. Assuming that Friedel's law does apply, then the minimum rotation ran

Re: [ccp4bb] Isothermal titration calorimetry

2013-03-24 Thread George Kontopidis
Chris, indeed nanoITC instrument analysis software is very robust and user friendly (probable more friendly than microcal, GE). Although when you need to subtract Q (heat) values (from 2 or 3 blank experiments) from your experimental data you cannot. NanoITC software can subtract Q values

Re: [ccp4bb] molecular replacement problem.

2013-03-24 Thread Appu kumar
I run the phenix.xtriage to evaluate the twining but it suggest no twining. When i reindex from C2221 to P21, the completeness of data reduced from 95 % to 35% whereas the map is very good and Rwork and Rfree are 26/31 for 2.2 resolution. I do not understand why the completeness of data reduced so

[ccp4bb] Question about DNA/RNA crystal annealing

2013-03-24 Thread Bernhard Spingler
Dear ccp4bb members, I would be most happy, if you could point me to any publications, in which results of crystal annealing by warming up a DNA/RNA/oligonuculeotide crystal and again cooling it down to low temperatures were reported. I am aware of 2 publications that discuss this for DNA/pro

Re: [ccp4bb] molecular replacement problem.

2013-03-24 Thread Appu kumar
Thank you for the quick reply. After molecular replacement , i have done only few cycle of refinement in refmac. I have not done any solvent modification or NCS averaging. I have initially indexed the data in C2221 but Rfree was not decreasing so i reindexed the data in data in P121 space group ke