[ccp4bb] PHENIX error: No refinement carried out (may need free R flags)

2012-02-24 Thread Naveed A Nadvi
Hello Fellow PHENIX users (and others!) I had been using PHENIX to generate iterative build composite OMIT maps. I was able to perform these runs with automated settings for two of my data. With the third one (1.2 A structure) I get an error. I am pasting a part of the message below:

[ccp4bb] Disulfide bonds

2012-03-03 Thread Naveed A Nadvi
Hello everyone, I was wondering if there is any information available regarding the range of Ca-to-Ca distances between two cysteine residues forming disulfide bonds. Is there any software available for analysing the PDB for this kind of information? Some old textbooks suggest a distance of 4.4

[ccp4bb] unique reflections vs unique observations

2012-04-15 Thread Naveed A Nadvi
Dear CCP4 users, I am a bit confused about the use of these terms in regards to structure refinement statistics. When I process my data with SCALA, the program outputs statistics in terms of "total and unique numbers of observations". However, when I use the MTZ files with REFMAC, the final PDB

[ccp4bb] Criteria for Ligand fitting

2012-04-23 Thread Naveed A Nadvi
Dear Crystallographers, We have obtained a 1.7 A dataset for a crystal harvested from crystallization drop after 2 weeks of soaking with inhibitor. The inhibitor has an aromatic ring and also an acidic tail derived from other known inhibitors. The active site hydrophobic crown had been reporte

Re: [ccp4bb] Criteria for Ligand fitting

2012-04-24 Thread Naveed A Nadvi
Dear Crystallographers, Thank you all for responding! I will try to respond to the suggestions collectively. I did however have some questions for some of these suggestions... @Herman Schreuder: I have performed refinement with alt conform as you suggested. I am not sure how to do group-occupan

[ccp4bb] Multiple structure alignment and citing CCP4bb

2012-05-14 Thread Naveed A Nadvi
Hello everyone, I was wondering if there is any software out there that can be used for multiple structure superimposition and output some graphical plot of residues based on their deviation from the reference molecule. I want to highlight how entire residues undergo conformational change in th