Re: [ccp4bb] radiation damage-induced phasing (RIP) tutorial

Dear Murpholino, I must apologize, there was a mistake in may last email. The critical parameter is, as you correctly pointed out, DSCA not RIPW and it is necessary to try a range of values for DSCA. For this reason I am CCing this to CCP4bb. As you will be discovering, RIP phasing is not

Re: [ccp4bb] CH-bond length discrepancies

Hi Bernhard, You touch a valid point. You get different clash scores in MP depending on how you add hydrogens when you run it (unless this was solved recently). So you can essentially cheat the program by choosing a different H addition function. I don't get why this option exists at all. If

Re: [ccp4bb] CH-bond length discrepancies

Thanks to all respondents. It seems the source of the discrepancy is that some programs use nuclear distances and some use electron density peak distances. Now, does it matter, for example, using nuclear distances for placing riding Hs in the VdW terms, (i.e., a model for dipole

Re: [ccp4bb] CH-bond length discrepancies

Also, see figure 4 here: http://phenix-online.org/papers/dz5209_reprint.pdf that illustrates the difference. Pavel On Fri, Apr 28, 2017 at 10:33 AM, Bernhard Rupp wrote: > Dear Fellows of the Bond, > > > > when validating a QM refined homology model with Molprobity, I

Re: [ccp4bb] CH-bond length discrepancies

It totally depends on what you define as your C-H bond length. For XRD work, the C-H is the distance between the electron center-of-masses. For neutron or high-resolution XRD work, you can determine the distance between the nuclear center-of-masses. They are different by about 0.1A. The

Re: [ccp4bb] CH-bond length discrepancies

'Most distances between bonded atoms weresettled longago to highaccuracy, but,in the caseof hydrogens, the values in common use often differ by as muchas 20%.' Phenix / MolProbity

Re: [ccp4bb] radiation damage-induced phasing (RIP) tutorial

Dear Murph, the reason we placed more emphasis on data collection and processing for this tutorial is that the course for which it was created is on data collection and processing. With respect to Auto-Rickshaw, we used it as a convenient tool to check whether the experiment was successful. The

Re: [ccp4bb] radiation damage-induced phasing (RIP) tutorial

Dear Murpholino, I suspect that the pipelines in CCP4i and CCP4i2 do not include RIP phasing (perhaps they should) but you can also run the SHELX programs from a command line since you don't like black boxes. SHELXC reads XDS_ASCII.HKL files and has some special facilities for RIP, you can

Re: [ccp4bb] CALL CCPFYP: Segmentation fault: 11 (macOS Sierra Version 10.12.4)

I think one cannot rely on being able to use libraries compiled with compiler X with a program compiled with compiler Y. And your ifort result supports this. But you should be able to compile the CCP4 libraries with your gfortran. Then you can link them for sure. But why not use the ifort