Re: [ccp4bb] Building static libs.

Having struggled through similar build problems, I'd like to suggest augmenting the existing source and binary distributions with a distribution that includes header files and static libraries. thanks, Alastair Fyfe UCSC On 03/14/2015 05:17 AM, Ian Tickle wrote: Hello All I want to

Re: [ccp4bb] Bulk solvent

uot;, FPART and SCPART. However, this does not re-calculate kSol and bSol to reflect the modified mask. Is there a way to simply supply the mask to be used rather than have refmac calculate it ? Thanks, Alastair Fyfe On 01/11/2015 08:04 AM, Eleanor Dodson wrote: Yes. If the model is incomplete

[ccp4bb] monitoring refmac refinement

0979 This seems to happen rather erratically relative to changes in the model and I've been unable to determine which restraints/weights are responsible. Thanks for any pointers, Alastair Fyfe UCSC

Re: [ccp4bb] 6.4.0.1 update questions

yond the sources used to build the last binary distribution? Alastair On 08/04/2014 11:11 AM, Marcin Wojdyr wrote: On Thu, Jul 31, 2014 at 08:08:32PM -0700, Alastair Fyfe wrote: 2)6.4.0 binary bundles no longer include header files or static libraries. Thus to build local utilities the binary

[ccp4bb] 6.4.0.1 update questions

those from the last release. thanks, Alastair Fyfe UCSC

[ccp4bb] CCP4-JHBuild: how to build both static and shared libs?

Is there a JHBuild setting for requesting both static and shared libs? The default seems to only build *.so(s) and setting _build_static=True in conf.py only yields *.a(s). Thanks, Alastair Fyfe

Re: [ccp4bb] correct pdb encoding for split-personality solvent HETATM?

d a blank chain ID corresponds to PART 0. You may have to assign different residue numbers to CA and HOH, but I think this is also the case for shelxl. Does this resolve your problem? Best, Tim On 05/14/2014 07:48 PM, Alastair Fyfe wrote: On the subject of not (willfully) contaminating the pd

[ccp4bb] correct pdb encoding for split-personality solvent HETATM?

r software, eg mmdb. thanks, Alastair Fyfe

Re: [ccp4bb] EDS server - R-value

ed in many of the available mmCIF files? I should check.. thanks, Alastair On 04/04/2014 09:52 AM, Nat Echols wrote: On Fri, Apr 4, 2014 at 9:36 AM, Alastair Fyfe wrote: The topic brings up a question that I've been wondering about for some time, perhaps someone can enlighten me. Why

Re: [ccp4bb] EDS server - R-value

The topic brings up a question that I've been wondering about for some time, perhaps someone can enlighten me. Why is it not standard practice to deposit map coefficients along with structure factors ? Unlike image deposition there are no significant storage or file format issues. This would

[ccp4bb] saving map isovalue surface to file?

ecular surfaces, but I haven't found a reference for maps. thanks, Alastair Fyfe

Re: [ccp4bb] monovalent cation binding sites

in the map. Best, Alastair Fyfe On 11/09/2013 11:27 PM, Jrh wrote: Dear Alastair, This reference:- http://dx.doi.org/10.1107/S0907444903004219 seems related to your email input below. I would be grateful though to be guided with a couple of references from you on the topics you raise. T

Re: [ccp4bb] monovalent cation binding sites

nyone suggest a relevant reference? This seems a useful adjunct to bond-valence/non-bonding contact methods. thanks, Alastair Fyfe On 11/09/2013 03:24 AM, Robbie Joosten wrote: Hi Ed, WHAT_CHECK checks water that may be ions and also checks the identity of ions already built. The check my metal serv

Re: [ccp4bb] Comparison of Water Positions across PDBs

Elise - after looking into a related problem for some time, I've come to the conclusion it's a bit harder than it seems. Two obstacles: (1) there is no good coordinate system for partitioning the overall solvent volume (fraction of unit cell not occupied by protein density) into suitable "nei

Re: [ccp4bb] Fo simulators - summary

crystallographers out there, but to this day nobody has come up with a "systematic error" that, when accounted for in refinement, gives you a small-molecule-style R/Rfree for pretty much anything in the PDB. Not even lysozyme. -James Holton MAD Scientist On 9/5/2013 9:35 AM, A

[ccp4bb] Fo simulators - summary

Below are some links to tools for simulating Fobs data: phenix.fake_f_obs: http://cci.lbl.gov/cctbx_sources/mmtbx/command_line/fake_f_obs.py phenix.fmodel: http://cci.lbl.gov/cctbx_sources/mmtbx/command_line/fmodel.py sftools (calc keyword): http://www.ccp4.ac.uk/html/sftools.html diffraction

[ccp4bb] Fo simulators?

Any pointers to open-source software for generating (for legitimate purposes) simulated Fo data starting from Fc or pdb would be much appreciated. I understand phenix.fmodel is an option - are there others? thanks, Alastair Fyfe

Re: [ccp4bb] Deposition of riding H + what to deposit in addition to the pdb

>The pdbe.org, for example allows to upload auxiliary files and in my opinion the >uploading of the final .ins-file (not the .res-file!) should be made mandatory >in the case of shelxl refinement. >all the input files, e.g. command scripts/cif-files for ligands/.ins files etc. >should be atta

[ccp4bb] calculating solvent volume from molecular surfaces

Does anyone know of software that will segment a unit cell into volume internal/external to a calculated molecular surface ? thanks! Alastair Fyfe