That makes perfect sense. Thanks for the quick and helpful reply Pavel. Oliver. On Tue, Aug 16, 2016 at 1:05 PM, Pavel Afonine wrote:

Hi Oliver,

it is only used to calculate correlation between experimental map and map calculated form the model (model-map CC). When you run phenix.real_space_refine you provide model and experimental map as inputs. To calculate model-map CC you need to calculate map from atomic model first. This is done by first calculating structure factors Fcalc from the model up to specified resolution and then FT'ing them into Fourier map that is then used to calculate CC.

Pavel

On 8/16/16 09:59, Oliver Clarke wrote:

...

Hi,

What exactly does phenix.real_space_refine do with the mandatory "resolution=" keyword when refining a model against a ccp4/mrc formatted map?

Is this purely for adjusting restraints etc, or does phenix internally low-pass filter or resample the map based on this parameter?

This seems like a basic question, so I apologize if the answer is staring me in the face, but I couldn't see it in the online documentation or in the output of phenix.real_space_refine --help.

Cheers Oliver.

?Hi Reza, Yes, if two crystals of your molecules are isomorphous then it is reasonable to guess that both the phases and the amplitudes for the two crystals are similar. In such a case, as a first approximation to the structure factors for either crystal, you could take the amplitudes from one and the phases for the other. You could also average phases or amplitudes from the two crystals. In all these cases you would want to be aware that you are using information from different crystals at this stage in structure determination and therefore that the maps that you would get would have mixed information about the two crystals. All the best, Tom T ________________________________ From: [email protected] on behalf of Reza Khayat Sent: Wednesday, August 24, 2016 5:48 AM To: [email protected] Subject: [phenixbb] Combining amplitudes and phases Hi, Is it possible to combine amplitudes from one dataset with phases from another? Assume that the systems are isomorphous. Thanks. Best wishes, Reza Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry New York, NY 10031

Hi Reza, In the simplest case, you can use the reflections editor in the GUI and select phases from one dataset and amplitudes from another. If you want to combine HL coefficients you can use a script to do it (see https://solve.lanl.gov/Resolve/html_resolve_manual/resolve_sample_scripts.ht... ). All the best, Tom T ________________________________ From: Reza Khayat Sent: Wednesday, August 24, 2016 6:28 AM To: Terwilliger, Thomas Charles; [email protected] Subject: Re: Combining amplitudes and phases Hi Tom, Thanks for the prompt response. This is what I'm trying to do. I'm having difficulty figuring out what Phenix programs to use for doing this. Best wishes, Reza ? Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry New York, NY 10031 ________________________________ From: Terwilliger, Thomas Charles Sent: Wednesday, August 24, 2016 8:23 AM To: Reza Khayat; [email protected] Cc: Terwilliger, Thomas Charles Subject: Re: Combining amplitudes and phases ?Hi Reza, Yes, if two crystals of your molecules are isomorphous then it is reasonable to guess that both the phases and the amplitudes for the two crystals are similar. In such a case, as a first approximation to the structure factors for either crystal, you could take the amplitudes from one and the phases for the other. You could also average phases or amplitudes from the two crystals. In all these cases you would want to be aware that you are using information from different crystals at this stage in structure determination and therefore that the maps that you would get would have mixed information about the two crystals. All the best, Tom T ________________________________ From: [email protected] on behalf of Reza Khayat Sent: Wednesday, August 24, 2016 5:48 AM To: [email protected] Subject: [phenixbb] Combining amplitudes and phases Hi, Is it possible to combine amplitudes from one dataset with phases from another? Assume that the systems are isomorphous. Thanks. Best wishes, Reza Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry New York, NY 10031

Dear Huanwang, Please find some about phenix.mtz_as_cif usage below. In the next nightly build it will be displayed if you run the tool without arguments. Please let me know if you need additional information. Best regards, Oleg Sobolev. phenix.mtz_as_cif: Convert mtz to CIF format. Usage: phenix.mtz_as_cif data.mtz [params.eff] [options ...] Usage examples: phenix.mtz_as_cif data.mtz ------------------------------------------------------------------------------- mtz_as_cif { mtz_file = None output_file = None mtz_labels = None cif_labels = None } On Thu, Aug 25, 2016 at 9:40 AM, Huanwang Yang wrote:

Dear developers,

Could you please let me know where I can find the documentation for phenix.mtz_as_cif? For other modules, if I type (--help) I can get good instruction of how to use it (for example, phenix.elbow --help). "phenix.mtz_as_cif --help" does not give useful information. I am using the latest public version.

Regards, Huanwang _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]

Dear Huawang, The tool will automatically recognize most of the labels from Phenix and CCP4 and convert them to appropriate labels for mmCIF format. If some labels are not recognized, or another mmCIF labels are needed for them, one may use mtz_labels and cif_labels parameters to provide pairs of mtz and cif labels. Note that provided cif_labels must comply with mmCIF format. Number of mtz_labels should be equal to number of cif_labels. In command-line, for example: phenix.mtz_as_cif data.mtz output_file=custom.cif mtz_labels="FOBS SIGFOBS" cif_labels="_refln.custom1 _refln.custom2" Or you can put these instructions in .eff file. Basically, mtz_labels and cif_labels are just white-space separated lists. In this example FOBS will become _refln.custom1 and SIGFOBS will become _refln.custom2. To find out what labels you have in mtz file you may use phenix.mtz.dump utility. Also note, that this functionality is available in GUI: Utilities-> Convert MTZ to mmCIF. Hope this helps, Best regards, Oleg Sobolev. On Thu, Aug 25, 2016 at 11:58 AM, Huanwang Yang wrote:

Dear Oleg,

Thank you so much for your help. In the parameter file, what should I give to the labels below

mtz_labels = None cif_labels = None

Could you provide an simple example for them? Thanks a lot.

Best, Huawang

On 08/25/2016 01:49 PM, Oleg Sobolev wrote:

Please find some about phenix.mtz_as_cif usage below. In the next nightly build it will be displayed if you run the tool without arguments. Please let me know if you need additional information.

Best regards, Oleg Sobolev.

phenix.mtz_as_cif: Convert mtz to CIF format. Usage: phenix.mtz_as_cif data.mtz [params.eff] [options ...]

Usage examples: phenix.mtz_as_cif data.mtz

------------------------------------------------------------ ------------------- mtz_as_cif { mtz_file = None output_file = None mtz_labels = None cif_labels = None }