On Sat, Mar 3, 2012 at 8:27 AM, Pavel Afonine wrote:

phenix.real_space_correlation

allows to compute correlations between nearly any user-defined maps, can use x-ray or neutron scattering dictionaries, accepts atoms selections, detail level (cc per residue, atom etc).

This doesn't let you define your own level of detail, e.g. CC for a domain, or a loop. It would need to be refactored to pick out map grid points corresponding to a user-input atom selection instead of each residue or each atom. This could theoretically be done for get_cc_mtz_pdb, but I think that uses RESOLVE internally to handle the origin shift, which makes it non-trivial to change. In this case it is probably overkill.

I don't remember if it is available in the GUI (Nat to confirm), if not then it would be good to have.

It's not in the GUI because I found it far too confusing - looking at the code again I am still not sure what some of the parameters mean. I assume this is because it's written to be flexible enough to handle two models or two maps in addition to model-vs-map, but this makes it far too cumbersome for routine use. The validation GUI includes the same residue-or-atom enumeration anyway, which is what 99% of users would use phenix.real_space_correlation for anyway. What Francis is asking for is something like this: phenix.some_awesome_new_command model.pdb data.mtz selection="rename LIG" which phenix.real_space_correlation cannot do, especially since it does not seem to be able to figure out what to do with model and data files automatically. -Nat

What does the validation in the GUI use? What is the CC being reported? atom or residue level? F On Mar 3, 2012, at 7:59 PM, Pavel Afonine wrote:

Also one needs to define which grid points to use: atom level, residue level or any user-defined (the latter is missing in phenix.real_space_correlation and can be trivially added). phenix.real_space_correlation automatically decides whether to use atom or residue level, depending on resolution (obviously, there is no much sense to compute cc per atom at say 4A resolution, while at 1A resolution cc per atom is justified and more informative than cc computed in any larger scale).

--------------------------------------------- Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

Dear All: I am using phenix-1.7.2 to refine my structure. Now i am facing a problem with .cif file. I could not generate cif files for a modified nucleic acid and MPD at same time with phenix.elbow or phenix.ready_set. If I use phenix.elbow to generate cif file for modefied nucleic acid only, phenix .refine complains about MPD cif not found, same for MPD. If I combine two cif files together, phenix.refine also complains. Is there better to generate cif file containing both modified nucleic acid and MPD? Many thanks for your help, Xue

Yes, I did try to import both cif files (for nucleic acid and MPD individually) into phenix.refine, but with no luck. any suggestion? Regards, Xue On Mon, 5 Mar 2012, Kelly Daughtry wrote:

Maybe I'm missing something here, but don't you just import both cif files (for nucleic acid, and MPD individually) into phenix.refine? Did you try that?Kelly Daughtry

******************************************************* Kelly Daughtry, Ph.D. Post-Doctoral Fellow, Raetz Lab Biochemistry Department Duke University Alex H. Sands, Jr. Building 303 Research Drive RM 250 Durham, NC 27710 P: 919-684-5178 *******************************************************

On Mon, Mar 5, 2012 at 12:29 PM, Xue-Yuan Pei wrote: Dear All: I am using phenix-1.7.2 to refine my structure. Now i am facing a problem with .cif file. I could not generate  cif files for a modified nucleic acid and MPD at same time with phenix.elbow or phenix.ready_set. If I use phenix.elbow to generate cif file for modefied nucleic acid only, phenix .refine complains about MPD cif not found, same for MPD. If I combine two cif files together, phenix.refine also complains. Is there better to generate cif file containing both modified nucleic acid and MPD? Many thanks for your help, Xue

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Hi Chen, You can set the target number of omit regions with the keyword n_box_target: n_box_target= None You can tell the Wizard how many omit boxes to try and set up (but it will not necessarily choose your number because it has to be nicely divisible into boxes that fit your asymmetric unit). A suitable number is 24. The larger the number of boxes, the better the map will be, but the longer it will take to calculate the map. The number of processors is up to you. The suggestion of 5 times the number of boxes is the maximum number of processors that would be useful. All the best, Tom T ________________________________________ From: [email protected] [[email protected]] on behalf of Qiang Chen [[email protected]] Sent: Monday, March 05, 2012 10:03 AM To: PHENIX user mailing list Subject: [phenixbb] SA-OMIT map/omit regions HI all, I want to use phenix.autobuild to calculate SA-OMIT map. BY default, it will be seperated into 16 regions. How could I set a different number of omit regions? Is there any difference of the final omit map by setting different regions? The phenix.autobuild manual says: If you are calculating an omit map, then use nproc=5 * number of omit regions (i.e., up to 100 or more, depending on how many processors you have). Does the * mean to use regions number to multiply 5? If my computer have 16 processors and I want to use 48 regions, so my command should be this: nproc=240. Am I right? Thank you! The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb