I know that feeling all too well! Cheers, Tristan ________________________________ From: [email protected] on behalf of Pavel Afonine Sent: Tuesday, 23 February 2016 1:47 AM To: [email protected] Subject: Re: [phenixbb] Feature request: multi-stage refinement protocols from the GUI? Hi Tristan, I've been willing to do this for years now. In fact it would help to automate refinement by dynamically casting refinement strategies and parameters as refinement progresses. Unfortunately no, this functionality is not available. It is not too difficult to implement, may be a week of focused work. The biggest problem is that the (only) way this can be done will brake a lot of backwards compatibility and will require a lot of changes in the GUI because the main{} scope of parameters will have to become of type "multiple". So far this was the major demotivator for me to do it. All the best, Pavel On 2/22/16 15:36, Tristan Croll wrote: Hi all, I'm personally a big fan of the Phenix GUI, in particular for its automated record keeping for different runs. One thing I really wish it had, though, is the option to define more complex refinement scenarios as a single run. An example of what I'm talking about is the following protocol that has been working very well for me on a 3.6 Å strucutre: - ~6 rounds of refinement of TLS, a single group B-factor and occupancies (the latter for a very small set of residues, mostly low-occupancy lead ions) with positions fixed - ~8 rounds of TLS and individual B-factor refinement, still with positions fixed and with no further occupancy refinement - ~8 rounds of TLS, B-factor and position refinement with torsion-angle restraints to the starting model - ~8 rounds of position refinement with no restraints other than standard stereochemistry and metal bonds. I know that all of this could be scripted quite easily from the command line, but it would be fantastic to be able to queue up such a protocol as a single continuous job in the GUI. Best regards, Tristan _______________________________________________ phenixbb mailing list [email protected]mailto:[email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]mailto:[email protected]

Hi Miyatake, could you please send me (and copy to Nigel) the PDB file (and any ligand CIF files you use) and tell what bonds you are expecting to have and that brake as result of refinement. Thanks, Pavel On 3/7/16 03:40, miyatake wrote:

Dear all,

I'm trying to a mutant of eYFP, which has fluorescence group, CR2.

During the refinement, however, the bonds between the CR2 and other amino acids were cleaved even I added the cif file created by the ReadySet.

Would some one give me suggestions to solve the problem?

Miyatake

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Miyatake The OXT atom in the restraints file is there because it can be in the model. You need to remove the atom from the model if you don't want it. Also, Coot's make link does not make a link in Phenix. You need to rely on the automatic linking or provide your own. You can check that the link is present in the refinement by checking the .geo file. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov On Mon, Mar 7, 2016 at 11:06 PM, miyatake wrote:

Dear Pavel,

Thank you for your e-mail.

The bonds I want to connect are between CR2 and amino acids like below;

C PHE A 64 N1 CR2 A 66 C3 CR2 A 66 N LEU A 68

so I made links by the "make link" of Coot.

Then I made .cif file by the Ready_Set, but I noticed it always contained OTX terminator atom of CR2, so the CR2 connections to the next amino acids were something wrong after refinement if I used the cif as it was.

Thus I deleted OTX in the cif file, and then in turn it went well.

I wonder why the cif file contained OTX, is it something a bug?

Thank you for your attention.

Miyatake

On Mon, 7 Mar 2016 08:40:21 -0800 Pavel Afonine wrote:

...

Hi Miyatake,

could you please send me (and copy to Nigel) the PDB file (and any ligand CIF files you use) and tell what bonds you are expecting to have and that brake as result of refinement.

Thanks, Pavel

On 3/7/16 03:40, miyatake wrote:

...

Dear all,

I'm trying to a mutant of eYFP, which has fluorescence group, CR2.

During the refinement, however, the bonds between the CR2 and other amino acids were cleaved even I added the cif file created by the ReadySet.

Would some one give me suggestions to solve the problem?

Miyatake

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Hi , I am solving a structure using selenium SAD using autosol. Autosol gave me nice solution but many loop and side chain density is missing. autosol gave me many different output MTZ files . for building further in coot which MTZ file i should use and for refinement in phenix refinement which MTZ file i should use . I tried doing refinement with .sca file it gave me increase Rfree afte single cycle of refinement . thanks for your suggestions. -Vandna