On 6/27/13 7:12 AM, Nathaniel Echols wrote:

On Wed, Jun 26, 2013 at 3:51 PM, Pavel Afonine wrote:

...

Hm.. this isn't easy.. phenix.refine automatically identifies disulfide bonds and creates restrains for them. This is controlled by disulfide_distance_cutoff=3 parameter. You can set it to some big number, so none desulfide bonds will be created automatically Are you sure it's not the reverse? I think this number sets the maximum distance allowed for disulfides; increasing it will just bond more distant atoms.

yes, I guess you are correct. One can quickly check using: phenix.pdb_interpretation model.pdb write_geo_files=true disulfide_distance_cutoff=0 Pavel

Hi Ursula, could you please send me the model and data files off list and indicate unwanted S-S bonds? I may just implement automatic (or at least easier than now) handling of this today or over the week-end. Thanks, Pavel

So how do people deal with this? I would think close cysteines are fairly common in metal coordination sites.

Ursula

On Thu, Jun 27, 2013 at 7:12 AM, Nathaniel Echols mailto:[email protected]> wrote:

On Wed, Jun 26, 2013 at 3:51 PM, Pavel Afonine mailto:[email protected]> wrote: > Hm.. this isn't easy.. phenix.refine automatically identifies disulfide > bonds and creates restrains for them. This is controlled by > disulfide_distance_cutoff=3 parameter. You can set it to some big number, so > none desulfide bonds will be created automatically

Are you sure it's not the reverse? I think this number sets the maximum distance allowed for disulfides; increasing it will just bond more distant atoms.

-Nat

In the short term, just lower the distance cutoff - I suspect 2.0 would be a good starting point as long as the initial model is fairly accurate. I wouldn't put it all the way at zero (this may have weird side effects), but any arbitrarily low value will eventually prevent any disulfides from being formed, if that's what you want. -Nat On Thu, Jun 27, 2013 at 9:17 AM, Ursula Schulze-Gahmen wrote:

So how do people deal with this? I would think close cysteines are fairly common in metal coordination sites.

Ursula

On Thu, Jun 27, 2013 at 7:12 AM, Nathaniel Echols wrote:

...

On Wed, Jun 26, 2013 at 3:51 PM, Pavel Afonine wrote:

...

Hm.. this isn't easy.. phenix.refine automatically identifies disulfide bonds and creates restrains for them. This is controlled by disulfide_distance_cutoff=3 parameter. You can set it to some big number, so none desulfide bonds will be created automatically

Are you sure it's not the reverse? I think this number sets the maximum distance allowed for disulfides; increasing it will just bond more distant atoms.

-Nat _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

-- Ursula Schulze-Gahmen, Ph.D. Assistant Researcher UC Berkeley, QB3 356 Stanley Hall #3220 Berkeley, CA 94720-3220

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

Sorry for duplicating the answer. I haven't seen Nat's comment. Vaheh -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Oganesyan, Vaheh Sent: Thursday, June 27, 2013 1:43 PM To: PHENIX user mailing list Subject: Re: [phenixbb] unwanted disulfids and geometry restraints I think it should be a smaller number, not bigger. Vaheh -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Pavel Afonine Sent: Wednesday, June 26, 2013 6:52 PM To: PHENIX user mailing list Subject: Re: [phenixbb] unwanted disulfids and geometry restraints Hi Ursula,

1) I am using phenix.refine on the command line with a .eff file as input that was modified from previous GUI phenix runs. My structure has several Zn atoms and readyset creates a geometry_restraints file for the Zn interactions. I am not sure if phenix.refine gets these restraints when I run it from the command line.

check *.geo file that lists all geometry restraints used in refinement. IF restraints in questions are not there then there is a problem.

Do I need to read this file in some specific way?

No, just specify it in the command line along with all other files.

2) The other question is: phenix refines several of the Cysteine neighbors in the Zn environment as disulfids, but they are not. How do I prevent this from happening?

Hm.. this isn't easy.. phenix.refine automatically identifies disulfide bonds and creates restrains for them. This is controlled by disulfide_distance_cutoff=3 parameter. You can set it to some big number, so none desulfide bonds will be created automatically, but then you will need to specify those that you want to have using "Custom bonds": http://www.phenix-online.org/documentation/refinement.htm#anch354 Sorry, not an easy solution but if desperate you can do it! Pavel _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb To the extent this electronic communication or any of its attachments contain information that is not in the public domain, such information is considered by MedImmune to be confidential and proprietary. This communication is expected to be read and/or used only by the individual(s) for whom it is intended. If you have received this electronic communication in error, please reply to the sender advising of the error in transmission and delete the original message and any accompanying documents from your system immediately, without copying, reviewing or otherwise using them for any purpose. Thank you for your cooperation. _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb To the extent this electronic communication or any of its attachments contain information that is not in the public domain, such information is considered by MedImmune to be confidential and proprietary. This communication is expected to be read and/or used only by the individual(s) for whom it is intended. If you have received this electronic communication in error, please reply to the sender advising of the error in transmission and delete the original message and any accompanying documents from your system immediately, without copying, reviewing or otherwise using them for any purpose. Thank you for your cooperation.