Re: [ccp4bb] [phenixbb] [ccp4bb] Phenix refine distorting a sidechain despite correct density

2020-12-03 Thread Igor Petrik
Thanks for the advice Pavel! I don't want to celebrate prematurely, but I just re-ran the same refinement in both the stable and in nightly 4070, and it _seems_ to be corrected in the nightly. Will let you know if it pops up again. - Igor Petrik, PhD On Thu, Dec 3, 2020 at 9:16 AM Pavel

Re: [ccp4bb] Phenix refine distorting a sidechain despite correct density

2020-12-03 Thread Igor Petrik
Thanks Nigel, I will put together the input and output file from my latest refinement and send them to you and Pavel later today. - Igor Petrik, PhD On Wed, Dec 2, 2020 at 9:46 PM Folmer Fredslund wrote: > Dear Igor > > There's a phenix bulletin board for question like this, which

[ccp4bb] Phenix refine distorting a sidechain despite correct density

2020-12-02 Thread Igor Petrik
the coordinates back into the correct density and refine it again in phenix, they get distorted again. What settings in phenix should I check to try to get it to properly refine the coordinates? Thanks, - Igor Petrik, PhD

Re: [ccp4bb] Depositing data reduced with HKL2000 - ~half as many reflections in log file statistics

2020-11-21 Thread Igor Petrik
a big red error message, so I assumed it had to be fixed, but maybe I can just explain it. I will fix the deposition with the right coordinates and final mtz file, and try to deposit. - Igor Petrik, PhD On Sat, Nov 21, 2020 at 12:27 PM Jon Cooper wrote: > Hello, > > so the structure was

[ccp4bb] Depositing data reduced with HKL2000 - ~half as many reflections in log file statistics

2020-11-21 Thread Igor Petrik
st (see Refinement page) [23562]" When I open the original sca file in Phenix, I see: Number of Miller indices: 31365 Bijvoet pairs: 15030 What is the correct way to reconcile these numbers for the deposition? Thanks, - Igor Petrik, PhD P.S. I collected and processed the data 5+ years ago, an

[ccp4bb] Positions open: Structural Biologist (Computational), Ambry Genetics, CA, USA

2016-12-19 Thread Igor Petrik
systems Igor Petrik, PhD Structural Biologist I Ambry Genetics Direct 949.457.4721 ipet...@ambrygen.com<mailto:ipet...@ambrygen.com> www.AmbryGen.com<http://www.AmbryGen.com/> [http://www.ambrygen.com/resources/signature/logo.png] Confidentiality Notice: This e-mail message, inclu

[ccp4bb] XDS orientation matrix inconsistent with Mosflm, DENZO

2014-12-28 Thread Igor Petrik
point. Why is this and what is the proper way to obtain the absolute reciprocal orientation at 0 deg from XDS? (If anyone wants to test this on their own, I can provide the frames I used to obtain these files.) Thanks, - Igor Petrik University of Illinois

Re: [ccp4bb] XDS orientation matrix inconsistent with Mosflm, DENZO

2014-12-28 Thread Igor Petrik
Takanori and Pierre, Thank you for your quick responses. If you read my post you will see that I used the xds2mos.py script to convert the xds orientation to Mosflm format, but this gives me a result that is inconsistent with the matrix calculated directly by moslfm or DENZO. For orthorombic