- phenixbb - phenix-online.org

Solving a protein - ligand structure
by Tom Vanmarcke 20 May '20

20 May '20

Dear, We are trying to solve a protein structure that contains a ligand (polyoxometalate). We found the ligand in the electron density but through the middle of the ligand goes a 2 fold axis. For this reason, we placed the occupendency of the ligand on 0.50. When we try to refine the structure using phenix.refine, the ligand breaks down even when adding a cif restrain file. The cif restrain file contains information about atoms, angles and bond lengths. Is there a way to fix this problem? Greetings Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

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Is there a way to evaluate batch pdb models with Malprobity in phenix?
by Jing Liu 19 May '20

19 May '20

Hi, I had generate a batch of pdb models (40-100) in rosetta and am wondering whether there is a way to evaluate these models in batch with Molprobity. For example, can I use phenix command line to do it and how? Or should I download the Molprobity and do it on my local computer? Really appreciate if anyone can share their experience. Jing Liu, PhD Ted Jardetzky lab Department of Structural Biology Stanford University

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Phenix 1.18 and rotamer outliers
by Xavier Brazzolotto 18 May '20

18 May '20

I’ve installed the latest stable Phenix version (1.18). I’ve noticed a clear difference in the final statistics (MOLprobity) compared to the previous version (1.17). A bit more of Rama outliers and the most noticeable in the Rotamer outlier score. Is there any reason that could explain such behaviour ? I am using Phenix under MacOS. Xavier Brazzolotto, PhD xavier.brazzolotto(a)chemdef.fr Département de Toxicologie et Risques Chimiques Unité Neurotoxiques Institut de Recherche Biomédicale des Armées 1 Place du Général Valérie André, BP 73 91223 Brétigny sur Orge France Phone +33 (0) 1 78 65 14 00 Alt Phone +33 (0) 4 57 42 87 19 Cell +33 (0) 6 58 36 39 09 The information in this e-mail may be privileged and confidential, intended only for the use of the addressee(s) above. Any unauthorized use or disclosure of this information is prohibited. If you have received this e-mail by mistake, please delete it and immediately contact the sender. This is not an official email address of the French Ministry of the Armed Forces. It does not allow diffusion of protected informations and does not necessarily complies to the ministry cyber security policy.

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unit cell dimesions
by Thomas, Leonard M. 13 May '20

13 May '20

Hello All, I have run into something that has me a bit puzzled. When finishing up a structure we ended reprocessing the data to get nice statistics for deposition, I don’t want to get into that discussion. Upon reprocessing the unit cell dimensions shifted slightly, 0.05 A or so. The PDB file used had the unit cell from the original solution/refinement while the data set cell dimensions were different. I ran the newly processed reflection data set through the reflection editor in order to transfer the Rfree set. Now the really odd thing is that I ended up reprocessing a couple times and transferring over the Rfree set once more. The cell dimensions on the final reflection file is from not the original reflection file/PDB but one that was used with an intermediate cutoff between the two, it is not the cell dimensions in the input reflection either. Just for completeness the data were processed using XDS at SSRL. My question is where does phenix.refine pick up the unit cell dimensions and were does the reflection file editor pick them up? Best Regards Len Leonard Thomas, Ph.D. Macromolecular Crystallography Laboratory Oklahoma COBRE in Structural Biology Price Family Foundation Institute of Structural Biology University of Oklahoma Department of Chemistry and Biochemistry Stephenson Life Sciences Research Center 101 Stephenson Parkway Norman, OK 73019-5251 Office: (405)325-1126 lmthomas(a)ou.edu<mailto:[email protected]> http://www.ou.edu/structuralbiology/cobre-core-facilities/mcl

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install fail in linux
by 안우찬 12 May '20

12 May '20

Hi, I have a problem with install phenix-1.18.1-3865 in linux. My linux version is NAME="Red Hat Enterprise Linux Atomic Host" VERSION="7.4.0.4". The error massage is ============================================================================= Traceback (most recent call last): File "./bin/install.py", line 244, in <module> installer(sys.argv[1:]).install() File "/home01/x1959a02/phenix/phenix-installer-1.18.1-3865-intel-linux-2.6-x86_64-centos6/li b/libtbx/auto_build/install_distribution.py", line 190, in install self.check_directories() File "/home01/x1959a02/phenix/phenix-installer-1.18.1-3865-intel-linux-2.6-x86_64-centos6/li b/libtbx/auto_build/install_distribution.py", line 268, in check_directories os.makedirs(i) File "/usr/lib64/python2.7/os.py", line 157, in makedirs mkdir(name, mode) ============================================================================= Thanks in advance, Teddy Ahn

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How to compare between electron density maps?
by Murpholino Peligro 12 May '20

12 May '20

I want to compare electron density features of map A from protein A and map B from protein B... Because each map has a different rmsd level... ...what is the best way to compare electron density between maps? Is there a way to normalize maps or something like that? Thanks

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Is there a way to search the phenixbb mailing list archive?
by Murpholino Peligro 11 May '20

11 May '20

With the ccp4bb at https://www.jiscmail.ac.uk/cgi-bin/webadmin I can search for a term in the archive. Is there something similar in the phenixbb? Thanks Or... is there a way to wget all the gz files?

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Online Course on Neutron Scattering Applications in Structural Biology
by Meilleur, Flora 11 May '20

11 May '20

ORNL Online Course on Neutron Scattering Applications in Structural Biology (https://conference.sns.gov/event/217/) June 1 - June 5, 2020 2:00 pm - 5:30 pm EST Registration (free) is now open and will close May 17, 2020. This online course is designed for graduate students, post-doctoral researchers and faculty with knowledge of structure and function of biological macromolecules but with limited to no experience with neutron sciences. The course will cover the basics of deuterium labeling, small angle neutron scattering, neutron reflectometry, neutron spectroscopy, neutron imaging and neutron crystallography. Instrumentation, sample preparation, data collection and processing will be introduced for each neutron technique.

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Boost 1.70 update for cctbx
by Billy Poon 09 May '20

09 May '20

Hi everyone, There is currently a pull request for cctbx that will update Boost to 1.70 ( https://github.com/cctbx/cctbx_project/pull/409). The update enables support for Python 3.7 and 3.8. The plan is to merge this next Friday, May 8, at 3 pm Pacific. After merging, developers should delete the build/lib/*boost* files and build/boost directory so that any remnants of the old Boost are removed and then rebuild. Let me know if you have any questions. Thanks! -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 Fax: (510) 486-5909 Web: https://phenix-online.org

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Phenix installation
by Sam Tang 06 May '20

06 May '20

Hi I am installing Phenix on a Fedora 30 station. It complains line 15: /usr/bin/python: No such file or directory. I have checked that there is python3.7.3 pre-loaded. So did I miss anything obvious...? Brs Sam

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