- phenixbb - phenix-online.org

Alternative conformation on special position occupancy wrong
by Kaiser, Jens T. 21 May '20

21 May '20

Hi, We have a case of a cofactor with 222 symmetry in two states on a special position ( 2-fold). When modelling one state, Phenix correctly restrains the occupancy to 0.5. When putting state 2 in alternative conformation group B, the occupancy of altconf A and B is restrained to 1.0, instead of 0.5; it seems like it does not recognize that the alternative conformations are on a special position. Cheers, Jens Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

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Phenix version 1.18 released
by Paul Adams 21 May '20

21 May '20

The Phenix developers are pleased to announce that version 1.18 of Phenix is now available (build 1.18.2-3874). Binary installers for Linux, Mac OSX, and Windows platforms, and the source installer, are available at the download site: http://phenix-online.org/download/ Please note that this recent publication should now be used to cite the use of Phenix: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Liebschner D, Afonine PV, Baker ML, Bunkóczi G, Chen VB, Croll TI, Hintze B, Hung LW, Jain S, McCoy AJ, Moriarty NW, Oeffner RD, Poon BK, Prisant MG, Read RJ, Richardson JS, Richardson DC, Sammito MD, Sobolev OV, Stockwell DH, Terwilliger TC, Urzhumtsev AG, Videau LL, Williams CJ, Adams PD: Acta Cryst. (2019). D75, 861-877. https://doi.org/10.1107/S2059798319011471 Highlights for the 1.18.2 version of Phenix: 1.18.2 Changes - Fix weighting for iron sulfur clusters 1.18.1 Changes - General bug fixes 1.18 Changes - Amber - Automatic creation of Amber files in phenix.refine GUI - Added AmberPrep GUI - Restraints - Engh & Huber restraints (2001) for cis-peptides now implemented - Restraints added for FeS - Metal coordination library is default to Zn+2 and FeS clusters - Rama-Z: New global Ramachandran score for identifying protein structures with unlikely stereochemistry in CLI (phenix.rama_z, mmtbx.rama_z) and GUI (validation reports). - Density modification for cryo-EM - Includes model-based density modification with automatic model generation - Optimized defaults and additional documentation - Real-space refinement - Hydrogen atoms no longer included in map target function, which improves fit. - Add NQH flip option (enabled by default) - Other - New tool for ordered solvent picking in cryo-EM maps (phenix.douse) - New map and model superposition tool (phenix.match_maps) - New FindProgram to find any Phenix program with a text search - Project details now has a button for opening the README file for tutorials For a full list of changes see: http://www.phenix-online.org/documentation/CHANGES Please note that this new publication should be used to cite the use of Phenix: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Liebschner D, Afonine PV, Baker ML, Bunkóczi G, Chen VB, Croll TI, Hintze B, Hung LW, Jain S, McCoy AJ, Moriarty NW, Oeffner RD, Poon BK, Prisant MG, Read RJ, Richardson JS, Richardson DC, Sammito MD, Sobolev OV, Stockwell DH, Terwilliger TC, Urzhumtsev AG, Videau LL, Williams CJ, Adams PD: Acta Cryst. (2019). D75, 861-877. https://doi.org/10.1107/S2059798319011471 Full documentation is available here: http://www.phenix-online.org/documentation/ There is a Phenix bulletin board: http://www.phenix-online.org/mailman/listinfo/phenixbb/ Please consult the installer README file or online documentation for installation instructions. Direct questions and problem reports to the bulletin board or: help(a)phenix-online.org and bugs(a)phenix-online.org Commercial users interested in obtaining access to Phenix should visit the Phenix website for information about the Phenix Industrial Consortium. The development of Phenix is principally funded by the National Institute of General Medical Sciences (NIH) under grant P01-GM063210. We also acknowledge the generous support of the members of the Phenix Industrial Consortium. -- Paul Adams Division Director, Molecular Biophysics & Integrated Bioimaging, LBL (http://biosciences.lbl.gov/divisions/mbib) Principal Investigator, Computational Crystallography Initiative, LBL (http://cci.lbl.gov) Vice President for Technology, the Joint BioEnergy Institute (http://www.jbei.org) Principal Investigator, ALS-ENABLE, Advanced Light Source (http://als-enable.lbl.gov) Division Deputy for Biosciences, Advanced Light Source (https://als.lbl.gov) Laboratory Research Manager, ENIGMA Science Focus Area (http://enigma.lbl.gov) Adjunct Professor, Department of Bioengineering, U.C. Berkeley (http://bioeng.berkeley.edu) Adjunct Professor, Comparative Biochemistry, U.C. Berkeley (http://compbiochem.berkeley.edu) Building 33, Room 250 Building 978, Room 4126 Building 977, Room 180C Tel: 1-510-486-4225 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 33R0345 Berkeley, CA 94720, USA. Executive Assistant: Ashley Dawn [ ashleydawn(a)lbl.gov ][ 1-510-486-5455 ] --

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Generating a polder map using coordinates
by Petr Kolenko 21 May '20

21 May '20

Dear colleagues, Is there a way to calculate the polder map in a selected box using coordinates instead of atom selection as shown in the "Generating a polder map with the compute_box option" website? Best regards, Petr

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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. 14 May '20

14 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 12 May '20

12 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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