- phenixbb - phenix-online.org

on ligand restraint
by Smith Lee 05 Oct '15

05 Oct '15

Dear All, Does phenix.refine can process some ligands without the process by eLBOW, for example ATP, ADP,etc? Smith

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Selection of Torsion NCS restraint groups
by Victor Xiao 03 Oct '15

03 Oct '15

Dear all, I have a protein-DNA structure that has six molecules in ASU. All six molecules share the same sequence and very similar structure. However, only three of them bind to DNA and conformations are slightly different from the other three. By default, PHENIX will consider six molecules into the same NCS group. Now I am trying to set up two NCS group, e.g. chain A,B,C are in one group (no-DNA), chain D, E, F are in another group (DNA-bound). So I did the following steps: 1. I used PHENIX GUI and go to 'Utilities' -> 'Detect NCS Groups'. 2. Put chain A, B, C in 'Torsion NCS restraint group 1'. 3. 'Add group' and put chain D, E, F in 'Torsion NCS restraint group 2'. 4. Click 'Update and exit'. However, after that, when I re-open 'Utilities' -> 'Detect NCS Groups', I found all six chains A-F are in group 1, and all six chains A-F in group 2. Did I do something incorrectly? Or any other suggestion for my purpose? Thank you! Best, Xiao

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Phenix eLBOW output cif missing Chi angle information
by Xiao Lei 02 Oct '15

02 Oct '15

Hi Phenix BB members, I tried to generate restraints of 3-METHYL-BETA-D-ASPARTIC ACID (PDB 3 letter code ACB, http://www.rcsb.org/pdb/ligand/ligandsummary.do?hetId=ACB). I am using this as a template for D-iso-aspartic acid in my model because I can not find a 3 letter code for the exact D-iso-aspartic acid (I know for L-iso-aspartic acid the code is IAS but no code for D-iso-aspartic acid) I can search in Phenix eLBOW (Mac Phenix Version 1.10pre) with code ACB and I can find the code and right compound, I tried to generate restraints of ACB using eLBOW and I got a cif and pdb output of the compound. However when I import the compound into coot, delete the methyl group to make the compound a D-isoAsp, and click "edit chi angles", I receive an error: This residue does not have assigned torsion/chi angles". I do not know what I should do to fix the problem. I thought eLBOW would automatically generate Chi angles but actually it did not in my case. I appreciate if you have any input on this. [image: Inline image 1]

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Non crystallographic symmetry
by Reza Khayat 01 Oct '15

01 Oct '15

Hi, I need to use icosahedral symmetry to refine a virus crystal structure. Does phenix support 60 NCS matrices? If not, how should I go about recompiling the program so that I can have 60 NCS matrices? Best wishes, Reza Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry New York, NY 10031

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on phenix.refine
by Smith Liu 30 Sep '15

30 Sep '15

Dear All, If my protein contains a metal ion (Mg2+ for example, do I need a cif for the metal for phenix.refine? If my protein contains another ligand, which server can produce the ligand PDB suitable for the eLBOW? If my protein contains 2 ligands, then do I need 2 cif files for the phenix.refine or the phenix.real_space_refine? I am looking forward to getting your reply. Best regards. Smith

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on Phenix10
by Smith Lee 28 Sep '15

28 Sep '15

Dear All, With the EM cryo data, I have compared the function of phenix.real_space_refine of Phenix10 and Phenix1.9-1692. For the Ramachandran favored, the new version is about 90%, the old version is about 92%. For the clashscore by Molprobity, the new version is about 30, the old version is about 20. Molprobity indicated the clashing atoms were systematically existing in the whole molecule, rather than on specific parts of the protein which may be indication of bad modelling. Clearly the clashscore of 30 is unacceptable. Will you please give some advise on how to improve the function of new version of Phenix, considering adding H was not suitable as for the resolution was poorer than 4.0 A? Smith

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Re: [phenixbb] Rosetta refine compilation issue Centos 7 (ludovic Pecqueur)
by Kay Diederichs 27 Sep '15

27 Sep '15

just a wild guess - could it be that, according to http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Phenix#Installa… the Phenix installer requires (on Fedora and RHEL) the openssl-devel and libXt-devel to be installed on the system ? HTH, Kay Am 28.09.15 um 03:24 schrieb phenixbb-request(a)phenix-online.org: > 8. Re: Rosetta refine compilation issue Centos 7 (ludovic Pecqueur) > > Message: 7 > Date: Wed, 23 Sep 2015 14:09:08 -0700 > From: Paul Adams <pdadams(a)lbl.gov> > To: ludovic Pecqueur <ludovic.pecqueur(a)college-de-france.fr> > Cc: phenixbb(a)phenix-online.org > Subject: Re: [phenixbb] Rosetta refine compilation issue Centos 7 > Message-ID: <68387823-8DAE-4C7F-84DF-5D79D36A3AD0(a)lbl.gov> > Content-Type: text/plain; charset=us-ascii > > Hi Ludovic, > > the problems seem to occur when scons is called to compile Rosetta. I notice that the scons.py file uses the python that appears first in your path (#! /usr/bin/env python). Is it possible that this is a python that is broken in some way? > > Cheers, > Paul > >> On Sep 23, 2015, at 9:11 AM, ludovic Pecqueur <ludovic.pecqueur(a)college-de-france.fr> wrote: >> >> Dear Developers, >> >> I have a fresh Centos 7 system and after installing Phenix I wanted to compile the Rosetta.refine module. (Rosetta from source version 2015.31.58019) >> >> I have succesfully compiled Rosetta but when I try to build the dedicated Rosetta for Rosetta_refine with rosetta.build_phenix_interface after setting up PHENIX_ROSETTA_PATH and ROSETTA3_DB I get the following error message: >> >> [XXX@...]$ rosetta.build_phenix_interface nproc=6 >> False >> scons: Reading SConscript files ... >> Running versioning script ... Done. (0.1 seconds) >> Could not find platform independent libraries <prefix> >> Could not find platform dependent libraries <exec_prefix> >> Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>] >> ImportError: No module named site >> CalledProcessError: Command '['./update_options.sh']' returned non-zero exit status 1: >> File "/usr/local/PROGRAMS/ROSETTA/PHENIX_Rosetta_refine/main/source/SConstruct", line 172: >> main() >> File "/usr/local/PROGRAMS/ROSETTA/PHENIX_Rosetta_refine/main/source/SConstruct", line 163: >> SConscript("SConscript", "build") >> File "/usr/local/PROGRAMS/ROSETTA/PHENIX_Rosetta_refine/main/source/external/scons-local/scons-local-2.0.1/SCons/Script/SConscript.py", line 614: >> return method(*args, **kw) >> File "/usr/local/PROGRAMS/ROSETTA/PHENIX_Rosetta_refine/main/source/external/scons-local/scons-local-2.0.1/SCons/Script/SConscript.py", line 551: >> return _SConscript(self.fs, *files, **subst_kw) >> File "/usr/local/PROGRAMS/ROSETTA/PHENIX_Rosetta_refine/main/source/external/scons-local/scons-local-2.0.1/SCons/Script/SConscript.py", line 260: >> exec _file_ in call_stack[-1].globals >> File "/usr/local/PROGRAMS/ROSETTA/PHENIX_Rosetta_refine/main/source/SConscript", line 28: >> subprocess.check_call(["./update_options.sh"]) >> File "/usr/local/PROGRAMS/XTAL/PHENIX/phenix-1.10-2155/base/lib/python2.7/subprocess.py", line 540: >> raise CalledProcessError(retcode, cmd). >> >> If you have any idea of what could cause the problem, I would welcome any suggestions. >> I updated Phenix and I could compile phenix.rosetta_refine without problems on Centos 6.7. >> >> Thank you very much for your time and help. >> >> Kind regards, >> >> Ludovic. >> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >> Unsubscribe: phenixbb-leave(a)phenix-online.org >

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Rosetta refine compilation issue Centos 7
by ludovic Pecqueur 24 Sep '15

24 Sep '15

Dear Developers, I have a fresh Centos 7 system and after installing Phenix I wanted to compile the Rosetta.refine module. (Rosetta from source version 2015.31.58019) I have succesfully compiled Rosetta but when I try to build the dedicated Rosetta for Rosetta_refine with rosetta.build_phenix_interface after setting up PHENIX_ROSETTA_PATH and ROSETTA3_DB I get the following error message: [XXX@...]$ rosetta.build_phenix_interface nproc=6 False scons: Reading SConscript files ... Running versioning script ... Done. (0.1 seconds) Could not find platform independent libraries <prefix> Could not find platform dependent libraries <exec_prefix> Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>] ImportError: No module named site CalledProcessError: Command '['./update_options.sh']' returned non-zero exit status 1: File "/usr/local/PROGRAMS/ROSETTA/PHENIX_Rosetta_refine/main/source/SConstruct", line 172: main() File "/usr/local/PROGRAMS/ROSETTA/PHENIX_Rosetta_refine/main/source/SConstruct", line 163: SConscript("SConscript", "build") File "/usr/local/PROGRAMS/ROSETTA/PHENIX_Rosetta_refine/main/source/external/scons-local/scons-local-2.0.1/SCons/Script/SConscript.py", line 614: return method(*args, **kw) File "/usr/local/PROGRAMS/ROSETTA/PHENIX_Rosetta_refine/main/source/external/scons-local/scons-local-2.0.1/SCons/Script/SConscript.py", line 551: return _SConscript(self.fs, *files, **subst_kw) File "/usr/local/PROGRAMS/ROSETTA/PHENIX_Rosetta_refine/main/source/external/scons-local/scons-local-2.0.1/SCons/Script/SConscript.py", line 260: exec _file_ in call_stack[-1].globals File "/usr/local/PROGRAMS/ROSETTA/PHENIX_Rosetta_refine/main/source/SConscript", line 28: subprocess.check_call(["./update_options.sh"]) File "/usr/local/PROGRAMS/XTAL/PHENIX/phenix-1.10-2155/base/lib/python2.7/subprocess.py", line 540: raise CalledProcessError(retcode, cmd). If you have any idea of what could cause the problem, I would welcome any suggestions. I updated Phenix and I could compile phenix.rosetta_refine without problems on Centos 6.7. Thank you very much for your time and help. Kind regards, Ludovic.

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a question on phenix refine
by Smith Liu 23 Sep '15

23 Sep '15

Dear All, If my protein is rather large, and I have the mtz file of the whole protein, when I do phenix.refine of a single domain PDB of the whole protein against the whole protein mtz, after several cycles of phenix.refine the domain will not fit in the map at all (or even the domain moves far away from its initial position in map which it fits best), perhaps because the phenix.refine has made the domain to seek suitable fit in the map. Is any possibility at the whole process of phenix.refine we keep the domain relatively surround the map position where it fit best, so that phenix.refine will really do the refine in this situation? Best regards. Smith

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ADP restraints under TLS+individual ADP
by Tristan Croll 23 Sep '15

23 Sep '15

Hi, When taking a structure I refined in Phenix (using a TLS + individual ADP model) into a different refinement package, a colleague noted a host of warnings related to mismatched B-factors between the sulfur atoms in disulfide bonds. If I understand correctly, this arises due to Phenix falling back to a Ulocal only ADP restraints scheme and, in particular, the choice to set adp_restraints.iso.sphere_radius = 2.0. The length of a disulfide bond being 2.05A, this means that as long as the geometry is correct the B-factors of the two sulfurs are never restrained to each other under these conditions. Cheers, Tristan Tristan Croll Lecturer Faculty of Health School of Biomedical Sciences Institute of Health and Biomedical Engineering Queensland University of Technology 60 Musk Ave Kelvin Grove QLD 4059 Australia +61 7 3138 6443 This email and its attachments (if any) contain confidential information intended for use by the addressee and may be privileged. We do not waive any confidentiality, privilege or copyright associated with the email or the attachments. If you are not the intended addressee, you must not use, transmit, disclose or copy the email or any attachments. If you receive this email by mistake, please notify the sender immediately and delete the original email.

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