- phenixbb - phenix-online.org

Answer regarding uploading 2Fo-Fc map into KiNG
by Christopher Williams 07 Oct '15

07 Oct '15

Hi Natalia, Thanks for your use of MolProbity and your interest in improving models. It means a lot to us. As you have noted, MolProbity indeed does not accept .mtz files. It accepts 3 file formats for electron density maps: OMAP, CCP4, and XPLOR. Fortunately, Phenix can generate maps for you. In the Phenix GUI, there are two relevant options under the "Maps" tab. The first one, "Calculate maps", can turn structure factors into .mtz or .ccp4 . The second one, "FFT map coefficients", can use a .mtz to generate a .ccp4 or a .xplor, and is probably the option you are looking for. Someone more familiar with the Phenix commandline may be able to tell you how to generate maps from the commandline in a more scriptable way. Hopefully this helps, -Christopher Williams ---Richardson Lab, Duke University

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on cif file
by Smith Lee 06 Oct '15

06 Oct '15

Dear All, For the phenix refine of a protein-ligand complex, is the ligand cif file a necessity? If we do not add the cif file, what will occur? Best regards. Smith

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Special position ambiguity
by R Sarath 06 Oct '15

06 Oct '15

Hi, I have to place two carbon atoms (C3 and C6 - in para positions) of a cyclohexane ring from a ligand in special positions (I4122 space-group), with C6' from the symmetry generated molecule overlapping on C3 of the ligand. Can someone please suggest me a way to do so. I tried changing the occupancies of C3 and C6 to 0.5. After refinement, I observe that they don't overlap but instead spoil the fitting of neighbouring atoms of the ligand. Thanks in advance, Regards,Sarath

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on ligand restraint
by Smith Lee 06 Oct '15

06 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 04 Oct '15

04 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 03 Oct '15

03 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 02 Oct '15

02 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 01 Oct '15

01 Oct '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 29 Sep '15

29 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 28 Sep '15

28 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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