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atom vdW dictionary for Python
by David Shin 11 Jul '15

11 Jul '15

Hi - I'm writing a Python script to measure the volume of pockets within protein structures - plus extra bells and whistles... thus a custom job. I was wondering just for speed, if someone could point me to values for van der Waals radii that are somewhat agreed upon for protein atoms, or if there is some dictionary already made that someone could point to that resides in phenix or some other structural biology package that would be ok for me to copy/use. Thanks, Dave

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Re: [phenixbb] [ccp4bb] Phenix; converting a map to structure factors
by Terwilliger, Thomas Charles 11 Jul '15

11 Jul '15

Hi Reza, Just use: phenix.map_to_structure_factors map.ccp4 d_min=2.5 or something like that, All the best, Tom T On Jul 10, 2015, at 11:27 AM, Reza Khayat wrote: Hi, Is it possible to convert a map to structure factors using Phenix? Thanks. Best wishes, Reza Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry New York, NY 10031

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NCS and R-Values Hung up at ~0.42/0.46
by John Bruning 11 Jul '15

11 Jul '15

Hi Everyone, I collected two datasets of the same ligand bound structure at 2.4 and 2.1 Å resolution. The apo structure has already been solved to 2.2Å resolution in P31 (and P3121 for SeMet). After processing each dataset as both P31 and P3121 in MOSFLM, I proceeded with MR with Phaser using sequential partial search models to place either 3 copies in the ASU for P3121, or 6 copies for P31. (The previously solved apo structure had 6 copies of the same protein in the ASU). *** in summary two datasets, processed as both P31 or P3121 After running xtraige for either .mtz, I get this warning about NCS: Largest Patterson peak with length larger than 15 Angstrom: Frac. coord. : 0.333 -0.333 -0.153 Distance to origin : 56.728 Height relative to origin : 26.388 % p_value(height) : 2.659e-03symmetry. Translational pseudo-symmetry is very likely present in these data. Be aware that this will change the intensity statistics and may impact subsequent analyses, and in practice may lead to higher R-factors in refinement. Regardless, I can proceed with the MR using sequential partial search models to place either 3 copies (P3121) or 6 copies (P31) with decent solutions (i.e. packing looks good upon inspection, scoring looks appropriate -> SOLU SET RFZ=2.8 TFZ=8.3 PAK=13*LLG*=-37 *LLG*=2199 as an example). However, I did get the following somewhat expected warnings: Number of known components (1) not divisible by 2: Translational *NCS* correction not applied Large non-origin Patterson peak indicates that translational *NCS* is present Upon any attempt at initial refinement (with a number of different strategies), the R-factors are hung up > 0.42 (for example in the P3121, 2.1Å case): Start R-work = 0.4966, R-free = 0.5133 Final R-work = 0.4231, R-free = 0.4477 *** best R-factors from ~ 15 different strategies My concern is that there is some pathology that is not being recognized (merohedral twinning) or that the NCS/pseudosymmetry is not being addressed appropriately. Any suggestions in troubleshooting this would be much appreciated, as I have pretty much exhausted everything I could think of. -- Cheers, John

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(no subject)
by Ashok Nayak 10 Jul '15

10 Jul '15

Dear Phenixites, I have a helical bundle structure, where in I wish to understand by what rotation and about which axis the dimers are inter-related. What I get from the superposition with Superpose is the transformation matrix and not the axis, and the angles are also elusive. Ashok Nayak CSIR-CDRI Lucknow, India --

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Axis of Rotation
by Ashok Nayak 10 Jul '15

10 Jul '15

Dear Phenixites, I have a helical bundle structure, where in I wish to understand by what rotation and about which axis the dimers are inter-related. What I get from the superposition with Superpose is the transformation matrix and not the axis, and the angles are also elusive. Thanks in advance -- Ashok Senior Research Fellow - Dr JV Pratap, Lab No-LSN 008 Molecular and Structural Biology Division Central Drug Research Institute, Janakipuram Extension Lucknow-226031 India

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rosetta.build_phenix_interface problem
by Appu kumar 10 Jul '15

10 Jul '15

Dear All, I have installed Rosetta on Linux machine. When i am issuing the command " rosetta.build_phenix_interface" it is giving me following error scons: Building targets ... scons: *** [build/src/release/linux/2.6/64/x86/gcc/4.4/python/libObjexxFCL.so] Implicit dependency `/usr/local/lib/libdl.so' not found, needed by target `build/src/release/linux/2.6/64/x86/gcc/4.4/python/libObjexxFCL.so'. scons: building terminated because of errors. Would you please give me your valuable suggestions to successfully carry out the Rosetta refinement. Thank you Appu

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Rosetta Refinement problem
by Appu kumar 10 Jul '15

10 Jul '15

Dear All, I have installed Rosetta successfully on Linux machine and after installation it say building done. While refining a structure with "phenix.rosetta_refine" it is giving following problem End of input processing Sorry: The RosettaScripts executable could not be located. Please add the appropriate directory to your PATH environment variable, or set the variable ROSETTA_BIN to point to it. In my .cshrc file i have setup the path as follow setenv PHENIX_ROSETTA_PATH /home/appu/2014_09_29_NSLS_X29/rosetta_bin_linux_2015.25.57927_bundle setenv ROSETTA_BIN /home/appu/2014_09_29_NSLS_X29/rosetta_bin_linux_2015.25.57927_bundle/main/source/bin setenv phenix /home/appu/software/phenix/phenix-1.9-1692 setenv ROSETTA3_DB /home/appu/2014_09_29_NSLS_X29/rosetta_bin_linux_2015.25.57927_bundle/main/database I would appreciate any help and suggestions in executing the Rosetta refinement Thank you Appu

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Problem with python while running Autobuild
by Tam＠em.uni-frankfurt.de 09 Jul '15

09 Jul '15

Dear all, I am currently facing a problem of python while running the Autobuild in Phenix. phenix.autobuild data=data1.mtz model=model.pdb seq_file=protein.dat rebuild_in_place=False \ composite_omit_type=iterative_build_omit then it stopped with error Error in `/home/mauricetam/software/phenix-1.9-1692/build/intel-linux-2.6-x86_64/base/bin/python2.7': free(): invalid next size (normal): 0x0000000003e100a0 *** I wonder what's wrong with it. Regards Heng-Keat

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problems with rosetta
by Benny Belviso 09 Jul '15

09 Jul '15

Dear all, I am trying to use rosetta with the Phenix Gui (Phenix is installed on Debian). I have downloaded the tar.gz file named "rosetta_bin_linux_2015.25.57927_bundle" that contains source and binary files. Becouse the tar.gz contains pre-compiled files, I have not compiled rosetta again (however, I have the same problems also in the case of tar.gz containing source after the compilation). According to the instructions showed on http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Phenix#Installa… I have setup my environmental variables in .bashrc as: export PHENIX_ROSETTA_PATH=/home/bbdanilo/program/rosetta_bin_linux_2015.25.57927_bundle export ROSETTA3_DB=$PHENIX_ROSETTA_PATH/main/database However, by opening MR-Rosetta on Phenix GUI, I get a first warning message that says me that rosetta directory seems to be not correct. By running rosetta, the program says that it is not able to find PHENIX_ROSETTA_PATH. I have tried to change the path also in the "Directory setup" by typing /home/bbdanilo/program/rosetta_bin_linux_2015.25.57927_bundle as directory for rosetta path /main/source/bin as Rosetta binary directory name mr_protocols.linuxgccrelease as binary of rosetta In this case, the program says that does not find the binary for rosetta (it requires mr_rosetta.default, instead I should use mr_protocols.linuxgccrelease). What am I doing wrong? Any help is welcome. Thanks. Danilo This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system, you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.

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Re: [phenixbb] on determination whether a protein is a monomer or complex by phenix
by Valerie Pye 07 Jul '15

07 Jul '15

Hi Smith, Your solvent content is most likely the 66% one (if you have diffraction to about 1A there's a chance it could be 33%.....in which case try to solve it with Balbes (ccp4)). You can not tell what the crystal packing is like until you solve the structure! Even if you know how many molecules you have in your a.s.u. you can not tell if the contacts are formed because of crystal packing or oligo formation! Its much better to look at your protein in solution for this (as i said before!) Cheers, val On 7 July 2015 at 03:17, Smith Liu <smith_liu123(a)163.com> wrote: > Dear Valerie and all, > > My space group is I422 (attached image for I422). There are 2 solutions > for Mathews coefficient, one is solvent content 66.76%, the other is > 33.52%. Based on this message and the attached images, how can we know > whether my protein is a monomer (for example, monomer protein only exist in > the "+" position), a tetramer (or crystal packing as a "tetramer", each > chain exist in the "+" position, and each chain so close to each other so > that they contact each other and a tetramer forms), a 8-subunit protein > complex (or crystal packing as a " 8-subunit protein complex ", each 2 > chains exist in the "+" position, and each 2 chians so close to each other > so that they contact each other and a 8-subunit protein complex form)? > > I am looking forward to getting a reply from you. > > Best regards. > > Smith > > > > > > At 2015-07-07 00:34:32, "Valerie Pye" <valpye(a)googlemail.com> wrote: > > Hi Smith, > > I'm fairly sure you can not tell the oligomeric state of your protein from > an mtz and your sequence. > What you can do is calculate the Matthews co-efficient with your given > unit cell parameters and size of monomer to see how many copies of your > monomer you may have in the a.s.u. > The difficulty lies in the fact that if say you have 4 copies of your > protein in the a.s.u - this doesn't necessarily mean you have a tetramer - > they could be 4 monomers related by n.c.s - or 2 dimers.... > Is it possible to solve your structure? Then you confirm your space group > and number of molecules in the a.s.u. - then look at the area of contact > between monomers to see if they are likely to be because of multimerisation > or crystal packing. > > Totally agree with Tim that a better way (which you'd probably want to do > to back-up a multimeric crystal structure) is by SEC or native PAGE. You > could also try SAXS, SEC-MALS, EM, or DLS depending on the size of protein > you're looking at. You'd also want to know that you have a clean oligomer > and not an aggregate ;) > > Good luck, > > val > > On 6 July 2015 at 12:21, Smith Liu <smith_liu123(a)163.com> wrote: > >> Dear Tim, >> >> I mean based on the mtz file, can I know whether I will get a PDB file of >> a monomer or dimer, or trimer, or tetramer or oligomer? >> >> Best regards. >> >> Smith >> >> >> >> >> >> At 2015-07-06 18:14:03, "Tim Gruene" <tg(a)shelx.uni-ac.gwdg.de> wrote: >> >Dear Smith, >> > >> >I would say that size exclusion chromatography or native PAGE are better >> >experimental techniques than crystallography for this type of question. >> > >> >Best regards, >> >Tim >> > >> >On 07/06/2015 11:20 AM, Smith Liu wrote: >> >> Dear All, >> >> >> >> >> >> Suppose I have got a mtz file, and I know the aa sequence of the protein from which I got the crystal and the corresponding mtz file, will you please tell me which phenix function (program) can tell me whether my protein crystal was formed by protein monomer or by protein complex, and if formed by protein complex, how many subunits existing in the complex? >> >> >> >> >> >> Best regards. >> >> >> >> >> >> Smith >> >> >> >> >> >> >> >> _______________________________________________ >> >> phenixbb mailing list >> >> phenixbb(a)phenix-online.org >> >> http://phenix-online.org/mailman/listinfo/phenixbb >> >> Unsubscribe: phenixbb-leave(a)phenix-online.org >> >> >> > >> >-- >> >-- >> >Dr Tim Gruene >> >Institut fuer anorganische Chemie >> >Tammannstr. 4 >> >D-37077 Goettingen >> >phone: +49 (0)551 39 22149 >> > >> >GPG Key ID = A46BEE1A >> > >> > >> >> >> >> >> _______________________________________________ >> 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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