November 2014 - phenixbb - phenix-online.org

Filtering CCP4 maps to lower resolution
by Barad, Ben 16 Nov '14

16 Nov '14

Hi All, I am currently trying to filter a CCP4-formatted real space map from the EMDB, which is at 3.2 Å resolution, to different resolutions from 3.2 to 5 Å, and I've been having a bit of a difficult time getting it to work. My first thought was to do an fft to get structure factors, then regenerate the map from those structure factors with a resolution cutoff. To do this, I used the tools "phenix.map_to_structure_factors" and "phenix.mtz2map" to generate a structure factor file, then convert it back into a map. When I do this, I end up with a very noisy map that is not usable for what I would like to do. Is there a better way to accomplish this in phenix (or another tool)? I've also tried some low-pass filtering with proc3d, without much success... Thanks, Ben Barad Fraser Lab @ UCSF

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Re: [phenixbb] simulated annealing omit map
by Pavel Afonine 15 Nov '14

15 Nov '14

Hello Bishal, as discussed before, computing ligand-omit map is tricky. Quoting my previous email: """ There are two commonly used options for omitting the ligand in order to demonstrate its presence/absence in Fo-Fc OMIT map: 1) Physically remove the ligand from PDB file. Then do some refinement and calculate Fo-Fc map. 2) Keep ligand in the file, set its occupancy to zero. Then, again, do some refinement and calculate Fo-Fc map. In this case you may want to ask refinement program to not move the ligand or move it only a little. Now, here is why these two options are poor and will not give you what you want. In the first case the bulk-solvent mask will be set in the ligand region and therefore it will mask ligand density (bulk-solvent will be filled into the ligand region). Depending on the strength of ligand density it may be masked completely or deteriorated. If you follow the second option you will always get positive density in ligand area. This density may correspond to bulk-solvent, ligand or mixture of both. That is there will be no simple way to differentiate whether this density arises from the ligand or bulk-solvent. """ Dale Tronrud offered a great alternative option: """ An alternative you might want to consider is what I call the "discovery map". At some point in the refinement process there was a map that convinced YOU that this ligand was present. You should be the hardest person to be convinced so that map will be both an omit map (because the model had been refined without the ligand prior to this) and clear enough to satisfy the reader. """ Now, recently I improved composite OMIT map calculation in phenix.composite_omit_map tool, see picture that illustrates how it works: https://www.dropbox.com/s/dbp8e0348v5p78h/fig_6.png?dl=0 I think at present that's the best option to follow if for some reason you cannot follow Dale's suggestion. Pavel On 11/13/14 6:58 AM, Singh, Bishal wrote: > Hello everybody, > I am generating figures showing the electron density map around the > ligands. I deleted the ligands from final co-ordinate file and then > performed refinement with identical parameters as before while > keeping simulated annealing=true. I shall be thankful if someone could > suggest me whether I consider mFo-DFc map or 2mFo-DFc map or both. > Kindly also tell me the minimum acceptable contour level required for > showing difference map. All structures are at 1.4 - 2.0 angstrom > resolutions. > > Regards, > Bishal

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CB outliers
by George Devaniranjan 14 Nov '14

14 Nov '14

Hi, I refined a structure using phenix.refine. The R/R free decreased slightly from 13.46/15.87 to 13.0/15.6. But, molprobity said there were 3 CB outliers (starting from 0). I looked at those residues in COOT. I could NOT really see a different between the refined and initial model. In addition I looked at COOT validate-->density fit analysis I cannot see ANY difference in the peak heights (same numerical value too). I looked at RSCC (using phenix validate tools as well). I still can't see a difference in the plots. I am not sure how to get rid of the 3 CB outliers that have crept in since I can't pick them out as worse off in the refined model. I ask since in another case > 3 CB outliers, with the same results in picking them out in COOT/RSCC. I am wondering if there is another way I can see the deviation and fix it? Thank you, George

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Rosetta compile problem
by miyatake 13 Nov '14

13 Nov '14

Dear all, I tried to compile Rosetta for rosetta_refinement, on Mac OX10.10. I run " /rosetta_2014.22.56873_bundle/main/source] user% sudo scons.py But it was in failure, showing the following message: g++-4.2 -o build/external/debug/macos/14.0/64/x86/gcc/4.2/default/dbio/cppdb/atomic_counter.os -c -isystem external/boost_1_55_0/ -isystem external/include/ -isystem external/dbio/ -pipe -ffor-scope -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -m64 -march=nocona -mtune=generic -O0 -g -ggdb -ffloat-store -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DCPPDB_EXPORTS -DCPPDB_LIBRARY_SUFFIX=\".dylib\" -DCPPDB_LIBRARY_PREFIX=\"lib\" -DCPPDB_DISABLE_SHARED_OBJECT_LOADING -DCPPDB_DISABLE_THREAD_SAFETY -DCPPDB_SOVERSION=\"0\" -DCPPDB_MAJOR=0 -DCPPDB_MINOR=3 -DCPPDB_PATCH=0 -DCPPDB_VERSION=\"0.3.0\" -DCPPDB_WITH_SQLITE3 -Ibuild/external/debug/macos/14.0/64/x86/gcc/4.2/default/dbio/sqlite3 -Iexternal/dbio/sqlite3 -Iexternal/boost_1_55_0 -Iexternal/dbio -I/usr/include -I/usr/local/include external/dbio/cppdb/atomic_counter.cpp sh: g++-4.2: command not found scons: *** [build/external/debug/macos/14.0/64/x86/gcc/4.2/default/dbio/cppdb/atomic_counter.os] Error 127 scons: building terminated because of errors. How can I resolve that? Best regards, H. Miyatake

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simulated annealing omit map
by Singh, Bishal 13 Nov '14

13 Nov '14

Hello everybody, I am generating figures showing the electron density map around the ligands. I deleted the ligands from final co-ordinate file and then performed refinement with identical parameters as before while keeping simulated annealing=true. I shall be thankful if someone could suggest me whether I consider mFo-DFc map or 2mFo-DFc map or both. Kindly also tell me the minimum acceptable contour level required for showing difference map. All structures are at 1.4 - 2.0 angstrom resolutions. Regards, Bishal

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Settings-Directories of MR-Rosetta wizard is altered when phenix-GUI is restarted?
by Martin Moche 13 Nov '14

13 Nov '14

Dear colleagues, When restarting phenix followed by opening the "MR-Rosetta(beta)" the Settings-Directories need to be reset each time? How can I set Rosetta binary directory name: Rosetta binary name: Rosetta script directory name: Rosetta database directory name: in Settings-Directories of "MR-Rosetta(beta)" wizard (or elsewhere) so that they do not change each time I restart the phenix-GUI? These settings are not changed: Base output folder: Rosetta path: Likely "Rosetta path" does not change between phenix-GUI restarts since PHENIX_ROSETTA_PATH is set in the shell as: echo $PHENIX_ROSETTA_PATH /software/apps/rosetta/2014.35/gcc01/rosetta_2014.35.57232_bundle The "Path to Rosetta" in "Phenix preferences - Wizards" is currently left blank since $PHENIX_ROSETTA_PATH is set in the shell. I have by accident started a few jobs with mixed (new and old) settings and phenix-GUI starts without error messages and all processors are running 100% CPU, however likely in some infinite loop since no work is performed beyond "place model"... Best regards, Martin Martin Moche, Ph.D. Head of Protein Crystallography Karolinska Institutet MBB/PSF Scheeles väg 2 171 77 Stockholm Sweden phone: +46-8-524 868 43 mobile: +46-73-322 93 27 fax: +46-8-524 868 68 email: Martin.Moche(a)ki.se

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fix atoms during refinement
by CPMAS Chen 10 Nov '14

10 Nov '14

Dear All Phenix Users, Is there a way to fix certain atoms position during refinement? I have some heavy atoms identified with MR-SAD, but when I build the whole molecule and have phenix to refine its position, the heavy atom's position is shifted from the anomalous signal. Therefore I would like to have these heavy atoms positions fixed during refinement. Thanks! Charles -- *************************************************** Charles Chen Research Associate University of Pittsburgh School of Medicine Department of Anesthesiology ******************************************************

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Ringer
by Ivan IVANOV 10 Nov '14

10 Nov '14

Dear All, I am trying to use ringer with a model I have. I followed the tutorial for Calmodulin and it worked very well for my protein. (http://bl831.als.lbl.gov/ringer/ringer/Tutorial/tutorial.htm). Now I have all files sigma vs chi angles for the residues I want and also the list of peaks identified above the sigma cutoff I selected. I am struggling to analyse the outputs as it is shown on the calmodulin exemple. I found this website (http://bl831.als.lbl.gov/ringer/ringer/Documentation/ringerManual.htm#Userp…) which is explaining very briefly how to plot all different conformation vs chi angles and how to show all selected amino acid conformation in the electron density (4.4 Plotting Accessory). I have to admit that this is not straigthforward for me to plot all outputs in a comprehensive way. Does anyone of you have a script to run with ringer outputs and get the final figures as it is shown on both websites ?? Kind regards, Ivan -- Ivan Ivanov, PhD PostDoctoral fellow at EMBL, European Molecular Biology Laboratory, Structural biology of RNA-protein complexes, Dr. Stephen Cusack, EMBL 71, avenue des Martyrs CS 90181 38042 Grenoble Cedex 9 T: +33 (0)4 76 20 7630 T(lab): +33 (0)4 76 20 7014 Email: ivanov(a)embl.fr Url: http://www.embl.fr

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"Femtosecond crystallography of membrane proteins in lipidic cubic phase (LCP)” Webinar
by Angela Criswell 04 Nov '14

04 Nov '14

Dear colleagues, I would like to draw your attention to an upcoming free, educational webinar to be presented by Dr. Wei Liu titled “Femtosecond crystallography of membrane proteins in lipidic cubic phase (LCP).” Despite recent technological advances in heterologous expression, stabilization and crystallization of membrane proteins, structural studies remain difficult. Wei’s presentation will describe the use of serial femtosecond crystallography of membrane proteins in LCP and how this approach holds promise to interrogate this difficult, yet important, class of proteins. This webinar is scheduled to occur on Thursday, November 13th at 11:00 AM CST (9:00 AM PST / 5:00 PM GMT). You can find an abstract and registration link for this webinar at: http://www.rigaku.com/webinars. We hope you will join us for the event. Best regards, Angela Criswell -- Angela Criswell VP, Life Science X-ray Products Rigaku Americas Corporation 9009 New Trails Drive The Woodlands, TX 77381 USA Ph: +1 281 362 2300 ext. 216 Fax: +1 281 364 3628 Email: angela.criswell(a)rigaku.com URL: http://www.rigaku.com Subscribe to Rigaku eNewsletters<http://www.rigaku.com/subscribe>

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