- phenixbb - phenix-online.org

NCS operators
by Dmitry A. Semchonok 19 May '23

19 May '23

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generating half maps for combined map using phenix.combine_focused_maps
by Manoj saxena 16 May '23

16 May '23

Hi all, I have a question for generating half half maps for the combined map in Phenix, I am combining 6 regions of a complex (using local refined maps) and supplying the reference map and a reference model for the complex. Additionally, I am supplying the 2 half maps for the whole complex as input fines. I was wondering if I need to supply 2 half maps for each of the local refined regions as input files in addition to the half maps for the reference map. Thank you regards Manoj

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Pb executing phenix.model_idealization
by CUNIASSE Philippe 15 May '23

15 May '23

Dear all, I tried to use the phenix.model_idealization code of phenix (in command line) following the syntax suggested inhttps://phenix-online.org/documentation/reference/model_idealization.html phenix.model_idealization xxxx.pdb But the code stops on the error : Traceback (most recent call last): File "/Applications/phenix-1.20.1-4487/build/../modules/cctbx_project/mmtbx/command_line/model_idealization.py", line 1118, in <module> run(sys.argv[1:]) File "/Applications/phenix-1.20.1-4487/build/../modules/cctbx_project/mmtbx/command_line/model_idealization.py", line 1106, in run mi_object.run() File "/Applications/phenix-1.20.1-4487/build/../modules/cctbx_project/mmtbx/command_line/model_idealization.py", line 548, in run self._setup_model_h() File "/Applications/phenix-1.20.1-4487/build/../modules/cctbx_project/mmtbx/command_line/model_idealization.py", line 478, in _setup_model_h params_h.pdb_interpretation = self.model._pdb_interpretation_params.pdb_interpretation AttributeError: 'NoneType' object has no attribute 'pdb_interpretation' Thanks in advance for any suggestion to solve this. Best regards. Philippe. ----------------------------------------------- Philippe Cuniasse, PhD/HDR. Institut de Biologie Integrative de la cellule. UMR 9198 CNRS-CEA-Univ Paris Sud Bat 144 CE-Saclay 91191 Gif-sur-Yvette Cedex France Tel: (33) 1 69 08 56 35 Fax: (33) 1 69 08 47 12 Email: philippe.cuniasse(a)cea.fr<mailto:[email protected]> Web: http://biodev.cea.fr/rasmot3d/ [signature_3031510868][signature_394100311][signature_2972121752] -----------------------------------------------

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How to exclude one part of a model to be taken into account during Real_Space_refinement ?
by CUNIASSE Philippe 15 May '23

15 May '23

Dear all, I am trying to do a phenix.real_space_refine in a CryoEM map at 4.2 Å with a model obtained by MDFF (NAMD, a protein DNA complex) because the resulting structure, despite a good CC and a good molecular geometry has a poor Ramachandran Map. When doing the phenix.real_space_refine, the CC is slightly increased with respect to the starting structure, the Ramachandran is dramatically increased but some part of the model ( in the case, the first three bases pairs a DNA duplex) are strongly distorted because of a lack of density in the corresponding region of the map. For some reason, this does not append with the MDFF method. I was wondering if there is a mean, in phenix.real_space_refine, to exclude a part of the model from being fitted in the map. Indeed, the distortion I observe in the DNA duplex is likely due to the fact that the real_space_refine tries to put the atoms at the extremity of the duplex in the closest density at the price of a strong distortion of the structure. Thank in advance for your suggestions. Best regards. Philippe. ----------------------------------------------- Philippe Cuniasse, PhD/HDR. Institut de Biologie Integrative de la cellule. UMR 9198 CNRS-CEA-Univ Paris Sud Bat 144 CE-Saclay 91191 Gif-sur-Yvette Cedex France Tel: (33) 1 69 08 56 35 Fax: (33) 1 69 08 47 12 Email: philippe.cuniasse(a)cea.fr<mailto:[email protected]> Web: http://biodev.cea.fr/rasmot3d/ [signature_3454313285][signature_3433042689][signature_3416814468] -----------------------------------------------

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phenix.combine_focused_maps
by Manoj saxena 10 May '23

10 May '23

Hi , I am trying the following command using PHENIX VERSION: 1.20.1-4487. to generate a composite map from locally refined maps (cryo-EM) of my complex. I have selected multiple regions each one correspond to one of the six locally refined maps that I wish to combine using this command. I would be grateful if you can suggest if this is the correct way to do it. In this test1.pdb contains the complete model. One of my doubts is that if instead of selection, I supply individual model files for each map region can they have multiple chain Ids. Asking because I was told that I would need to combine all chains and rename them as one chain (per map region) to have the correct weighted map. Many thanks Manoj phenix.combine_focused_maps map_file=Relion_deepEmhancer_reference_.mrc map_file=Base_map4.mrc map_file=Base_map1.mrc map_file=Base_map2.mrc map_file=Base_map3.mrc map_file=Base_map5.mrc map_file=Base_map6.mrc model_file=test1.pdb region_selection="(chain P and resid 366-401) or (chain P and resid 179-297) or \ (chain O and resid 401-555) or (chain N and resid 458-530) or (chain N and resid 311-457) or (chain R and resid 13-79) or \ (chain N and resid 726-577) or (chain N and resid 823-880) or (chain I and resid 350-409) or (chain N and resid 577-726) or (chain O and resid 667-722) or \ (chain Q and resid 264-276) or (chain N and resid 928-981) or (chain O and resid 926-971) or \ (chain O and resid 875-899) or (chain Q and resid 208-244) or (chain O and resid 717-739) or (chain N and resid 877-898) or \ (chain M and resid 7-101) or (chain L and resid 2047-2141) or (chain L and resid 1718-1746) or (chain L and resid 2001-2025) or (chain N and resid 880-900) or (chain P and resid 430-440) or (chain L and resid 1954-1965) or (chain P and resid 131-154)" composite_map_file=composite_map.mrc composite_half_map_1_file=composite_half_A_map.mrc composite_half_map_2_file=composite_half_B_map.mrc local_weighting=True rigid_body_refinement_single_unit=False nproc=8 resolution=4.0

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Issue resorting water chain
by Victor Rangel 05 May '23

05 May '23

Dear bb, I'm using phenix.sort_hetatms to sort my water molecule chain based on their bfactor. My macromolecule and water chains are separated, and I'd very much like them to remain so. When adding *preserve_chain_id=True*, the program outputs: *"Warning: no corresponding macromolecule chain match for C 1"*. The program still writes the output pdb, but it changes the water chain name from "C" to "X", and it does not sort them by bfactor. I'm using Phenix 1.20.1-4487 My command is: *phenix.sort_hetatms file_name="refine.pdb" output_file="resorted_refine.pdb" preserve_chain_id=True sort_waters_by=*b_iso* Not sure where my mistake is. Any suggestions? Best, Victor

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Advanced Methods for Ambient Crystallography at ESRF-EBS Workshop - 21-23 November 2023
by Matthew BOWLER 05 May '23

05 May '23

Dear all The ESRF and EMBL Joint Structural Biology Group, with the support of EU project Streamline, is organizing a workshop on sample preparation, data collection and data processing for Ambient Temperature Crystallography. ESRF and EMBL have been laying the groundwork for the future development of this field with two main projects: the refurbishment of MASSIF1 (https://www.esrf.fr/MASSIF1), including a CrystalDirect Harvester, allowing full automation of single crystal RT data collection and the new ID29 (https://www.esrf.fr/id29) for Time Resolved Serial Crystallography experiments with microseconds X-ray pulses. This 2.5 days workshop will cover the different practical and theoretical aspects of room temperature data collection and structure determination on the first day, followed by practicals at the beamlines and data processing on the following days. A total number of 10 participants will be selected and we will accept a limited number of participants’ samples to be tested during the workshop. There is no registration fee and meals and accommodation during the workshop will be provided free of charge. Bursaries are available to cover travel expenses for the participants. Deadline for application for the workshop is on 15th August. Applications can be submitted at the following link https://survey.esrf.fr/index.php/212282?lang=en More information is available at the following link https://www.esrf.fr/home/events/conferences/2023/amax2023.html Confirmed speakers and tutors include: Robert Thorne (Cornell) Marcus Fischer (St Jude) Daniel Keedy (CUNY) Silvia Russi (SSRL) Chia-Ying Huang (PSI) Sasha Popov (ESRF) Clemens Vonhrein (GPhL) Nicolas Coquelle (IBS) -- Matthew Bowler Project Leader MASSIF1@ESRF European Molecular Biology Laboratory 71 avenue des Martyrs CS 90181 F-38042 Grenoble France =================================================== Tel: +33 (0) 4.76.20.76.37 Fax: +33 (0) 4.76.20.71.99 http://www.embl.fr/ http://www.esrf.eu/MASSIF1 https://twitter.com/id30_massif1 https://www.embl.org/people/person/71918b7a010f129de27b37236c7ca90085113d74… ===================================================

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Cryo_fit execution data test GTPases fails
by CUNIASSE Philippe 04 May '23

04 May '23

Dear all, After installing cryo_fit in phenix and gromacs_cryofit on my Macbook Pro M1, I now try to test the code using the example data GTPase. The job encounters immediately a problem but the GUI suggests that the job is still running. The log suggest that the first step did not run successfully (below). I presume setting the topology of the protein but I don’t know. Another question is how is it possible to set other parameters for cryo_fit (like ff…) in the GUI or should I run it in command line ? Thank you for your help and suggestions. Philippe. User's computer's operating system: Darwin ############################################################################################### #################### Step 1: Make gro and topology file by regular gromacs #################### ############################################################################################### Current working directory: /Applications/phenix-1.20.1-4487/modules/cryo_fit/tutorial_input_files/CryoFit_1/steps/1_make_gro command: python 1_before_pdb2gmx_prepare_pdb.py GTPase_activation_center_tutorial.pdb 0 0 0 True Current working directory: /Applications/phenix-1.20.1-4487/modules/cryo_fit/tutorial_input_files/CryoFit_1 This pdb file, /Applications/phenix-1.20.1-4487/modules/cryo_fit/tutorial_input_files/GTPase_activation_center_tutorial.pdb , has 6489 atoms Approximately, for this number of atoms, one 3.1 GHz Intel Core i7 took 7 seconds to make a gro file. command: python 2_runme_make_gro.py /Applications/phenix-1.20.1-4487/modules/cryo_fit/ amber03 True True /usr/local/cryo_fit/cryo_fit/bin// Step 1 didn't run successfully User's command was phenix.cryo_fit /Applications/phenix-1.20.1-4487/modules/cryo_fit/tutorial_input_files/.phenix/project_data/run_1.eff phenix.cryo_fit alone without any arguments introduces full options. If a user sees a message like "Fatal error: Atom xx in residue xx xxx was not found in rtp entry xx with xx atoms while sorting atoms." or "Fatal error: Residue xxx not found in residue topology database" Solution if these residue/atoms are important: Fix wrong names of atoms/residues. Running real_space_refine via phenix GUI will show which atoms need to be fixed. If gromacs amber03 force field doesn't have parameters for these residue/atoms, you may need to add appropriate parameters. If you added parameters, please email me (doonam.kim(a)pnnl.gov), I want to recognize your contribution publicly. Most MD simulation force fields do not support all kinds of rare residue/atoms. cryo_fit2 is under development to address this issue using phenix.eLBOW Solution if these residue/atoms are not important: Remove these "wrong" atoms/residues from user's input pdb file. Run cryo_fit again. Solution if user's input pdb file is big: Probably cryo_fit will change conformation just minimally, I would extract out these "wrong" atoms/residues from user's input pdb file, then add these extracted lines to cryo_fitted file later. Email phenixbb(a)phenix-online.org or doonam.kim(a)pnnl.gov for any feature request/help.

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Re: [phenixbb] Pb installing cryo_fit gromacs
by Luca Jovine 03 May '23

03 May '23

Hi Philippe, It’s not an optimal workaround, but you can try using CFLAGS="-Wno-error=implicit-function-declaration" … Best, Luca - Luca Jovine, Ph.D. Professor of Structural Biology, Member of EMBO and the Nobel Assembly Karolinska Institutet Department of Biosciences and Nutrition Medicinaren 25 Neo Blickagången 16, SE-141 83 Huddinge, Sweden E-mail: luca.jovine(a)ki.se W3: http://jovinelab.org From: <phenixbb-bounces(a)phenix-online.org> on behalf of CUNIASSE Philippe <Philippe.CUNIASSE(a)cea.fr> Date: Wednesday, 3 May 2023 at 15:09 To: "phenixbb(a)phenix-online.org" <phenixbb(a)phenix-online.org> Subject: [phenixbb] Pb installing cryo_fit gromacs You don't often get email from philippe.cuniasse(a)cea.fr. Learn why this is important<https://aka.ms/LearnAboutSenderIdentification> Dear all, I tried to install Cryo_fit on my labtop Macbook pro M1 running OSX 13.0. The installation of the Cryo_fit itself in Phenix went well. I then tried to install gromacs (gromacs-4.5.5_cryo_fit) following the instructions found on https://phenix-online.org/documentation/tutorials/cryo_fit_install.html#id1 But during the compilation, I encoutered the following error that stops the process. cc -DHAVE_CONFIG_H -I. -I../../src -I/usr/include/libxml2 -I../../include -DGMXLIBDIR=\"/Applications/phenix-1.20.1-4487/modules/cryo_fit/cryo_fit/share/top\" -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 -std=gnu99 -I./include -MT md.o -MD -MP -MF .deps/md.Tpo -c -o md.o md.c md.c:414:9: error: call to undeclared function 'please_cite'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration] please_cite(stderr,"Kim2019"); ^ md.c:421:23: warning: passing 'const char *' to parameter of type 'char *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers] init_em_map(fplog,ftp2fn(efEMM, nfile, fnm), emmap, ir, state_global,cr); ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../include/cryoem.h:43:44: note: passing argument to parameter 'emfile' here extern void init_em_map(FILE *fplog, char *emfile,t_emmap *emmap, t_inputrec *ir, t_state *state, t_commrec *cr); ^ 1 warning and 1 error generated. I did it under a bash shell, Python version : 2.7.15 cc --version Apple clang version 14.0.3 (clang-1403.0.22.14.1) Target: arm64-apple-darwin22.1.0 Thread model: posix InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin Any suggestion to solve it ? Thanks in advance for your help. Philippe. ----------------------------------------------- Philippe Cuniasse, PhD/HDR. Institut de Biologie Integrative de la cellule. UMR 9198 CNRS-CEA-Univ Paris Sud Bat 144 CE-Saclay 91191 Gif-sur-Yvette Cedex France Tel: (33) 1 69 08 56 35 Fax: (33) 1 69 08 47 12 Email: philippe.cuniasse(a)cea.fr<mailto:[email protected]> Web: http://biodev.cea.fr/rasmot3d/ [signature_1537351220][signature_732259530][signature_3011392973] ----------------------------------------------- När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. Här finns information om hur KI behandlar personuppgifter<https://ki.se/medarbetare/integritetsskyddspolicy>. Sending email to Karolinska Institutet (KI) will result in KI processing your personal data. You can read more about KI’s processing of personal data here<https://ki.se/en/staff/data-protection-policy>.

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Pb installing cryo_fit gromacs
by CUNIASSE Philippe 03 May '23

03 May '23

Dear all, I tried to install Cryo_fit on my labtop Macbook pro M1 running OSX 13.0. The installation of the Cryo_fit itself in Phenix went well. I then tried to install gromacs (gromacs-4.5.5_cryo_fit) following the instructions found on https://phenix-online.org/documentation/tutorials/cryo_fit_install.html#id1 But during the compilation, I encoutered the following error that stops the process. cc -DHAVE_CONFIG_H -I. -I../../src -I/usr/include/libxml2 -I../../include -DGMXLIBDIR=\"/Applications/phenix-1.20.1-4487/modules/cryo_fit/cryo_fit/share/top\" -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 -std=gnu99 -I./include -MT md.o -MD -MP -MF .deps/md.Tpo -c -o md.o md.c md.c:414:9: error: call to undeclared function 'please_cite'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration] please_cite(stderr,"Kim2019"); ^ md.c:421:23: warning: passing 'const char *' to parameter of type 'char *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers] init_em_map(fplog,ftp2fn(efEMM, nfile, fnm), emmap, ir, state_global,cr); ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../include/cryoem.h:43:44: note: passing argument to parameter 'emfile' here extern void init_em_map(FILE *fplog, char *emfile,t_emmap *emmap, t_inputrec *ir, t_state *state, t_commrec *cr); ^ 1 warning and 1 error generated. I did it under a bash shell, Python version : 2.7.15 cc --version Apple clang version 14.0.3 (clang-1403.0.22.14.1) Target: arm64-apple-darwin22.1.0 Thread model: posix InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin Any suggestion to solve it ? Thanks in advance for your help. Philippe. ----------------------------------------------- Philippe Cuniasse, PhD/HDR. Institut de Biologie Integrative de la cellule. UMR 9198 CNRS-CEA-Univ Paris Sud Bat 144 CE-Saclay 91191 Gif-sur-Yvette Cedex France Tel: (33) 1 69 08 56 35 Fax: (33) 1 69 08 47 12 Email: philippe.cuniasse(a)cea.fr<mailto:[email protected]> Web: http://biodev.cea.fr/rasmot3d/ [signature_1537351220][signature_732259530][signature_3011392973] -----------------------------------------------

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