June 2021 - ChimeraX-users - RBVI Mailing Lists

Python API Inquiry
by Nathan Wood 29 Jun '21

29 Jun '21

To Whom it May Concern, My name is Nathan Wood and I am currently a Google Summer of Code Intern with the OpenChemistry Group. Currently I am currently in the process of replacing Visualizing Molecular Dynamics (VMD) with ChimeraX as a means to visualizing computationally generated electrostatic potential diagrams. To accomplish this I am having to use the Python API in a script. However, I am having difficulties enabling the Python API. When I execute a Tutorials example found in the online developer's documentation, I receive the error: /ImportError: No module named chimerax.core.commands// / which suggests that the python modules were never installed properly. I also recieve similar errors when attempting to import the toolshed. Otherwise, the ChimeraX GUI and its shell work properly and I am unsure how to resolve the API error. I am currently using the Generic Linux 64 Bit Daily Release and can provide more information if necessary. Any assistance would be greatly appreciated ------------------------------------------------------ Very Respectfully, Nathan Wood Undergraduate Year 3, GSOC Intern University of Florida

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Fit crystal structure into mrc
by SHIQING LIAO 29 Jun '21

29 Jun '21

Hi, I am trying to build an illustration using marker/color zone. I successfully colored my mrc file. Now, I want to fit a crystal structure I downloaded from pdb into the mrc. But they apparently have different sizes. I tried voxelSize to scale up my mrc, but then all my markers don’t fit with the enlarged mrc. However, voxelSize doesn’t seem to work with the crystal structure (.pdb1) as I got an error message “no volumes specified” when I indeed wrote “volume #5 voxelSize 2”. I am wondering is there any function like voxelSize to scale down the crystal structure? Thank you!

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Generating surfaces from a specific selection
by Diego Amaya 29 Jun '21

29 Jun '21

Hello, I have a pdb trajectory of 50 frames (in separated pdb files). I want to generate only the solvent accessible surface around amino acid 31 within a radius of 15 A. I want to use the same set of atoms when generating each surface with respect to the first frame of the trajectory. I'm using the python script here below but it doesn't work, I get a segmentation error in the else block. It works if I use "*rc(session, 'surface zone #1.1 nearAtoms :{} distance {}'.format(resid, radius))*" in the else block but in that way I don't use exactly the same atoms each time. Any suggestions? Thanks in advance. Here the code : ########################################################### *from chimerax.core.commands import run as rcdef get_surfaces(resid, radius): from chimerax.core.commands import run as rc from chimerax.atomic import selected_atoms with open('list_pdbs.txt', 'r') as list_pdbs: flag = 0 for pdb_file in list_pdbs: if flag == 0: list_atoms = [] rc(session, 'open ' + pdb_file.strip()) rc(session, 'sel :{} @<{}'.format(resid, radius)) cur_sel = selected_atoms(session).unique_structures[0].atoms.serial_numbers for a in cur_sel: list_atoms.append('@@serial_number='+str(a)) sel_atoms = ' | '.join(list_atoms) rc(session, 'surface #1 enclose #1') rc(session, 'surface zone #1.1 nearAtoms :{} distance {}'.format(resid, radius)) rc(session, '~ribbon') rc(session, '~disp') rc(session, "save {}_resid_{}_radius_{}.stl format stl".format(pdb_file.strip()[:-4], resid, radius)) rc(session, 'surface close') rc(session, '~sel') rc(session, "close all") flag = 1 else: rc(session, 'open ' + pdb_file.strip()) rc(session, 'sel {}'.format(sel_atoms)) rc(session, 'surface {} enclose #1'.format(sel_atoms)) rc(session, '~ribbon') rc(session, '~disp') rc(session, "save {}_resid_{}_radius_{}.stl format stl".format(pdb_file.strip()[:-4], resid, radius)) rc(session, '~sel') rc(session, 'surface close') rc(session, "close all") resid = 31radius = 15get_surfaces(resid, radius)rc(session, "quit")* ############################################################# -- Diego A. Amaya Ramírez -- *Aviso legal:* El contenido de este mensaje y los archivos adjuntos son confidenciales y de uso exclusivo de la Universidad Nacional de Colombia. Se encuentran dirigidos sólo para el uso del destinatario al cual van enviados. La reproducción, lectura y/o copia se encuentran prohibidas a cualquier persona diferente a este y puede ser ilegal. Si usted lo ha recibido por error, infórmenos y elimínelo de su correo. Los Datos Personales serán tratados conforme a la Ley 1581 de 2012 y a nuestra Política de Datos Personales que podrá consultar en la página web www.unal.edu.co <http://www.unal.edu.co/>.* *Las opiniones, informaciones, conclusiones y cualquier otro tipo de dato contenido en este correo electrónico, no relacionados con la actividad de la Universidad Nacional de Colombia, se entenderá como personales y de ninguna manera son avaladas por la Universidad.

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Accessing Chain IDs
by Diana Lee 29 Jun '21

29 Jun '21

Hi team! I have what I hope is an easy question. I'm accessing ChimeraX commands via python script, and I need a list of the Chain IDs. I'm currently getting the number of chains using the num_chains property. I've done quite a bit of digging through documentation and can only find ways to rename, or view interfaces, but I can't seem to find any specific command to list them. I feel as though it must be so basic, no one has needed to ask. :) Thanks for your help, Diana Lee Graduate Student Luque Lab, SDSU VII

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Global Fit List and Model Seperation
by Christian Tüting 28 Jun '21

28 Jun '21

Dear ChimeraX-Team & MailingListUsers, My question is actually two different questions: I would like to perform a global fitting in ChimeraX and seperate all fitting solutions into independent models. I loaded the map (#1) and a dimeric model (#2) into ChimeraX and perform the global fitting by: fit #2 inMap #1 search 50 My map represents a homo-oligomeric model with 40+ monomers (20+ dimers), so multiple fitting solutions are probably correct solutions. This is the log of the fitting: "Found 41 fits. List window not yet implemented." which matches with my assumption. I would like to now (a) inspect all fittings, but the list window is not implemented yet. Can I access the fitting solutions via console commands? And (b) I would like to save each fitted solution as an indepent object, reconstruction the entire model in the map for furhter refinement. Again, could this be done via commands like: "fit #2 inMap #2 search 50 saveFit fittings.pdb", which results in a multi-state pdb? The "Save PDB" button is probably only available in the List windows, which is not implemented yet. Thanks in advance Best Christian

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Fwd: Problem with preset original command in Chimerax 1.2.5
by Tom Goddard 28 Jun '21

28 Jun '21

Saverio reports his problem where ChimeraX "preset original" hung was solved by updating his graphics driver. Tom > Begin forwarded message: > > From: svle(a)tiscali.it > Subject: Re: [chimerax-users] Problem with preset original command in Chimerax 1.2.5 > Date: June 26, 2021 at 1:21:04 AM PDT > To: Tom Goddard > > I have upgraded the graphics driver by a program from AMD website and now it seems that all is working fine and the graphics operations are more responsive and faster. > The picture is very nice. > I have used the Report a Bug before and after the driver upgrading to give driver version information. > > Many thanks. > Saverio > Il 25.06.2021 21:05 Tom Goddard ha scritto: > >> These commands work fine for me in ChimeraX 1.2.5 on Windows 10. It is likely a bug in your graphics driver. Updating your graphics driver might fix it. You can use ChimeraX menu entry Help / Report a Bug and then we will see what graphics card and driver you are using which may give us further ideas. >> By the way maybe you will like preset cylinders/stubs shown below. >> Tom >> >> >>> On Jun 25, 2021, at 12:34 AM, svle--- via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >>> >>> Hi, >>> I have a problem with Chimerax 1.2.5 on windows 10. >>> In the command line I use the following: >>> >>> open 5u1c ( ok ) >>> preset riboon (ok) >>> preset original >>> >>> After the last command the application freezes and I must to kill it. >>> >>> What I can do? >>> >>> Thanks >>> >>> Saverio >>> >>> >>> >>> >>> Con Tiscali Mobile Smart 70 hai 70 GB in 4G, minuti illimitati e 100 SMS a soli 7,99€ al mese http://tisca.li/Smart70 <http://tisca.li/Smart70> >>> >>> _______________________________________________ >>> ChimeraX-users mailing list >>> ChimeraX-users(a)cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> >>> Manage subscription: >>> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users > > > > Con Tiscali Mobile Smart 70 hai 70 GB in 4G, minuti illimitati e 100 SMS a soli 7,99€ al mese http://tisca.li/Smart70 <http://tisca.li/Smart70> >

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saving coordinates with respect to map in ChimeraX
by khaja faisal tarique 28 Jun '21

28 Jun '21

Hello everyone While doing rigid body fit we know that after placing the coordinate to its correct position we can save it with respect to the map. Does anyone know if a similar feature exists in ChimeraX ? Is there a way where the coordinates .pdb/cif file can be saved with respect to its map in ChimeraX ? Thank you -- Faisal Tarique Khaja

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Problem with preset original command in Chimerax 1.2.5
by svle＠tiscali.it 25 Jun '21

25 Jun '21

Hi, I have a problem with Chimerax 1.2.5 on windows 10. In the command line I use the following: open 5u1c ( ok ) preset riboon (ok) preset original After the last command the application freezes and I must to kill it. What I can do? Thanks Saverio Con Tiscali Mobile Smart 70 hai 70 GB in 4G, minuti illimitati e 100 SMS a soli 7,99€ al mese http://tisca.li/Smart70

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access to current selection
by Diego Amaya 25 Jun '21

25 Jun '21

Hello everyone, I would like to find the equivalent to chimera expression "chimera.selection.currentAtoms()" in ChimeraX. Any idea ? Thanks in advance. Best regards -- Diego A. Amaya Ramírez -- *Aviso legal:* El contenido de este mensaje y los archivos adjuntos son confidenciales y de uso exclusivo de la Universidad Nacional de Colombia. Se encuentran dirigidos sólo para el uso del destinatario al cual van enviados. La reproducción, lectura y/o copia se encuentran prohibidas a cualquier persona diferente a este y puede ser ilegal. Si usted lo ha recibido por error, infórmenos y elimínelo de su correo. Los Datos Personales serán tratados conforme a la Ley 1581 de 2012 y a nuestra Política de Datos Personales que podrá consultar en la página web www.unal.edu.co <http://www.unal.edu.co/>.* *Las opiniones, informaciones, conclusiones y cualquier otro tipo de dato contenido en este correo electrónico, no relacionados con la actividad de la Universidad Nacional de Colombia, se entenderá como personales y de ninguna manera son avaladas por la Universidad.

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Chimerax 1.2.5/CentOS-7 Rizen cpu: WARNING: RDRND generated: 0xffffffff 0xffffffff 0xffffffff 0xffffffff
by Tru Huynh 25 Jun '21

25 Jun '21

Hi I have just installed the centos7 rpm (and rpm2cpio into our NFS shared software installation tree). tru@sillage ~]$ chimerax WARNING: CPU random generator seem to be failing, disabling hardware random number generation WARNING: RDRND generated: 0xffffffff 0xffffffff 0xffffffff 0xffffffff is diplayed upon startup on my desktop: /proc/cpuinfo: model name : AMD Ryzen 9 3900X 12-Core Processor stepping : 0 microcode : 0x8701012 .. fpu : yes fpu_exception : yes cpuid level : 16 wp : yes flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx mmxext fxsr_opt pdpe1gb rdtscp lm constant_tsc art rep_good nopl nonstop_tsc extd _apicid aperfmperf eagerfpu pni pclmulqdq monitor ssse3 fma cx16 sse4_1 sse4_2 movbe popcnt aes xsave avx f16c rdrand lahf_lm cmp_legacy svm extapic cr8_legacy abm sse4a misalignsse 3dnowprefetch osvw ibs skinit wdt tce topoext perfctr_core perfctr_nb bpext perfctr_l2 cpb cat_l3 cdp_l3 hw_pstate sme retpoline_amd ssbd ibpb stibp vmmcall fsgsbase bmi1 avx2 smep bmi2 cqm rdt_a rdseed adx smap clflushopt clwb sha_ni xsave opt xsavec xgetbv1 cqm_llc cqm_occup_llc cqm_mbm_total cqm_mbm_local clzero irperf xsaveerptr arat npt lbrv svm_lock nrip_save tsc_scale vmcb_clean flushbyasid decodeassists pausefilter pfthreshold avic v_vmsave _vmload vgif umip overflow_recov succor smca ... No error is shown on other machines equipped with: Intel(R) Xeon(R) Silver 4114 CPU @ 2.20GHz Cheers Tru -- Tru Huynh (PhD) | mailto:tru@pasteur.fr | tel +33 1 45 68 87 37 https://research.pasteur.fr/en/team/structural-bioinformatics/ Institut Pasteur, 25-28 rue du Docteur Roux, 75724 Paris CEDEX 15 France

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