June 2021 - ChimeraX-users - RBVI Mailing Lists

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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Your site is not working
by Moradkhan, Tiglath A 24 Jun '21

24 Jun '21

Hi, I'm trying to download a daily build of ChimeraX but when I try to access the UCSF ChimeraX website it seems to be down. Also when I try to access user guides, I'm also not able to access them. Are you experiencing some system-wide issue today? Thanks Tiglath

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Open a PDB-formatted file and a MTZ file
by Wen-Jin Winston Wu 23 Jun '21

23 Jun '21

Hi, I am trying to inspect electron density of X-ray data. I have the PDB-formatted coordinate file a.pdb (not been submitted to PDB yet) and a mtz file (a.mtz). I have downloaded Clipper to Chimera X (1.2.5) running on Window 10. I have opened my a.pdb, and I then tried to open my a.mtz file from the File-Open and I specified the file type with "*.mtz", and opened the a.mtz file, but I then got the error message: "Must specify a structure model to associate with crystallographic data". I know that I was not doing it correctly (e.g. not typing proper commands with correct syntax.). I looked into the description in the URL below. However, I just could not get it work. Any help will be appreciated. Thanks! http://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#clipper Best wishes, Winston

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Chimerax 1.2.5 Ubuntu 16.04 failed to start
by Zhou, Bing-Rui (NIH/NCI) [E] 22 Jun '21

22 Jun '21

Hello ChimeraX developer, I am trying to update ChimeraX from v1.1 to v1.2.5 on a Ubuntu 16.04 Linux machine, but Chimerax v1.2.5 failed to start with the following error message: > sudo apt-get install ~/Downloads/ucsf-chimerax_1.2.5_amd64.deb >chimerax qt.qpa.plugin: Could not load the Qt platform plugin "xcb" in "" even though it was found. This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem. Available platform plugins are: eglfs, linuxfb, minimal, minimalegl, offscreen, vnc, wayland-egl, wayland, wayland-xcomposite-egl, wayland-xcomposite-glx, xcb. Fatal Python error: Aborted Current thread 0x00007f5866636700 (most recent call first): File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/ui/gui.py", line 157 in __init__ File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/ChimeraX_main.py", line 577 in init File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/ChimeraX_main.py", line 1015 in <module> File "/usr/lib/ucsf-chimerax/lib/python3.8/runpy.py", line 87 in _run_code File "/usr/lib/ucsf-chimerax/lib/python3.8/runpy.py", line 194 in _run_module_as_main Aborted (core dumped) I could downgrade to ChimeraX v1.1 and it works fine, just wondering what has changed in v1.2.5 and if there is a fix for this issue. Thanks, Bing-Rui

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Ball-and-stick model modification
by Volodymyr Dvornyk 21 Jun '21

21 Jun '21

Hello, I wonder whether it is possible to modify the ball-and-stick model shape, i.e., change color, ball diameter, stick length, etc. Right now, the only available presentation style is like one in the attachment. Maybe there is some way to modify it but I was unable to find. Thank you, Volodymyr ________________________________ DISCLAIMER: This electronic mail transmission contains confidential information intended only for the person(s) named. Any use, distribution, copying or disclosure by any other person is strictly prohibited. If you received this transmission in error, please notify the sender by reply e-mail and then destroy the message. Opinions, conclusions, and other information in this message that do not relate to the official business of Alfaisal University shall understand to be neither given nor endorsed by Alfaisal University. The contents of any attachment to this e-mail may contain software viruses, which could damage your own computer system. While "Alfaisal University" has taken every reasonable precaution to minimize this risk, we cannot accept liability for any damage which you sustain as a result of software viruses. You should carry out your own virus checks before opening the attachment.

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Fwd: Troubles when saving a map
by Tom Goddard 18 Jun '21

18 Jun '21

Stephane's problem with the MRC map written by ChimeraX looking like noise in Coot was because the map origin was not correct. Tom > Begin forwarded message: > > From: Stéphane ROCHE > Subject: RE: [chimerax-users] Troubles when saving a map > Date: June 18, 2021 at 5:37:12 AM PDT > To: "Vadim Kotov" , "Tom Goddard" > > Thanks to both of you for your help ! > > I have finally understood what was happening, the origin of my map was changed and it was a very long way from its old position given that the box was quite large. So basically, when if I was looking around for densities, I was only scrolling inside the solvent. > > Thanks again, > Stephane Roche > > > On 17.06.21 10:07, Stéphane ROCHE via ChimeraX-users wrote: >> Dear Mr/Mrs, >> >> I am new to ChimeraX (v 0.7) and I have a trouble when saving a map. >> >> I am working with a .ccp4 map from an electron microscopy project. I would like to slightly change the pixel size that was inaccurately estimated during data processing and chimeraX seems to be the program for doing that. >> - Opening the map is fine. >> - Then I change the pixel voxelsize which is also fine. >> - I then save the modified map (I use the .mrc format here given that I do not find a .ccp4 format). >> - However if I then use the map with my usual softwares (phenix, coot) it looks like pure noise. But the map looks normal with some other softwares (e.g. pymol). I also have no problem usually with my .mrc maps with any software so I would assume the problem is with the .mrc map I created >> >> Do you know what I could do to solve this problem ? >> >> Thanks, >> Stephane Roche >> Institut de Biologie Intégrative de la Cellule >> 91198 Gif sur Yvette >> France >>

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Assistance
by Priyanka Abeyrathne 18 Jun '21

18 Jun '21

Hi, Could someone assist me to sort out the following? In Chimera, we can save PDB relative to the electron microscopy density map. Can we save the electron microscopy density map relative to the PDB? Any suggestion? Thank you. Priyanka

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ChimeraX-users June 2021