- Chimera-users - RBVI Mailing Lists

Fwd: Split, Crash out
by Tom Goddard 07 Sep '21

07 Sep '21

MJ reports that rebooting the computer fixed the Chimera crashes. > Begin forwarded message: > > From: Jeremy Jin > Subject: Re: [Chimera-users] Split, Crash out > Date: September 5, 2021 at 10:28:02 PM PDT > To: Elaine Meng <meng(a)cgl.ucsf.edu>, Tom Goddard <goddard(a)sonic.net> > > Hi Elaine adb Tom, > Sorry to bother, I tried again today, it worked, seems something wrong with my system or reboot several times works. I am also will try ChimeraX! Thanks! > > Best Regards! > MJ > > MJ, Mingliang Jin > Postdoc of Yifan Cheng’s Lab > Genentech Hall, UCSF Missionbay > Main Email: m.jin(a)msg.ucsf.edu > Tel: 415-2835-171 > > > >> On Sep 3, 2021, at 12:53, Tom Goddard <goddard(a)sonic.net> wrote: >> >> Hi MJ, >> >> Most Chimera crashes are caused by graphics driver bugs. Updating your graphics driver is the usual fix. You might try our newer program ChimeraX. We have only done basic maintenance on Chimera for the past 5 years. ChimeraX does a better job reporting diagnostics if a crash happens. >> >> Tom >> >>> On Sep 3, 2021, at 12:26 PM, Jeremy Jin via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: >>> >>> Hi, >>> >>> When I use chimera, I want to split a mode, as long as I split, the software just crashes out. >>> >>> It works very well before. Also it worked this morning, but after I split the model, fit to my map, it crashed out, then I restart, it showed the same problem. Then I re-installed the program, 2020-12-08 version, it crashed out even when I do split command. >>> >>> Best Regards! >>> MJ >>> >>> MJ, Mingliang Jin >>> Postdoc of Yifan Cheng’s Lab >>> Genentech Hall, UCSF Missionbay >>> Main Email: m.jin(a)msg.ucsf.edu >>> Tel: 415-2835-171 >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> _______________________________________________ >>> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu >>> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >>> >> > >

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Copy protein orientation
by SANDOVAL, KENNETH 06 Sep '21

06 Sep '21

Hello, I wish to generate two images. The first is of protein A which is in session 1. The second is of protein A aligned with protein B using TM-Align which is in session 2. I wish for the alignment of the second image to be in the same orientation as the first with respect to protein A. Is there a feature which lets me do the following: 1) Identify orientation of protein A in session 1 2) Copy that orientation 3) Apply that orientation to protein A in session 2 4) Have protein B in session 2 remain aligned to protein A despite the new orientation Thank you, Kenneth Sandoval

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Split, Crash out
by Jeremy Jin 03 Sep '21

03 Sep '21

Hi, When I use chimera, I want to split a mode, as long as I split, the software just crashes out. It works very well before. Also it worked this morning, but after I split the model, fit to my map, it crashed out, then I restart, it showed the same problem. Then I re-installed the program, 2020-12-08 version, it crashed out even when I do split command. Best Regards! MJ MJ, Mingliang Jin Postdoc of Yifan Cheng’s Lab Genentech Hall, UCSF Missionbay Main Email: m.jin(a)msg.ucsf.edu Tel: 415-2835-171

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matchmaker for more than one chain
by manikandank 02 Sep '21

02 Sep '21

Hi ChimeraX-users, I have used recently the mmaker cmd to align two pdb each have multiple chains as below. mmaker #12/L,M,N to #5/S,A,B matrix blosum-62 showAlignment true But the sequence view shows only the alignment of chain L and S. 1. I would like to have aligned sequences of all chains used in mmaker alignement. 2. Is it possible to open the saved RMSD header values in a file later just to color the pdb? 3. Do mmaker align entire pdb based on selected chains and Can calculate RMSD for all residues in the pdb? 4. I also would like to change the displayed text for the sequence name. Presently it puts the filename as sequence name. [similar to 'Edit sequence name' in the sequence viewer in chimera] Please let me know how this can be done. thank you very much with kind regards Mani.

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Ribbon scaling in a script
by Esser, Lothar (NIH/NCI) [E] 01 Sep '21

01 Sep '21

Hi, despite a good amount of search in the documentation, I was unable to find a way to set the dimensions of a ribbon coil, helix width etc. with a commandline statement. I can do it in Ribbons Style Editor but I need to be able to do it from a script. I am sure it is terribly obvious but I just think it may be easier if I get a hint at this point. Thanks, Lothar Dr. Lothar Esser National Institutes of Health 37 Convent Dr. Rm2122B Bethesda, MD 20892

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Re: [Chimera-users] Making oligomers from Alphafold predictions
by Tom Goddard 01 Sep '21

01 Sep '21

Hi Tiru, If the center of symmetry is at 0,0,0 for your model and it just needs 6 rotated copies placed use Chimera command sym #0 group c6 where #0 is the model number of your monomer. If you do not know the center of symmetry or how the monomers interface with each other (ie their orientation in the hexamer), then that is a protein-protein docking problem and the sym command does not solve that. For that case you would need to fit in a cryoEM or X-ray map of the hexamer, or align the monomer to a known homologous hexamer, or find some amazing oligomeric structure prediction tool. Tom > On Sep 1, 2021, at 11:24 AM, Tiru Hcu <tiru.hcu09(a)gmail.com <mailto:tiru.hcu09@gmail.com>> wrote: > > Hi Tom, > > Thank you for your response. My protein symmetry is a hexamer. Please would you mind sharing a little elaborate how to to do in chimera. Thank you. > > Best regards, > Tiru > > On Wed, 1 Sep 2021, 21:10 Tom Goddard via Chimera-users, <chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>> wrote: > Hi Smith, > > Do you know the symmetry of the oligomer you are trying to make? Is it just a matter of applying positions that you already know? Or do you need some computational protein-protein docking to figure it out (a vastly harder problem)? If you know the symmetry you want the Chimera and ChimeraX sym command can place copies of a structure using standard symmetries or a list of position matrices (rotation + translation). > > tom > > >> On Sep 1, 2021, at 1:29 AM, tim smith via Chimera-users <chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>> wrote: >> >> Thank you, Elaine and Kevin, for your response. >> The Rosetta Symmetry docking is up to 400 amino acids, and mine is 800. I can't use it as it is. Wondering there is any other server for predicting symmetry. >> >> Thank you. >> >> Best >> Smith >> >> On Tue, Aug 31, 2021 at 7:02 PM Kevin Jude <kjude(a)stanford.edu <mailto:kjude@stanford.edu>> wrote: >> Hi Smith, you can use Rosetta Symmetric Docking. It's available on the ROSIE server >> >> https://rosie.rosettacommons.org/symmetric_docking <https://rosie.rosettacommons.org/symmetric_docking> >> -- >> Kevin Jude, PhD (he/him/his) >> Structural Biology Research Specialist, Garcia Lab >> Howard Hughes Medical Institute >> Stanford University School of Medicine >> Beckman B177, 279 Campus Drive, Stanford CA 94305 >> Phone: (650) 723-6431 <tel:%28650%29%20723-6431> >> On Tue, Aug 31, 2021 at 4:30 AM tim smith via Chimera-users <chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>> wrote: >> Hi All, >> Apologies for the nonrelated question!! >> >> Wondering if there are any tools (can make in chimera/chimerax/Pymol) that predict or build protein oligomers based on alphfold structure. Please let me know. I will be grateful for your kind responses. Thank you >> >> Best >> Smith >> _______________________________________________ >> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> >> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users> >> _______________________________________________ >> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> >> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users> > > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> > Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>

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Making oligomers from Alphafold predictions
by tim smith 01 Sep '21

01 Sep '21

Hi All, Apologies for the nonrelated question!! Wondering if there are any tools (can make in chimera/chimerax/Pymol) that predict or build protein oligomers based on alphfold structure. Please let me know. I will be grateful for your kind responses. Thank you Best Smith

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Capture click event
by jeni_zen2004＠yahoo.co.in 30 Aug '21

30 Aug '21

Hi, Is there a way to capture the Chimera click event or a way to work around?I'm trying to do something from python code like., when a user clicks on a residue, it pops up a tooltip or shows the centroid. Thanks,Catherine

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ITasser model looks different once PDB opened in UCSF Chimera
by Athena Andreosso 25 Aug '21

25 Aug '21

Hi, I recently submitted a sequence to get a model in PDB format. When I opened the PDB file of model 1 in Chimera it looked completely different than the model on the ITasser results page - it had less beta strands. When I clicked on model 2 it was better but there's still a visible discrepancy. Am I doing something wrong? Am I supposed to give chimera more info than just the PDB file ? Any help is appreciated. Cheers Athena Andreosso, D.Phil. | Research Officer Mucosal Immunology QIMR Berghofer Medical Research Institute e AthenaAndreosso(a)qimrberghofer.edu.au<mailto:AthenaAndreosso@qimrberghofer.edu.au> | www.qimr.edu.au<http://www.qimr.edu.au/> 300 Herston Road, Herston QLD 4006

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3D Visualization
by Song, David 25 Aug '21

25 Aug '21

Hi, My name is Dave Song, and I am a graduate student interested in visualizing protein structures in 3D. I was wondering if you had any recommendations in regards to computer hardware requirements for maximum performance while using Chimera/ChimeraX. Additionally, do you have any suggestions on monitors and 3D glasses that work well with Chimera? Thank you for your time, and I look forward to hearing from you. Best, Dave

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Chimera not responding
by Pritam Dey 23 Aug '21

23 Aug '21

Cannot execute 'gzip': no automatic decompression of .Z files Return code: -1073741819 Press return or enter to to exit

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Hollow Sticks When Exporting as STLs?
by Josh Moon 17 Aug '21

17 Aug '21

Hello, I hope to make this question as direct and simple as I can! When I export a scene of a molecule displayed as a ball-and-stick as a STL, I find that many of my "stick" portions are hollow. This creates thin, weak walls for 3D printing. I've included a screenshot of an intended plane cut from Meshmixer so that you can see the internal structure. What am I doing incorrectly? Is there something I can do in Chimera to export a solid object with no "hollow tubes." Fixing this with 3d programs can be time consuming. Sincere thanks, Josh ----------------------------------------- Josh Moon, Ph.D. (he/him/his) Educational Technology Specialist Kalamazoo College (269) 337-7415

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Fc dimer fall apart after fusion with a GS linker
by tiger wang 16 Aug '21

16 Aug '21

Dear Ms/Mr helper: I encounted an issue when I try to fuse one (G4S)x linker to one of the Fc "C" terminal using "join bond". Once selected the "C" atom on Fc C terminal and "N" atom on (G4S)x N terminal and hit "apply" button, the Fc dimer fall apart but the (G4S)x linker was connected to the C terminal of Fc. How to avoid the Fc dimer from falling apart? Thanks very much for your help Sincerely TW

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How to get random velocities?
by Seera Suryanarayana 11 Aug '21

11 Aug '21

Dear chimera users, Dear VMD users, I was asked to do simulations five times with the same starting structure and number of processors. But the velocities should be different. Here my query is "How do you generate velocities in the gromacs?". I request you to guide me how to do it. Thanks in advance Surya Graduate student India.

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Problems with installing on a Windows 10 expedition Dell laptop
by Alice Chen 10 Aug '21

10 Aug '21

Hello, I'm on a Dell XPS 9500 laptop running Windows v. 10.0.2.1000. When my IT specialist tried to install it, it would run the install program but at the very end the install would fail. We were able to install the old non-X version of Chimera. Is there something we should/can do to check, settings-wise? Cheers-Alice Kitterman Alice Y Chen AY Chen Illustration and Design https://www.facebook.com/AYCIAD https://vimeo.com/user13507144/videos www.aliceychen.com

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How to recreate point of view
by achatz 06 Aug '21

06 Aug '21

Hello, I have two Chimera sessions which originate from the same pdb. Through rotations and movements the sessions viewpoints diverged over time. Is there a way to synchronize one session with the other so it has the exact same viewing angle? Thanks Stefan

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Question about peptide connection
by Nicole Ostrovsky 27 Jul '21

27 Jul '21

Hello, I have a structure which I've cut a section out of and I am working on connecting the two loose ends together. I wanted to connect them with two glycine residues - since they are easiest to work with and have no side chains. I am doing this using the Modify Structure option under the Build structure tool and adding one atom at a time. However, when I try to minimize my newly created glycine, I get the error message "No MMTK name for atom "H1" in standard residue "GLY"" (I've attached a picture of my reply log). I'm not sure how to troubleshoot this. Is there a better way to connect two ends of a peptide, or should I change the way I am using the modify structure tool? Thank you. Nicole Ostrovsky

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Changing DNA sequence
by Tom Goddard 26 Jul '21

26 Jul '21

Hi Gary, The swapna command lets you change a nucleic acid base, for example, to change residue 18 in chain C from a T to a G use open 1rsb swapna G :18.C Documentation for swapna https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/swapna.html <https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/swapna.html> Tom > On Jul 26, 2021, at 1:31 AM, <gren(a)lbl.gov> <gren(a)lbl.gov> wrote: > > Dear Tom > Thanks for many answers to our previous questions. > > I have one more question to our loved Chimera program. > > I have a NDA model (PDB), but the sequence is not right. Is there any way to use this DNA model to generate a new model with a right order of sequence? In other word, if is there an automatic/ simple method (by comment lines) to replace the sequence by the correct one in Chimera? > > Thanks a lot!! > Gary > > > Gang (Gary) Ren, PhD > Lawrence Berkeley National Laboratory > Molecular Foundry, Room: 2220 > 1 Cyclotron Road, MS 67R2206 > Berkeley CA 94720-8197 > Phone: (510) 495-2375; Fax: (510) 486-7268 > Email: gren(a)lbl.gov <mailto:gren@lbl.gov>; > https://rengroup.lbl.gov/ <https://rengroup.lbl.gov/>

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Query: Saved pdb doesnt have mutated residue
by ZUNERA JAMAL 26 Jul '21

26 Jul '21

Respected Chimera team! I have a pdb file in which i have done mutation by using swapaa command in IDLE python but once i saved the structure then new saved structure doesn't have mutated residues in it. commands: 1.rc("open filename.pdb") 2.rc("swapaa val #0:2.a") 3.new_file_name="val.pdb" 4.rc("write format pdb #0 C:\\Users\\folder" + new_file_name) 5.rc("save newsession") 6.rc("close session") 7.rc("close all")

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color pdb based on rmsd
by manikandank 21 Jul '21

21 Jul '21

Hi Chimera-users, I have aligned three pdbs using MatchMaker and would like to color one based on rmsd (per residue or per CA atoms). I see that i can use 'rmsd' to calculate CA-CA distance between two models, but i would like to write the distance difference in a file so that the file can be read in 'attribute' coloring scheme. Please let me know how to do this. thanking you with kind regards Mani.

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Doubts about DOCK6.9 and ZINC20
by Francesca Magarotto - francesca.magarotto2＠studio.unibo.it 20 Jul '21

20 Jul '21

Hi, I’m a student and I’m currently doing a thesis. I’ve never used Dock or Chimera before, so I followed some tutorials but now I’m a bit confused. 1. For five months I’ve saved the prepared receptors and the ligands as mol2, but I didn’t choose “write current selection to @SETS section of file”. I’ve just read on Chimera that it “makes the currently selected atoms as a SET (as used to specify the rigid portion of a ligand in DOCK)”. The docking I’ve performed seemed to go, but is actually everything wrong because I didn't select the option? 2. I’ve generated the receptor without hydrogens after dockprep (so after assigning charges and hydrogens). I’ve deleted only hydrogens but maybe the charges are still there, is that an error? 3. I’ve always saved the receptor without hydrogens in mol2 instead of pdb, because I’ve seen this in some tutorials, but now I’ve read tutorials that save it in pdb. Is this another error? I was able to generate the surface even with mol2 no hydrogens receptor and I’ve always toggle on “use untrasformed coordinates”, but obviously the options to save the file change for mol2 and pdb. 4. I follow a tutorial online to download 3D molecules from ZINC20. Anodyne means there are no PAINS and no reactive groups? Is the most “clean” reactivity pattern? 5. I don’t know how to organize all the directories and subdirectories downloaded with ZINC. I downloaded them in format mol2 and method curl, is that correct or shoul I use fot the virtual screening another format and method? To perform a virtual screening, I need to save them in a single mol2 file? How can I do that without errors? I've seen the option "flat" in downloading method in ZINC, is this a way to download the molecules correctly for virtual screening? 6. I need to use Chimera, but even with ViewDock I’m not able to open so many molecules (190 822), how can I look at the results in the end? 7. I’ve saved the ligands’ mol2 files using sybyl-style hydrogen naming. Is that an error? 8. To perform the virtual screening using 3D molecules from the tranche browser of ZINC20, can I use them as they are or I need to edit them in some way (for example after downloading them, open them in Chimera and using add H and/or add charge)? I need very specific indications about all these questions, because I’ve never done something similar, it’s the very first time with all and I’m afraid of making mistakes. I apologize for the many questions, but I hope that someone can answer all my doubts. Thank you, Francesca.

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Help: Suitable graphic driver
by Nur Nadia Razali 20 Jul '21

20 Jul '21

Hi, I am Nadia, I am a newbie for Chimera UCSF. When I started using Chimera, fetch under uniprot search, the message popped up. [image: image.png] I really need you help regarding this. Is it the issue of graphic card? Could you suggest what is the suitable driver for me to buy. I do have this kind of problem with other software that requires me to have the driver. Thank you, Sincerely, Nadia *ChM. NUR NADIA BINTI RAZALI* Science Officer UKM Medical Molecular Biology Institute (UMBI) *p:* +603-91459187 *f:* +603-91717185 *w:* www.ukm.my/umbi *e:* nadiarazali(a)ukm.edu.my <azrulhisham(a)ukm.edu.my> *a:* Jalan Yaacob Latiff, Bandar Tun Razak, 56000 Cheras, Kuala Lumpur, MALAYSIA. -- *PENAFIAN*: E-mel ini dan apa-apa fail yang dikepilkan bersamanya ("Mesej") adalah ditujukan hanya untuk kegunaan penerima(-penerima) yang termaklum di atas dan mungkin mengandungi maklumat sulit. Anda dengan ini dimaklumkan bahawa mengambil apa jua tindakan bersandarkan kepada, membuat penilaian, mengulang hantar, menghebah, mengedar, mencetak, atau menyalin Mesej ini atau sebahagian daripadanya oleh sesiapa selain daripada penerima(-penerima) yang termaklum di atas adalah dilarang. Jika anda telah menerima Mesej ini kerana kesilapan, anda mesti menghapuskan Mesej ini dengan segera dan memaklumkan kepada penghantar Mesej ini menerusi balasan e-mel. Pendapat, rumusan, dan sebarang maklumat lain di dalam Mesej ini yang tidak berkait dengan urusan rasmi Universiti Kebangsaan Malaysia (UKM) adalah difahami sebagai bukan dikeluar atau diperakui oleh mana-mana pihak yang disebut. _*DISCLAIMER *: This e-mail and any files transmitted with it ("Message") is intended only for the use of the recipient(s) named above and may contain confidential information. You are hereby notified that the taking of any action in reliance upon, or any review, retransmission, dissemination, distribution, printing or copying of this Message or any part thereof by anyone other than the intended recipient(s) is strictly prohibited. If you have received this Message in error, you should delete this Message immediately and advise the sender by return e-mail. Opinions, conclusions and other information in this Message that do not relate to the official business of The National University of Malaysia (UKM) shall be understood as neither given nor endorsed by any of the aforementioned._

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Minimization troubleshooting
by Nicole Ostrovsky 19 Jul '21

19 Jul '21

Hello, I am trying to perform minimizations on some structures I'm examining and each time the minimization is done and I open the reply log, the gradient norm says "-nan" and it tells me that no atoms were updated. I wasn't able to find anything online about how to fix this, so I'm emailing to ask if anyone would know how to troubleshoot this. Thank you. Nicole Ostrovsky

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Blast protein webservice error
by Stefan Dobrev 14 Jul '21

14 Jul '21

Hello! I'm trying to run a homology model on a protein sequence using BLAST, but my Blast: query window shows up empty. At first I got this error in the reply log: File "C:\Program Files\Chimera 1.15\share\blastpdb\pdbinfo.py", line 151, in fetch_pdb_info import replyobj ImportError: No module named replyobj I solved it by changing the code to "from python import replyobj". Now I can actually see what the error is. A few more functions are called until we get to this: File "C:\Program Files\Chimera 1.15\bin\lib\socket.py", line 480, in readline data = self._sock.recv(self._rbufsize) error: [Errno 10054] An existing connection was forcibly closed by the remote host I've allowed chimera through the firewall and I have a modeller license key, I believe I've entered it somewhere in Chimera at some point. Any ideas what might be causing this? Thanks for any advice, Stefan Dobrev

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Flipping the map - resolution question
by Dmitry Semchonok 14 Jul '21

14 Jul '21

Dear colleagues, I heard that flipping the map in Chimera with the command vop zflip # will decrease the resolution of the map https://www.cgl.ucsf.edu/chimerax/docs/user/commands/volume.html#notes <https://www.cgl.ucsf.edu/chimerax/docs/user/commands/volume.html#notes> Did I understand that statement correctly? If yes, how to flip the map without losing the quality (resolution)? Thank you Sincerely, Dmitry

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