- ChimeraX-users - RBVI Mailing Lists

Re: Help_saving
by Elaine Meng 21 Jun '24

21 Jun '24

Sure, if you tell me that works. I wasn't sure if #2 had all 60 or just the other 59 and it would have been another several minutes experimenting. Elaine > On Jun 21, 2024, at 1:53 PM, Tom Goddard <goddard(a)sonic.net> wrote: > > How about execute the second sym command with copies true on model #2 which has the first 60 copies? > > Tom > > >> On Jun 21, 2024, at 1:50 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: >> >> Sigh, I was trying to enlist help in answering the question directly considering I've already spent hours messing around with it... especially if you think it is simple to explain. I don't think it is obvious to expect different numbers of copies just because you wanted them to be atomic instead of graphical. >> >> If she wants 3600 full atomic copies how would she do that?? >> >> Elaine >> >>> On Jun 21, 2024, at 1:35 PM, Tom Goddard <goddard(a)sonic.net> wrote: >>> >>> Hi Elaine, >>> >>> If you don't use copies true, then the first sym command changes model #1 rendering to include 60 graphical clones, and then the second sym command also on model #1 makes 60 graphical clones of the previous 60 graphical clones, so you now have 3600 graphical clones in model #1. You can see this with "info #1" which says "3600 instances". >>> >>> If you use the "copies true" option then the sym command makes a new model #2 with 60 copies. The second sym command on #1 with copies true makes 60 more copies as model #3. Of course that is a very different result then the sequence without copies true because the copies true version makes new models instead of modifying the original model. >>> >>> This all makes sense to me. >>> >>> Tom >>> >>> >>>> On Jun 21, 2024, at 1:25 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: >>>> >>>> Hi Tom, maybe you can figure it out?? >>>> >>>> OK I give up, I did extensive tests and can't figure it out either. I regenerated the original starting molecule (I think), attached as temp.pdb >>>> >>>> Then the overall result visible with the following, which is what she apparently wants (except with real atomic copies) although I worry it may have double copies in places, is a very packed-looking sphere: >>>> >>>> sym #1 i,2n5 center 20,20,20 >>>> sym #1 i,2n3 center 20,20,20 >>>> >>>> However if you start over with temp.pdb and then do the following, you get something much more patchy/holey >>>> >>>> sym #1 i,2n5 center 20,20,20 copies true >>>> sym #1 i,2n3 center 20,20,20 copies true >>>> >>>> I thought it might have something to do with copies replacing other copies but I tried with newModel true and still had seemingly the same issues. >>>> >>>> Maybe the more-packed appearance is actually a bug if sym w/o copies true makes more graphical copies of ones that are already graphical copies. >>>> >>>> Elaine >>>> >>>> <temp.pdb> >>>> >>>> >>>> >>>>> Begin forwarded message: >>>>> >>>>> From: "Noriega, Heather via ChimeraX-users" <chimerax-users(a)cgl.ucsf.edu> >>>>> Subject: [chimerax-users] Re: Help_saving >>>>> Date: June 21, 2024 at 12:14:50 PM PDT >>>>> To: ChimeraX Users Help <chimerax-users(a)cgl.ucsf.edu> >>>>> Reply-To: "Noriega, Heather" <heather.noriega(a)bison.howard.edu> >>>>> >>>>> Hello, >>>>> >>>>> It is quite baffling to me why it does this. I am going to add different sessions to show you what I see. I have included each session to try and separate to explain myself and not confuse. Three of the sessions do not include the copies true command: (sym_2n3, sym_2n5, sym_both). The one with both (sym_2n3 and sym_2n5) gives me the niosome I am quite interested in with an aqueous and lipophilic compartment. I want to do a simple measure of the volume inside the large compartment, but would like to minimize the niosome as a whole first, hence needing a pdb file. However, I have done the same with the next three sessions, but adding copies true command and it is not coming up with the same result for sym_both_copiestrue. >>>>> >>>>> I hope this helps to try and understand what I am looking for, and maybe you have an answer as to why there are different results for Sym_both and Sym_both_copiestrue. >>>>> >>>>> Thank you, >>>>> >>>>> Heather Noriega >>>>> PhD-Pharmaceutical Science student >>>>> Howard University >>>>> heather.noriega(a)bison.howard.edu >>>>> 520-203-1883 >>>>> >>>>> >>>>> On Fri, Jun 21, 2024 at 2:33 PM Elaine Meng <meng(a)cgl.ucsf.edu> wrote: >>>>> Hi Heather, >>>>> >>>>> I don't really understand why you needed two sym commands instead of one (must be something specific about your structure(s)), but whenever you want to actually save the PDB of any parts that "sym" adds you would need to include "copies true" when you add them. >>>>> >>>>> You could just do the experiment with and without it yourself and see what you get. Or save two separate PDB files, one from each command, to make sure you aren't getting duplicates of the same atoms exactly on top of each other from using sym twice. >>>>> >>>>> Elaine >>>>> >>>>>> On Jun 21, 2024, at 9:45 AM, Noriega, Heather via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: >>>>>> >>>>>> Hello, >>>>>> >>>>>> I do not want to save the shape of a sphere. I was using that for something else while creating the nano. >>>>>> >>>>>> Ok, that is what I did wrong. I did not include the copies true command. I have a question. I used the commands: >>>>>> >>>>>> Sym #1 i,2n3 center 20,20,20 and Sym #1 2n5 center 20,20,20 to create the sphere. Would I have to add copies true to both commands? >>>>>> >>>>>> sym#1 i,2n3 center 20,20,20 copies true >>>>>> sym#1 i,2n5 center 20,20,20 copies true >>>>>> >>>>>> And then continue with the saving process for PDB >>>>>> >>>>>> >>>>>> Thank you, >>>>>> >>>>>> Heather Noriega >>>>>> PhD-Pharmaceutical Science student >>>>>> Howard University >>>>>> heather.noriega(a)bison.howard.edu >>>>>> 520-203-1883 >>>>>> >>>>>> >>>>>> On Fri, Jun 21, 2024 at 12:37 PM Elaine Meng <meng(a)cgl.ucsf.edu> wrote: >>>>>> Hi Heather, >>>>>> I can't tell what you are trying to save exactly but here are two issues: >>>>>> >>>>>> (1) when you used "sym" the Log said it was making graphical clones. (The log contents are included in the session file.) If you want full atomic copies instead of graphical clones you have to use "copies true" as explained in the help: >>>>>> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/sym.html#copies> >>>>>> >>>>>> (2) The big sphere seems to be a surface model, and you can't save a surface model as PDB format. Maybe you used the "shape" command, which creates surface models. But I can't tell from your message whether you are trying to save that in the file or not. >>>>>> >>>>>> I hope this helps, >>>>>> Elaine >>>>>> ----- >>>>>> Elaine C. Meng, Ph.D. >>>>>> UCSF Chimera(X) team >>>>>> Resource for Biocomputing, Visualization, and Informatics >>>>>> Department of Pharmaceutical Chemistry >>>>>> University of California, San Francisco >>>>>> >>>>>> >>>>>>> On Jun 21, 2024, at 9:16 AM, Noriega, Heather via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: >>>>>>> >>>>>>> Hello, >>>>>>> >>>>>>> I have a question. I created this sphere nanoparticle and have been trying to save it as a PDB (the whole sphere). But when I save "selected atoms, " I try to re-open the PDB file. It only shows the original single Span-60 that was used. Is there a way to save the copies and nanoparticles as a whole so I can minimize them altogether? >>>>>>> >>>>>>> I attached the session below for your reference. >>>>>>> >>>>>>> Thanks, Happy Friday! >>>>>>> >>>>>>> Thank you, >>>>>>> >>>>>>> Heather Noriega >>>>>>> PhD-Pharmaceutical Science student >>>>>>> Howard University >>>>>>> heather.noriega(a)bison.howard.edu >>>>>>> 520-203-1883 >>>>>>> <nano_span_60.cxs> >>>>> >>>> <sym_2n5_copiestrue.cxs> >>>> <sym_2n3_copiestrue.cxs> >>>> <sym_2n5.cxs> >>>> <sym_2n3.cxs> >>>> <sym_both.cxs> >>>> <sym_both_copiestrue.cxs> >>>>> _______________________________________________ >>>>> ChimeraX-users mailing list -- chimerax-users(a)cgl.ucsf.edu >>>>> To unsubscribe send an email to chimerax-users-leave(a)cgl.ucsf.edu >>>>> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ >>>> >>> >> >> > >

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Sequence viewer colour by B factor
by isaphan＠uw.edu 21 Jun '24

21 Jun '24

How do I colour a sequence by B factor? There's an option to 'Load a sequence coloring file'. Sounds good, but how do I produce an .scf file from a structure coloured by B-factor ? There's a format explanation, but how do I get the actual data ? Grateful for any hints.

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question about coloring
by Artur Biela 21 Jun '24

21 Jun '24

dear all, I would like to color my structure (atoms) according to the LocalResolution of the map that the model is fitted in. There is a simple way to color a map according to the colors of the molecular model, but can it be done the other way around? best Artur =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Artur BIELA, PhD tel: +48-518-459-652 @: artur.biela(a)uj.edu.pl [cid:ced8e93e-4e29-47d8-b709-419b04837a3b] cryoEM faciliy manager SOLARIS National Synchrotron Radiation Centre Jagiellonian University Czerwone Maki 98, 30-392 Kraków www.synchrotron.pl<http://www.synchrotron.pl/> https://synchrotron.uj.edu.pl/en_GB/linie-badawcze/cryo-em

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Adjusting Torsion Angles
by Eleanor Streeper 20 Jun '24

20 Jun '24

Hi Chimera X, I hope you are well. I am a student at Swarthmore College and am currently trying to use Chimera X to adjust the torsion angles of glycans on a protein I have glycosylated. I tried using the same notation in your user guide, but the program says I am only entering 3 atom into the command bar. I attached images of the command and the numbering of those atoms (2nd entry in the angle/torsion measurement picture). I am trying to get the 2nd entry torsion to be 178.6 degrees. Can you let me know what I am doing wrong and how to adjust the torsion angle. Best, Ellie Streeper [image: Screenshot 2024-06-20 at 1.28.34 PM.png][image: Screenshot 2024-06-20 at 1.28.24 PM.png] [image: Screenshot 2024-06-20 at 1.35.46 PM.png]

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Re: CHimeraX and Chimera website down
by Elaine Meng 19 Jun '24

19 Jun '24

Hi Yaikhomba, Yes, we had a planned outage for server maintenance the last few days. Usually our email is out at the same time so it will not help to send email either, sorry! There was an announcement about it to this chimerax-users email list and also a news item on the ChimeraX home page, although of course you can't see the home page when the website is down. You can change the map origin with the ChimeraX "volume" command option "origin" or "originIndex", see the help for what these mean and how to use them: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#dimensions> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco > On Jun 19, 2024, at 8:49 AM, M Y <yai25ram(a)gmail.com> wrote: > > Hi Elaine > > I hope you are well. > > I had trimmed the box size of a cryoEM-map using the RELION software (to 375 pixels from 600 pixels). To fit in a PDB model to the trimmed map, I also rescaled the trimmed map to 1.048 A/pixel from 1.07 A/pixel. However, these 2 maps do not overlay with one another (image attached). > > I wanted to change the origin of the trimmed map such that 2 maps overlay with one another. How could I do this in ChimeraX? > > I tried looking at the Chimera or the ChimeraX website. But, the website is either down or I am not able to access it (Screenshot attached). > > Your suggestions will be helpful. > > Many thanks > Yaikhomba > <image.png> > <image.png>

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Creating bond between two selected atoms
by Eleanor Streeper 17 Jun '24

17 Jun '24

Hi Chimera X, I hope you are well. I am a student at Swarthmore College and am currently trying to use Chimera X to covalently attach glycans to asparagine residues. I was able to get 3 out of 5 of the glycans attached by selecting both atoms > structure editing > build structure > adjust bonds > add reasonable bonds. I did the same process for the other 2 glycans and no bond was made. The log says bond sel, 0 bonds. The glycans are combined with the protein using the combine command. I believed it may be an issue with an unreasonable binding distance but when I moved the glycan closer, the bond still didn't work. What else should I try? Also, do you know why it is working for some glycans but not others? Best, Ellie Streeper

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Updating pdb SEQRES record with a loaded .fasta file
by Samuel Haysom 14 Jun '24

14 Jun '24

Hello, I would like to use a .fasta file that I have loaded into ChimeraX to update the SEQRES records of a PDB file that is also loaded into ChimeraX. Currently the loaded PDB file only has SEQRES records for the residues that are modelled, while the .fasta file has the full, sequence with no gaps. I have tried loading in the .fasta file and then using the $ sequence associate command to associate it with the relevant pdb chain. However, when I then save out the pdb file (using the $ save command) and then examine the pdb file it still only records the modelled residues. Is there any way to force the written pdb file to have the full sequence as uploaded in the .fasta file? I am running chimeraX version 1.7 (2023-12-19). Thanks for your help, Sam Samuel Haysom Research Scientist • Biophysics Nxera Pharma UK Limited +44 (0)1223 949201 • Steinmetz Building, Granta Park, Great Abington Cambridge, CB21 6DG, United Kingdom The information in this e-mail is confidential and may be legally privileged. It is intended for the exclusive attention of the addressee stated above and should not be copied or disclosed to any other. If you have received this transmission in error, please contact the sender immediately, make no use of its contents and delete this message from your system. Contact and registered office address: Nxera Pharma UK Limited, Granta Park, Great Abington, Cambridge, CB21 6DG. Company No: 06267989.

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RBVI downtime
by Eric Pettersen 13 Jun '24

13 Jun '24

Hi all, The RBVI compute cluster will be down for scheduled maintenance Monday and Tuesday of next week (June 17/18) which means that the Chimera and ChimeraX web sites (including the ChimeraX toolshed) and mailing lists will be down during that time. This also means that web services from Chimera/ChimeraX that access our compute cluster will not work (Blast Protein, Modeller tools, sequence realignment). We are sorry for any inconvenience. --Eric Eric Pettersen UCSF Computer Graphics Lab

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Resizing an ion model representation
by Ioannis Skalidis 13 Jun '24

13 Jun '24

Dear all, I want to show a metal ion surrounded by some side-chains for a figure panel, but the ion ball representation is quite small and gets lost in the figure panel. Is there a way to select only the specific ion and increase its size? I tried a bit with the "size" command, including the ballScale option but I had no luck. Any suggestions? Thanks a lot, Ioannis. Dr. Ioannis Skalidis | Structural Biochemist | Twitter: @imjohnskal <https://twitter.com/imjohnskal>

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Feature Request: Visual feedback on selecting menu items
by Cam McMenamie 12 Jun '24

12 Jun '24

Hello! I'm just suggesting a UI feature that I think would be very helpful. Currently, there are several menu items that do not show any feedback if they are "selected" or not, for example, in the screenshot below (hard to tell which options have been selected / toggled). This is especially the case for mutually exclusive selections such as in the 'coloring' section in the "molecule display" tab. [cid:34830b00-bed7-4734-b191-dc4fd0fad018] Thanks in advance, Cam

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