- ChimeraX-users - RBVI Mailing Lists

Re: [chimerax-users] Model panel for multi-state objects of dimeric protein
by Elaine Meng 01 Aug '22

01 Aug '22

Hi Enrico, I haven't figured out why this doesn't work on your example (omitted since mailing to the list): close #1 & ~ #1.5 However, this works: delete #1 & ~ #1.5 Also if you didn't have other models (#2 etc.) that you were trying to keep you could just use delete ~#1.5 I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Aug 1, 2022, at 6:39 AM, Enrico Martinez <jmsstarlight(a)gmail.com> wrote: > > Hello Elaine, > I just faced the same problem that has been indicated in this topic > Thi time I am dealing with the monomeric multi-model complex obtained > from docking. > Here is the example of a pdb file consisted of 80+ docking poses. To > keep only the 1.5 sub-modeli've tried to use > close #1 & ~ #1.5 > but this produced nothing, while for other pdbs it works fine. Could > you tell me what's wrong with it? > Many thanks in advance > Cheers > Enrico

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Reduce figure size for export for publication
by Fossati, Andrea 01 Aug '22

01 Aug '22

Hi, How to best export figure at high-ish resolution to then add it to an already made illustrator panel? After some googling seems vector-based export is not possible so what is the recommended format and which resolution is best for 3x3 inch illustrator panel? At the moment I am exporting as TIFF with transparent background and size 5000 and supersampled 4 times to keep high res but the file has like 15Mb per structure which is not feasible/handy to modify. What is the suggested solution for paper figures? Best, Andrea Fossati, Ph.D Krogan Lab

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How to estimate 2dlabels fading?
by Edoardo D Imprima 01 Aug '22

01 Aug '22

Hi, Could you please explain more how the frames option works when changing 2dlabels? Let’s say I have 100 frames and I wish to have an arrow to appear at frame 10 for 5 frames? Many thanks in advance, Edoardo ------------------------------------------------------ Dr. Edoardo D'Imprima Postdoctoral fellow Structural and Computational Biology Unit EMBL Heidelberg - Mahamid Group Meyerhofstraße 1 69117 Heidelberg Germany Phone: +49 6221 387-8531

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Side view in command line
by HONG ZHAN 31 Jul '22

31 Jul '22

Hi all, I would like to setup a movie sequence using cxc file. It is very useful to setup in the UI window, however, any tricks could I use to set the clip plane in the command line to generate a view as in the attached picture? So that I can run my cxc file together with other actions? Many thanks! Hong [cid:12317B70-9FE5-4C25-933C-E56EF2888E9D]

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ChimeraX on Mac
by Lisa Käshammer 30 Jul '22

30 Jul '22

Dear developers, I have problems to get chimeraX to work on my computer. It had a previous version installed (1.1) which did not work anymore. So I removed that version and installed the newest version, however, it does not open. There is no error message so I am a bit lost at what I can do to resolve this issue. The macOS is 10.15.7. Thank you very much in advance. Best, Lisa

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command inquary
by Kwangjun Lee 30 Jul '22

30 Jul '22

Hello, Do you have any command that displays a selected region only? For example, I have a protein structure AA1 to AA300. I only want to display AA100 to AA200. Thanks!

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Re-scaling maps
by Nebojsa Bogdanovic 29 Jul '22

29 Jul '22

Hello, I have two maps. One from cryosparc @ 1.06 A/pix and another EM-gan sharpened map @ 1.0 A/pix. They are different in size upon visual inspection in chimeraX so I tried relion_image_handler --i cryosparc.mrc --angpix 1.0 --rescale_angpix 1.06 --o cryosparc-rescaled.mrc however, the resulting map is still smaller than the original input. I also tried to rescale in this way to several different angpix values but maps are still not the same. Is there any command in chimeraX or chimera to play with pix sizes to find the right one? Thank You and regards, Nebojša Bogdanović, Ph.D Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University

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Application to enter the chimeraX user's group
by Xiaofeng CHU 28 Jul '22

28 Jul '22

Dear chimeraX team Sorry for the interruption. My name's Xiaofeng Chu, the phd candidate in Misha Kudryashev's group working on cryoET and structural biology. Could you please help me to enter the group of chimeraX users? So I can raise some questions about how to use it. Thank you very much in advance! And have a nice day. Best regards Xiaofeng -- Xiaofeng Chu (he/him) Ph.D. candidate in M. Kudryashev's research group, Max Delbrück Center for Molecular Medicine in the Helmholtz Association 13125 Berlin, Germany

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Re: [chimerax-users] Assembling 2 proteins
by Elaine Meng 27 Jul '22

27 Jul '22

Hi Tata Santosh Rama Bhadra Rao, I already gave my suggestions in the previous message, so there is not really anything else I can do to teach you. Since you didn't give the details of all the steps that you tried and which step(s) gave results you didn't like, I can't tell you how to do it differently. My only idea is to go back to what I already suggested: you could use Matchmaker if you already had a pentamer, which you show in the bottom figures. So, following the instructions in my first reply, maybe you can take the chains shown in the top figures and match them onto the chains in the bottom figures to make the pentamer. However, that will only work if the proteins are very similar. If you did it already and it gave the bad result, maybe these proteins are not similar enough to use that approach. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On May 30, 2022, at 9:22 PM, SANTOSH RAMA BHADRA RAO TATA <19807877(a)students.latrobe.edu.au> wrote: > > Hi Elaine, > > I tried doing and it came out like this. Final 2 figures are homomeric pentamers. First 2 are heteromers with 3A subunits (A, B, D chains) and 2D (C, E chains) subunits. Could you please help me or teach me assembling them properly. > > Thanking you, > > With best wishes, > Tata Santosh Rama Bhadra Rao, > PhD Scholar, > C/O Prof Helen Irving, > La Trobe university, > Bendigo, Vic-3550, > Australia. > Email: 19807877(a)students.latrobe.edu.au; > S.Tata(a)latrobe.edu.au > Phone: 0499263974 > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Sent: Wednesday, 25 May 2022 2:08 AM > To: SANTOSH RAMA BHADRA RAO TATA <19807877(a)students.latrobe.edu.au> > Cc: chimerax-users(a)cgl.ucsf.edu <chimerax-users(a)cgl.ucsf.edu> > Subject: Re: [chimerax-users] Assembling 2 proteins > > Hello Tata Santosh Rama Bhadra Rao, > It all depends on what information you have already. If you don't know how the pentamer is supposed to look (how the proteins fit together), then there may not be enough information: ChimeraX is not going to predict the pentamer structure for you. > > You said "5 different proteins" which I interpret to mean they are not 5 copies of the same thing, that it is a heteropentamer and not a homopentamer. If they were 5 copies of the same thing (homopentamer), then you might be able to use the "sym" command to build it from one copy, if the input file contains symmetry matrices in the header, or you know the symmetry and can specify it separately: > <https://rbvi.ucsf.edu/chimerax/docs/user/commands/sym.html> > > Otherwise: > You would only use Matchmaker if you also have an already-known structure of a similar pentamer. Then you would open the structure of that pentamer, open the structures of your five proteins (if the same one is multiple copies in the pentamer, you would open it multiple times), and then match each one of them to the similar subunit of the known pentamer. In other words, you would open 6 different PDB files and then use Matchmaker 5 times, once to match each of your proteins to the corresponding subunit of the pentamer. > > Just start Matchmaker (menu: Tools... Structure Comparison... Matchmaker) and in that dialog's Chain Pairing, choose "Specific chain(s) in reference structure with specific chain(s) in match structure". Choose one of your protein chains as the match structure and choose the corresponding chain in the known pentamer as the reference. Apply. Repeat with your second protein chain, etc. > > Here is the Matchmaker help with detailed explanations of all the options: > <https://rbvi.ucsf.edu/chimerax/docs/user/tools/matchmaker.html#top> > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > > > > On May 23, 2022, at 9:49 PM, SANTOSH RAMA BHADRA RAO TATA via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: > > > > Hi, > > > > I would like to create a pentamer, how can I assemble 5 different proteins subunits into a pentamer. I was trying to use matchmaker but I couldn't. can you please help me with some video how to get in use it or if there is any other way to use the software and create pentamer please let me know. > > > > Thanking you, > > > > With best wishes, > > Tata Santosh Rama Bhadra Rao, > > PhD Scholar, > > C/O Prof Helen Irving, > > La Trobe university, > > Bendigo, Vic-3550, > > Australia. > > Email: 19807877(a)students.latrobe.edu.au; > > S.Tata(a)latrobe.edu.au > > Phone: 0499263974

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FitMap/FitList scripting
by Christian Tüting 27 Jul '22

27 Jul '22

Dear ChimeraX DevTeam, I am currently working on a project which requires fitting a single model multiple times in a map. This is easy doable with the global search parameter, and if n is big enough, all correct locations are found. My collegue Ioannis wrote you a couple of weeks ago to implement a copy function to the fitlist, but this includes only the statistics, but not the translation information of each model. This is only possible by clicking the button "Place Copy", which creates a copy of the model and applies the translation to this model. In the log, there is only the best model with the translation matrix, but if my map does have multiple correct locations, I'm missing this information. I extended the fitmap function in fitcmd.py, so it writes this to a file to the current location called fitmap.txt. This file contains all the statistics and the rotation/translation information. This might be handy for some users. Here is the code: f = open("fitmap.txt", "w") if len(flist) == 0: f.write("No fit found") else: for i, f0 in enumerate(flist): msg = f0.fit_message() f.write(f"Fit #{i+1}\n" + msg + "\n") f.close() Maybe you can include an option "to_text" (which is false by default), to actually add this functionality. Best Christian

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