August 2022 - ChimeraX-users - RBVI Mailing Lists

Sorting the required molecules in cvc file
by Dmitry Semchonok 02 Aug '22

02 Aug '22

Dear colleagues, I would like to find out about the possibilities. I have a model that contains apart from the other data, the pigment molecules – chlorophylls, carotenoids etc. Is there a way sort certain types of molecules in a *.cvc file by chimeraX so that the following information will be shown? Mol,Label,Element,X,Y,Z CHL,n 606,NC,267.342,151.989,253.363 CHL,n 606,MG,266.202,151.941,255.073 CHL,n 607,NB,275.512,153.952,252.428 CLA,n 610,MG,273.005,139.807,270.918 CLA,n 611,NB,288.916,127.885,266.725 Thank you! Kind regards, Dmitry

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Superposing protein structures
by Alicia Gardiol 02 Aug '22

02 Aug '22

We have experimental protein structures in PDB, and Alpha Fold predicted structures. Which is the best software to superpose these structures using a MAC computer. - Two different predicted proteins (predicted 1 to predicted 2) and - Same protein predicted and experimental (predicted 1 to experimental 1) Thank you and best wishes. Alicia Gardiol, PhD

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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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