April 2016 - Chimera-dev - RBVI Mailing Lists

Labeling and coloring chains
by Deniz Simsek Buck 27 Apr '16

27 Apr '16

Hi, I am very new to Chimera. If you have time, I would really appreciate your answers. I am working with a structure that contains 80 chains. 1. I would like to color 40 chains at once the same color, rather than manually doing it one by one. How do I do this? 2. Also, I would like to add labels to the individual chains I choose on the structure. How do I do this? Thank you, Deniz

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suggestions for better STL export - remove internal, reduce atom vertices
by Jakob Suckale 15 Apr '16

15 Apr '16

Dear Chimera developers, Chimera has the great feature of STL export, very useful for 3D printing models for research and teaching. May I make two suggestion to improve this feature even further. 1 - Remove invisible internal and therefore unnecessary structures. Chimera generates a lot of internal structures that complicate printing and are pointless for STLs. This includes inside surfaces at the end of ribbon cartoons (red below). [image: Inline images 1] as well as copious amounts of invisible internal surfaces for wire and ball and stick models. [image: Inline images 2] If these were automatically removed, STLs would not only be much smaller but also much easier to print without remashing. 2 - Reduce the number of vertices for atom models. Ribbon conversion to vertices is already good, but as can bee seen above atom models are converted using far too many vertices inflating the resulting STL files. I'm aware that this has been discussed and listed previously as a bug but the problem remains and makes for difficult to use STLs and bad 3D prints. Best regards, Jakob Suckale, PhD Lecturer in Biochemistry University of Tübingen +49-7071-29-73363

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surface calculation failed, mscalc returned code -11
by Sunny Sharma 07 Apr '16

07 Apr '16

Hi, I have been trying to generate a surface model of a relatively larger molecule yet a single chain and have been getting the error (surface calculation failed, mscalc returned code -11). I have tried several options like splitting but have failed to get rid of this error and generate the surface model. Looking forward to your help Best Regards Sunny -- Sunny Sharma, PhD RNA Molecular Biology FRS/F.N.R.S. Université Libre de Bruxelles Rue Profs Jeener & Brachet, 12 B-6041 Gosselies, Belgium. Mobile: +32 484656127

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a more logical command for atom view
by Jakob Suckale 04 Apr '16

04 Apr '16

Dear Chimera dev't team, As a new user to Chimera, I always found the command to show atoms counterintuitive and I would like to suggest to add a synonym that is logically consistent with the other options to show a molecule. How about "atom achain"? If you asked any new user to complete the following series, the answer would not be "display" - surface achain, ribbon achain, ? achain. This is probably not something that veterans of Chimera still notice but it's illogical to new users and could be easily remedied with a synonym in addition to "disp". This wouldn't affect any old users while being consistent and logical. All the best, Jakob Jakob Suckale, PhD Lecturer in Biochemistry University of Tübingen +49-7071-29-73363

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