- Chimera-users - RBVI Mailing Lists

chimerax mesh commands doesn't work
by Yehuda Halfon 20 Sep '18

20 Sep '18

Hi all, I wanted to use chimeraX to use some commands on mesh display. Some works like meshLightning but others like lineThickness doesn't I use volume #1 lineThickness 10 (or any other integer) but nothing seems to change. What am I doing wrong? Yehuda Halfon

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change the center of a pdb model
by C.J. 19 Sep '18

19 Sep '18

Dear specialists, When I opened two pdb files of icosahedral model(two structures of the same virus), I found both center didn't overlap. My question is how to change the origin of a pdb model to overlap both. Thank you! -- Best regards! Jianhao Cao

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How to show ligand pocket as wireframe mesh
by leifepeterson＠sbcglobal.net 19 Sep '18

19 Sep '18

I ran a ligand-receptor prediction for a protein at Site-hound, and downloaded all the files. Is there a Chimera tutorial which shows how to display the volume a selected cluster inside the protein as a wireframe mesh? My guess is that the volume will be between all the AA residues in the given cluster(?) Once I can show the mesh, I will then go through the Autodock Vina run using ligands in a mol2 file, to sort their energies.

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FW: Question for using Chimera 1.8
by Williams, Joanne 17 Sep '18

17 Sep '18

From: Shabnam Nadjafi <shabnam.nadjafi(a)gmail.com> Date: Monday, September 17, 2018 at 12:29 AM To: "chimera(a)cgl.ucsf.edu" <chimera(a)cgl.ucsf.edu> Subject: Question for using Chimera 1.8 Dear Manager I am a pharmacologist and I decide to publish a book about drugs and some biochemicals by in silico evaluation of the chemical structures with biologic targets. I have to use the impressive software "Chimera 1.8". Would you please give me some information about this? Is it enough to cite "Chimera 1.8" in "Foreword" or "Preface" sections of the book? Is it free to use "Chimera 1.8" for publishing a book? Sincerely Yours Shabnam Nadjafi M.D. PhD of Pharmacology Neuroscience Research Center, Iran University of Medical Sciences, Tehran, Iran

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Add to discussion group
by Ayala Carl 17 Sep '18

17 Sep '18

To whom this may concern, I am a chimera user and have been having some difficulty opening structural measurement file. I would like to join the discussion group to post a question regarding this topic. Thanks, Ayala

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Atom specifiers for selected atoms
by BuddySphinx 16 Sep '18

16 Sep '18

Dear Chimera users, I have a simple question, if I have selected some atoms from my coordinates using mouse and draw a square. How do I know which atoms I have selected? Is there any way to show the atom specifier? Best, Yangqi Sent from Mail for Windows 10

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Calculating surface area
by Yangqi Gu 14 Sep '18

14 Sep '18

Dear Chimera users, I am trying to visualize the interface surface of my two monomers. Is there anyway to show the interacting surface from Chimera by using the EM map? Or should I do it from PDB coordinates? Best, Yangqi -- Yangqi Gu Graduate Student Malvankar Lab Yale University, West Campus

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Morph colors
by Rajan Prabu 14 Sep '18

14 Sep '18

Hello again, Following another old thread, http://plato.cgl.ucsf.edu/pipermail/chimera-users/2016-September/012743.html I could morph/play the coordinates and Volume at the same time. The script is given below. ---------------------------------------------------- # Open maps and set threshold open 1.mrc open 2.mrc open start_full.pdb open end_full.pdb vol #0,1 level .025 # Create a marker for coloring measure center #2 mark true radius 20 color red ~display #4 # Create morph volume vop morph #0,1 frames 0 model #5 # Create morph models model #6 morph start #2 frames 200 morph interpolate #3 frames 200 morph movie # marker on morph measure center #6 mark true radius 20 color red # Color near marker scolor #5 zone #6 range 50 coordset #6 1,100; vop morph #0,1 start 0 playstep 0.01 frames 100 model #6 ---------------------------------------------------- Still the color is at centre of of the first Frame of morph. If I understand correct I have to measure the centre for each Frame and add marker and color it. But I still can't make it. Any help/directions in this regard would be very helpful. Thanks in advance for your time and help. best regards Rajan

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Open Structural Measurement table
by Ayala Carl 13 Sep '18

13 Sep '18

Hi, I have been having difficulty opening a previously saved table of measured distances. I cannot open in as any file type listed by chimera and unfortunately I did not save the session that I measured the distances. If I open my models is there a way to impose the distances saved to the opened models? Thanks in advance

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Morph colors
by Rajan Prabu 13 Sep '18

13 Sep '18

Hello all, First please accept my apologies for to open a topic which is discussed already, but I couldn't get it working. I would like to morph a volume and colour its subregions. I made the following script ( adopting old messages in this forum ) open 1.mrc open 2.mrc open start_full.pdb open end_full.pdb vol #0,1 level .025 # Create a marker for coloring measure center #2 mark true radius 20 color red ~display #4 # Create morph vop morph #0,1 frames 0 model #5 # Color near marker scolor #5 zone #4 range 50 #Play morph vop morph #0,1 model #5 frames 200 interpolateColors false In the above script everything works, but color stays at place. Unfortunately for my morphing the marker has to move along with the morph. But I dont know how to do that. Any help in this regard would be very helpful. best regards Rajan

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