September 2020 - Chimera-users - RBVI Mailing Lists

(no subject)
by Reeki Emrizal 02 Sep '20

02 Sep '20

Dear Chimera team, I'm attempting to dock small molecule ligand on a RNA molecule using chimera autodock vina. However, the docking process ended prematurely after the receptor.pdb (the RNA molecule) file is made. Please find attached a screenshot of the reply log. I'm suspecting the error comes from the receptor.pdb file made by chimera. Please find attached the screenshots of receptor.pdb files for a RNA molecule and a protein molecule. The receptor.pdb for protein has the column for residue names parsed correctly (e.g. "THR") but not for the receptor.pdb for RNA (e.g. "G" which I believed should be " G"). My questions are: (1) Is chimera allows docking of small molecule ligand on RNA molecule and (2) Is the a parameter that I've overlooked to allow this? Kind Regards

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Why is molmap changing the grid spacing and origin of simulated map
by Ouadou, Anes (MU-Student) 01 Sep '20

01 Sep '20

Hello, I am using molmap to simulate cryo-em density maps from protein pdb file. I follow the two steps outlined in Chimera tutorial (http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html#onGrid). I first create an empty map with specific size, grid spacing, and origin. vop new #1 size 116,96,152 gridspacing 1 origin -99.0,-39.0,-58.0 Then simulate the pdb file on the empty map using the option the grid spacing molmap #0 3 onGrid #1 the resulting simulated map has grid spacing changed from 1A to 2A and the origin coordinates are also changed to half the values I provided. This does not happen with all cases. The following commands work perfectly and generate a simulated map with grid spacing of 1A vop new #1 size 78,88,121 gridspacing 1 origin -32.73,-28.64,-63.42 molmap #0 3 onGrid #1 I can re-sample the map to obtain 1A grid spacing, but it adds extra work (I doing this to 100s of examples) and seems to affect the resolution of the simulated map. Could you please adive me to why is this phenomenon is happening and how to solve it. best regards Anes Ouadou CS PhD Student University of Missouri-Columbia aomqc(a)mail.missouri.edu Mobile: (573 )-289-9073

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on mrc map splitting without losing resolution
by Smith Lee 01 Sep '20

01 Sep '20

Dear All, Suppose my protein complex pdb contains A,B,C and D subunits, and its mrc map is available. With Chimera, can we and how to get the mrc map for this protein complex with the part for subunit D cut out, without losing the resolution of the protein complex with subunit A, B and C? Smith

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Chimera, Modeller, and socket modules
by Casey Becker 31 Aug '20

31 Aug '20

Hello, I'm attempting to do some loop refinements using Modeller in Chimera while making use of Modeller's parallel job feature to use multiple CPUs. When I run the scripts directly through python's IDLE interface, it works. However, when I attempt to run a custom script including parallel jobs directly through the Chimera interface, I receive an error stating that I'm missing a socket module. I've contacted the Modeller help email and they referred me to you after suggesting I replace the mod9.24.exe with python.exe in the "Modeller executable," but that didn't work. In fact, it froze my Chimera. I've attached copies of my scripts and the error I get. Any assistance appreciated. Thank you.

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Chimera-users September 2020