- Chimera-users - RBVI Mailing Lists

How to set the contour level correctly?
by Selenschik, Philipp 18 Oct '21

18 Oct '21

Hello, my apologies if this is a recurring (and potentially trivial) question that does not directly concern Chimeras functionalities. I am wondering how to properly set the value of the contour level to visualize a Coulomb potential map. When I use the approximation of 1 Da = 1.2 [cid:image003.png@01D7C06B.AA8F9850] ³ to adjust the displayed volume in the Volume viewer dialog almost no secondary structure, but a lot of dust is visible. The same problem occurs when I’d like to visualize, for example, an α-helix of a subunit rigid-body fitted to the density. I use the “zone” command to trim the density at a pre-defined 2 Å around the α-helix. But is there any general guideline on how to properly set the contour level? I often find values between 1 σ to 3 σ. I assume this is the standard deviation of the map. If so, can it be measured via the “Volume Mean, SD, RMS” command? Kind regards Phil

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Select coloured residues with Chimera
by Javier Sanchez Utges (PG Research) 13 Oct '21

13 Oct '21

Hello, my name is Javier and I am a Bioinformatics PhD student in Dundee. I am using UCSF Chimera v1.14 and I am trying to select residues according to the colour they are coloured in, using the following command for blue-coloured residues for example: "sel @/color=blue". This works just fine, however, I struggle when using other colours such as "medium blue" or "dark green". "sel @/color=darkgreen" does not work. It looks like all colours with a single word name work fine, but 2-word name colours do not. Moreover, I can colour residues using RGB codes, such as "col #da70d6 sel" to colour selected residues in orchid. Nevertheless, "sel @/color=#da70d6" does not work. "sel @/color=orchid" works, though. So, is there a way that I can use two-word named colours when selecting by colours, and also, use RGB codes or other colouring codes to select coloured residues? Many thanks, Javier The University of Dundee is a registered Scottish Charity, No: SC015096

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Questions on moving lables automatically
by 夏前程 12 Oct '21

12 Oct '21

Hi, I've noticed that Chimera can help us to label a lot of things, including atomic partial charge, on chemical systems like a compound. Those atomic labels were set just a distance from atoms' positions. However, I want to set these labels exactly on those atoms. I've known that such operations can be realized through moving them with mouse manually and one by one. Thus, I'm wondering if there is an alternative approach in Chimera that can allow me to set those labels directly on their corresponding atoms automatically. I think this function should exist here. But I've searched for hours and find almost nothing related. With Regards, Qiancheng Xia 2021/10/12

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addh command not working
by Prathvi Singh 12 Oct '21

12 Oct '21

Hi, I have a PDB file which I have trimmed such that it contains only two residues, say residue-10 and residue-25 (I have given the numbers to denote that the residues are far apart from each other in the primary structure of the protein) and saved as a new PDB file. In order to prevent formation of any pseudobonds between the two residues, I manually added a TER row in the PDB file, just after the entry of the last atom of residue-10. Now, when I delete all the atoms of residue-10 except the atoms of its carbonyl group i.e., its backbone C-atom and covalently linked backbone O-atom and run the "addh" command, chimera adds H-atoms to the relevant atoms of residue-25 but doesn't adds H-atoms to the C-atom of residue-10 due to which its valency remains incomplete. Can you please tell me why it is happening? Is there any way to overcome this problem? -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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Is there any way to export chimera settings
by Prathvi Singh 08 Oct '21

08 Oct '21

Is there any way to export chimera settings to a file & then import those settings to chimera program installed on a different PC? -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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superimpose models from inside a python script and access the transformation matrix
by Engeholm, Maik 06 Oct '21

06 Oct '21

Hi there, I'm trying to superimpose two models from inside a python script and get back the transformation matrix. I know I can do something like chimera.runCommand("match #1 #0 showMatrix true") but then the matrix is written to the ReplyLog. (Of course I could save the ReplyLog and then read it in from my script to access the matrix, but that seems quite cumbersome.) Is there a better way to do this? Cheers, Maik

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Blast PDB in Chimera version 1.15
by Feixia Chu 06 Oct '21

06 Oct '21

Hi there, I am teaching a Protein and Function course this semester, and show students how to use Chimera, and integrated Modeller to carry out homology modeling. I use the older version Chimera 1.11.2 and they downloaded current version Chimera 1.15. For some reason, when they use "info" tool and select "blast proteins" in FASTA file window, the Blast query window show blank and never progressed. I don't have any the problem with the older version Chimera installed in my old laptop. Can you advise how to process from here? Thank you! Feixia _________________ Feixia Chu, Ph.D. Associate Professor Molecular, Cellular & Biomedical Sciences University of New Hampshire 46 College Road Durham, NH 03824

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Atomistic Simulation Center - Invitation to virtual inauguration symposium
by Harald Lanig 04 Oct '21

04 Oct '21

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Error to run chimera remotely on a GPU computer from Mac computer
by Zongli Li 30 Sep '21

30 Sep '21

Dear listers, I ssh with "-Y" from my Mac desktop to a GPU computer and process my data there. Quite often I need to look at the 3D volumes with chimera. This had been working nicely for long time. But all suddenly it stopped working and game the error 3: X Error of failed request: GLXBadCurrentWindow Major opcode of failed request: 149 (GLX) Minor opcode of failed request: 5 (X_GLXMakeCurrent) Serial number of failed request: 1400 Current serial number in output stream: 1400 Did anyone encounter the same error? Any suggestions or tips to overcome this problem would be appreciated. Thanks, Zongli

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Surface exposed residue in a protein assembly
by Alessandro Strofaldi 30 Sep '21

30 Sep '21

Dear Chimera developers, I’m working on a protein complex and I’d like to analyse the SASA and hydrophobicity on the surface. I have worked with Chimera before so I know how to do those basic tasks for a monomeric protein; however, since I have five monomers interacting together I was wondering how to calculate the SASA (and later showing the hydrophobic residues of the surface) excluding the monomer-monomer interfacial regions. I would also need those values tabulated to show hydrophobicity vs primary sequence but still excluding the monomer-monomer interfaces! It seems like there is no basic tool to do that (or am I missing something?); is there any procedure I could apply? Unfortunately I can’t code in Python so I’m looking for a solution that involves using the GUI. Thank you, Best regards, Alessandro Strofaldi, PhD University of Bristol

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