January 2019 - Chimera-users - RBVI Mailing Lists

babel-type not found
by Ryan Cairns 25 Jan '19

25 Jan '19

Hi, When using AutoDock vina, I keep getting the message 'AttributeError: member babel_type not found'. I have uninstalled and reinstalled to try and fix it with no luck. Any suggestions on how to fix this? Thanks, Ryan Ryan Cairns PhD student School of Chemistry University of Nottingham pcxrc5(a)nottingham.ac.uk O'Reilly Research Group http://www.oreillyresearchgroup.com/ This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please contact the sender and delete the email and attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. Email communications with the University of Nottingham may be monitored where permitted by law.

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Select multiple chains
by Racaniello, Vincent R. 25 Jan '19

25 Jan '19

In pdb 4CTF there are multiple identical chains, e.g. A0, A1, A2, A3, A4 etc. I can select one with select :.A0 How do I select multiple chains, e.g. A0-A4? ______________________________ Vincent Racaniello, Ph.D. | Higgins Professor Department of Microbiology & Immunology Columbia University, New York virology.ws | microbe.tv "Tanto sa ciascuno quanto opera"

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Chimera Issue: Surface Calculation Failed - MSCalc returned code 5
by Megan Yung 25 Jan '19

25 Jan '19

Hello, I'm having some trouble generating surface models of large antibodies for an urgent project. I keep getting the mscalc return code 5 error message. I read through the forums and it seems that using the split command is the way to go, but I would not like to split this antibody. I'm trying to get a full rendition of the surface model of the antibody so that it is possible to 3D print the antibody. Can you please let me know if that would be possible? The pdb files of the 4 antibodies are attached. Thank you very much, Meg

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Re: [Chimera-users] Update VDW Dots During Torsion Rotation
by Eric Pettersen 24 Jan '19

24 Jan '19

Glad it did what you needed! —Eric > On Jan 24, 2019, at 11:29 AM, Brian E Coggins <bec2(a)duke.edu> wrote: > > Eric, > > Hack or not, this does the job perfectly! Many thanks. > > Brian > > >> On Jan 23, 2019, at 6:36 PM, Eric Pettersen <pett(a)cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu>> wrote: >> >> Hi Brian, >> It seems the vdw command caches the computed surface points and that therefore various tricks with ~vdw/vdw don’t update the surface. However changing the dot density does clear the cache and cause a recomputation, so you can use this awful hack to get the vdw surface to update as you adjust torsions: >> >> perframe “vdwdens 5.1; vdwdens 5” >> >> Every frame, the density will be changed to 5.1 and then back to the (default) 5. You might want to use different numbers. I prefer not to be “credited” with this idea. :-) >> >> >> not Eric Pettersen >> not from the UCSF Computer Graphics Lab >> >> >>> On Jan 23, 2019, at 3:14 PM, Elaine Meng <meng(a)cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> wrote: >>> >>> Hi Brian, >>> This is not a direct answer to your question, but alternatives to showing VDW dots are: >>> >>> (A) show sphere representation (VDW spheres) instead of stick representation of atoms >>> >>> (B) show molecular surface, which will update as bonds are rotated. You could make it transparent and/or show it as mesh, e.g. commands: >>> >>> surftrans 75 >>> surftrans 0 >>> surfrep mesh >>> >>> There is also a “dot” style (as opposed to mesh and solid) but then you’d want to crank up the vertex density to put the dots closer together… e.g. select the surface with Ctrl-click and then use the Selection Inspector (open by clicking green magnifying glass icon), inspect: MSMS surface, increase “vertex density” and maybe dot size. >>> >>> Depending on the structure, however, molecular surface calculation may be slow and/or fail as you change the structure by rotating bonds. >>> >>> I hope this helps, >>> Elaine >>> ----- >>> Elaine C. Meng, Ph.D. >>> UCSF Chimera(X) team >>> Department of Pharmaceutical Chemistry >>> University of California, San Francisco >>> >>>> On Jan 23, 2019, at 1:29 PM, Brian E Coggins <bec2(a)duke.edu <mailto:bec2@duke.edu>> wrote: >>>> >>>> Hello, >>>> >>>> If I am displaying atomic dots using the “vdw” command, is there any way to get the dots to update as structural changes are made? For example, if I am adjusting torsions in the Adjust Torsion box, is there a way to get the dots to follow along as the structure changes? >>>> >>>> Thanks, >>>> Brian >>>> >>>> --- >>>> Brian E. Coggins, Ph.D. >>>> Assistant Research Professor of Biochemistry >>>> Duke University, Durham, NC >>> >>> >>> _______________________________________________ >>> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> >>> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <https://urldefense.proofpoint.com/v2/url?u=http-3A__plato.cgl.ucsf.edu_mail…> >>> >> > > --- > Brian E. Coggins, Ph.D. > Assistant Research Professor of Biochemistry > Duke University, Durham, NC > > > >

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Update VDW Dots During Torsion Rotation
by Brian E Coggins 23 Jan '19

23 Jan '19

Hello, If I am displaying atomic dots using the “vdw” command, is there any way to get the dots to update as structural changes are made? For example, if I am adjusting torsions in the Adjust Torsion box, is there a way to get the dots to follow along as the structure changes? Thanks, Brian --- Brian E. Coggins, Ph.D. Assistant Research Professor of Biochemistry Duke University, Durham, NC

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Visualize dot_surface dat file in chimera
by Ashok Nayak 23 Jan '19

23 Jan '19

Hi, I have a HOLE dot surface fie exported from coot in the .DAT format. Unfortunately I cant display it in chimera. Could you suggest me the compatible format in chimera to visualize the dot surface files Its in X Y Z r g b Hexcol format 234.17638 238.94343 268.17244 0.44800 0.47168 0.80000 #7278cc 234.33047 238.06957 268.17244 0.44800 0.47168 0.80000 #7278cc 234.63396 237.23575 268.17244 0.44800 0.47168 0.80000 #7278cc 235.29419 242.56321 267.72878 0.44800 0.47168 0.80000 #7278cc Any suggestion will be appreciated

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Serine 371 in a protein (ATR)
by leifepeterson＠sbcglobal.net 22 Jan '19

22 Jan '19

Hi Elaine, A particular protein binds with e.g. Serine-371 of another protein (ATR). In order to find that pocket in a PDBQT image of ATR, can I simply look for AA=371? Thanks, Leif Peterson

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how to get chimera to use the auth_seq_id in .cif format files
by Carmen San Martin 21 Jan '19

21 Jan '19

Hi all, I am using chimera to display a structure with a 10-residue gap. When I use a pdb format file, the gap appears as a dashed line and everything is fine. However, when I convert the coordinate file to cif format, chimera draws a very long bond across the gap. Further, the residue numbering seems to have changed, so that now instead of skipping the 10 figures in the gap, the residues at both sides are consecutively numbered, and therefore the numbering in the rest of the protein is wrong. I understand this happens because chimera is using the cif column "label_seq_id" instead of "auth_seq_id" to identify the residue number. Is there a way to make chimera use the auth_seq_id column instead? Sorry if this has already been answered, I googled it and saw similar questions but not the actual answer to this one. Best, ------------------------------------------------------------- Carmen San Martín, Ph. D. Centro Nacional de Biotecnología (CNB-CSIC) Darwin, 3 28049-Madrid (SPAIN) Email: carmen(a)cnb.csic.es Phone: 34-91-5855450 Fax: 34-91-5854506 <http://www.cnb.csic.es/> http://tinyurl.com/carmensanmartinlab https://sites.google.com/site/adenonet/ ------------------------------------------------------------

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I-TASSER secondary structure
by nadineh.1991＠web.de 21 Jan '19

21 Jan '19

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match command
by Hernando J Sosa 20 Jan '19

20 Jan '19

Dear Chimera, Can somebody clarify the syntax of the match command. I am specifically trying to move several atoms (residues or ligands) to match their location in another model *without* moving the rest of the model. e.g. match #0:ADP.A #1:ADP.A works fine but moves the whole model #0 But match #0:ADP.A #1:ADP.A atoms Or using any other option after the atom specifications generate the following error: "an even number of space-separated atom specs are required" According to the user-guide website the syntax is: match atom-spec1 atom-spec2 options Not sure what the problem is. Thanks H.

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Chimera-users January 2019