- Chimera-users - RBVI Mailing Lists

fetching EDS files from the web (python script)
by Laleh 31 May '13

31 May '13

Hello. I'm wondering how I can fetch a bunch of EDS files (from the EDS server) and save them in my local machine in .mrc format. I don't want to do this manually one by one from the user interface... I tried to use open_volume_file with different settings; but it is not working... I'm surprised because this is very starightforward with pdb files. I appreciate your help. Thanks in Advance, Laleh

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castP, Chimera and atom numbers
by Boaz Shaanan 29 May '13

29 May '13

Hi, Apparently Chimera insists on consecutive serial atom numbers (the first column after ATOM in the pdb file) when it reads in castp files. If that's not the case (as most often happens when hydrogens are attached during the refinement run but are not written out to the final pdb) Chimera complains about incompatibility between the mouth file and coordinates and refuses to read in the castp files. This is my first encounter with a program that cares about the atom number column but I learnt it the hard way. Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan(a)bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710

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Tube representation picture of the eigenvector
by Prasanna Venkatesh 29 May '13

29 May '13

Dear Chimera users and supporters, I would like to generate a tube representation picture similar to one in the article (Figure 5 in "MD Simulations of Papillomavirus DNA-E2 Protein Complexes Hints at a Protein Structural Code for DNA Deformation"). Through Gromacs, I have average.pdb and extreme.pdb of my protein for the MD simulations. Please help me by providing the steps to make the picture. I asked the question earlier but not getting the similar picture with the answer provided. I don't know I asked it right the last time. Thank you in advance. Regards, Prasanna.

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How to deselect a subset of atoms in a non-standard residue
by felipe vasquez 28 May '13

28 May '13

Hi, I am trying to select all hydrogens atoms in a protein structure to achieve an energy minimization process. However, I would like to discard of the selection the hydrogen atoms of a non-standard residue (in my case a cofactor, NADPH). How can I deselect only this subset of hydrogen atoms of the whole hydrogens selection? Best regards, *Andrés Felipe Vásquez J., MSc.* Grupo de Fisiología Molecular Instituto Nacional de Salud Avenida calle 26 No. 51-20 - Zona 6 CAN Bogotá, D.C., Colombia

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How to delete range of solvent molecules
by felipe vasquez 22 May '13

22 May '13

Hi, I am trying to prepare a protein structure for docking, and I want to keep just one or a couple of water molecules. How can I do achieve this goal, deleting the rest of solvent molecules? Thanks in advance. Best regards, * * * * *Andrés Felipe Vásquez J., MSc.* Grupo de Fisiología Molecular Instituto Nacional de Salud Avenida calle 26 No. 51-20 - Zona 6 CAN Bogotá, D.C., Colombia

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Distance measuring
by T-I 22 May '13

22 May '13

Dear Chimera, I want to know something very simple which is making my life very difficult at the moment. I have an EM map of a virus capsid and I would like to make various distance measurements. I simply want to draw a strait line and measure it or place two points on the map and measure the distance between them. I have read all your help files on this matter and I cannot make any sense out of the instructions Can you help me out ? Thankyou Mr A.I

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Fitmap in batch mode
by ingvar 22 May '13

22 May '13

Hello, I am trying to run fitmap on a set of volumes on a server without a display. I would like to collect the results of the top hits to store in a database – correlation coefficients, inclusion scores, and the transforms. The only way I found to collect the fitting results is to save the session after displaying the listFits dialog. The listFits dialog cannot be displayed when running Chimera in –nogui mode, otherwise this would have been a solution. I tried to use a virtual display, with Xvfb. I have used Xvfb with some java applications in the past. When I use Xvfb with Chimera, it appears that Chimera do not want to start up properly, the process just hangs, i.e. no cpu usage. Is there a way around this, or am I asking for an enhancement, e.g. a “writeListFile toFile” option. I am on RHEL 6.2/6.3 if that matter. Noticed that there is a local correlation option in the pipeline for Chimera 1.8, looking forward to try it out. Kind Regards, Ingvar Typical python script: from chimera import runCommand as rc rc("open emd_5500.map") rc("volume #0 level 1.34 transparency 0.5") rc("open emd_2017.map") rc("volume #1 level 0.58 transparency 0.5") rc("fitmap #1 #0 search 200 metric overlap envelope true inside 0.2 listFits false") #rc("fitmap #1 #0 search 200 metric overlap envelope true inside 0.2") rc("save session5500_2017") rc("stop now") Setup to run with Xvfb (in bash): i=0 while [ -f /tmp/.X$i-lock ] do i=$[$i+1] done Xvfb :$i & pid=$! export DISPLAY=:$i chimera fit5500_2017.py kill $pid

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Pipes and planks representation
by Ernesto Arias Palomo 21 May '13

21 May '13

Dear chimera developers, I have noticed that in the last Chimera releases you have significantly improved the 'pipes and planks' representation. I find it particularly useful because, in my opinion, it makes the structures look simpler and clearer, especially when you are displaying large PDBs. I would like to suggest an improvement. It would be really useful if you could make that representation an attribute of the structure (like the 'ribbons' one) instead of a separate object. That way one could easily show, hide or color different regions of the structure without having to modify the actual PDB file. Thank you very much for your help, and congratulations for your great work. Cheers, Ernesto.

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Re: [Chimera-users] RMSD i.b and RMSD u.b
by Elaine Meng 20 May '13

20 May '13

Please send Chimera questions to chimera-users(a)cgl.ucsf.edu instead of just my address. The RMSD lb (lower bound) and RMSD ub (upper bound) of a docked ligand are calculated by AutoDock Vina and are described in the manual for that program: <http://vina.scripps.edu/manual.html> (go to that page and search for "RMSD") I believe they just indicate how similar each position is to the best-scoring position found. I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On May 20, 2013, at 6:10 AM, Muhammad ALi <muh.ali741(a)yahoo.com> wrote: > AOA > > sir > when I check my result with ViewDock their are two RMSD values i.e RMSD i.b and RMSD u.b plz tell me about them.....

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3D Printing our protein
by Bart Janssen 19 May '13

19 May '13

Hi My apologies for what are likely to be stupid questions. We are plant developmental biologists and we just obtained our first X-ray crystal structure for a new hormone receptor in plants. We'd really like to make a 3D model of the protein using one of the 3D printers at our institute. I've been trying to use and understand Chimera for the last week and I'm a bit out of my depth :). I can import our protein 4DNP.pdb and display it using solid surface or using the sphere representations of atoms. I can also display it with the "lid" domain hidden and vice versa. My problem has been getting files that our 3D printer can read. The solid surface model of the whole protein can be exported as a scene in .stl format and that can be printed just fine. Although I can't figure out how to adjust resolution or the smoothness of the exported file. But I'd really like to print the two domains of the protein separately. If I use Solid surface model with the lid hidden what I get is an eggshell like model which has no internal detail. If I use atoms shown as spheres instead I get the internal detail I want BUT when I try and export the scene I get a 2 Gb+ file that is unreadable by the printer. If I export .obj format instead the colleague who runs the printer says the file won't load and appears to have errors. I have a horrible feeling I am going about this entirely the wrong way but I can't find a tutorial that describes what I'm trying to achieve. I do realise chimera is not really written for the somewhat trivial use that I am attempting but it really would be helpful if we had a physical model of the protein to look at. Is there a tutorial I should follow or another part of Chimera (or another program) that I should be using instead? Any advice would be much appreciated. Cheers Bart Bart Janssen Scientist Plant Development team Breeding and genomics Plant and Food Research Private Bag 92169 Auckland 1142 New Zealand Ph +64 09 9257179 bart.janssen(a)plantandfood.co.nz The contents of this e-mail are confidential and may be subject to legal privilege. If you are not the intended recipient you must not use, disseminate, distribute or reproduce all or any part of this e-mail or attachments. If you have received this e-mail in error, please notify the sender and delete all material pertaining to this e-mail. Any opinion or views expressed in this e-mail are those of the individual sender and may not represent those of The New Zealand Institute for Plant and Food Research Limited.

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