- Chimera-users - RBVI Mailing Lists

command line: how to add hydrogens to a phosphate group?
by Sara Luz Gomez Maya 15 Jun '21

15 Jun '21

Hi, I have a system consisting of a molecule intercalated into DNA. For a very specific application, I need to remove all the Sodium atoms from a PDB file and, in turn, add hydrogens to all the DNA phosphate groups (whatever the oxygen). Since for chimera that atom type is identified as O3- (possibly resonance-equivalent terminal oxygen on tetrahedral center (phosphate, sulfate, N-oxide), I have tried: labelopt info idatmType label #0 addh spec O3- but it did not work. You can find attached herewith the pdb file. Any help is appreciated. Regards, Sara

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Sending Chimera MD job to remote computer
by Cowie, Connor 14 Jun '21

14 Jun '21

Hello, I am using Terminal to try to run Chimera MD simulations on a remote server/computer. I have been able to successfully connect using the command ssh username@detroit05 (and then entering the password). However, I want to be able to send a command to a remote computer to improve the computational time especially when running multiple MD simulations; right now, I am running MD simulations on the same computer. I was first thinking of a sequence of commands below: Ctrl+Z bg ssh -y username@detroit05 I know that the Ctrl+Z command temporarily pauses a command, but I believe that the jobs command is first needed to list the current running jobs (that Ctrl+Z can be performed on). However, the running jobs are not listed when I type “jobs”. After using the “top” command to list all of the processes, I have verified that the Kill command works by typing these in succession: Kill -STOP PID# Kill -CONT PID# Can you walk me through how to first have a listing of jobs running in Chimera and then sending it to a remote computer? Best, Connor

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getting surface patches
by Diego Amaya 13 Jun '21

13 Jun '21

Hello all, I'm trying to get surface patches of PDB structures in VTK format. So I want to define a patch as the set of atoms within a given radius of a specific residue, build the surface corresponding to that patch and export the result in VTK format. Additionally, I want to do all this with a python script. Here the code I'm trying but doesn't work : *import pychimerapychimera.patch_environ()pychimera.enable_chimera()import osimport chimerafrom chimera import runCommand as rc* *list_resid = [31, 64]* *radius = 3list_pdbs = ['ensayo.pdb']for resid in list_resid: for line in list_pdbs: list_atoms = [] rc('open '+line) rc('sel :{} za<{}'.format(resid, radius)) for a in chimera.selection.currentAtoms(): list_atoms.append('serialNumber=' + str(a.serialNumber)) sel_atoms = ' or '.join(list_atoms) rc('surfcat patch @*/{}'.format(sel_atoms)) rc('surface patch') rc("export format VTK {}_resid_{}_radius_{}.vtk".format(line[:-4], resid, radius)) rc("close all")* Thanks in advance for your help. -- Diego A. Amaya Ramírez -- *Aviso legal:* El contenido de este mensaje y los archivos adjuntos son confidenciales y de uso exclusivo de la Universidad Nacional de Colombia. Se encuentran dirigidos sólo para el uso del destinatario al cual van enviados. La reproducción, lectura y/o copia se encuentran prohibidas a cualquier persona diferente a este y puede ser ilegal. Si usted lo ha recibido por error, infórmenos y elimínelo de su correo. Los Datos Personales serán tratados conforme a la Ley 1581 de 2012 y a nuestra Política de Datos Personales que podrá consultar en la página web www.unal.edu.co <http://www.unal.edu.co/>.* *Las opiniones, informaciones, conclusiones y cualquier otro tipo de dato contenido en este correo electrónico, no relacionados con la actividad de la Universidad Nacional de Colombia, se entenderá como personales y de ninguna manera son avaladas por la Universidad.

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Minimize hydrogens in water molecules
by Francesca Magarotto - francesca.magarotto2＠studio.unibo.it 11 Jun '21

11 Jun '21

Hi, I need to minimize two water molecules in the binding site of the protein: I don't want to move the oxygen, so I've selected only hydrogen atoms and then I' ve used the Minimize Structure tool (keeping fixed all atoms that are unselected). I can't do the minimization because there's an error: Chimera/MMTK cannot minimize structure, probably because there is no parameter for ''No parameters for bond Atom 0.CYS_394__0_0_1_397__A.N (atom type n) - Atom 0.GLY_393__0_0_1_396__A.peptide.C (atom type C)'' I don't known what this means and what I should do to fix it. I've tried to use the command line, but there's another error. Does anyone have suggestions? Thank you. Francesca

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search a sequence in UCSF chimera
by Xiao Lei 10 Jun '21

10 Jun '21

Dear chimera-users, Is there a way to search a short amino acid sequence (for example: DDDDK) in an openned protein structure in UCSF chimera? Thanks ahead, Xiao

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Removing specific water molecules
by Francesca Magarotto - francesca.magarotto2＠studio.unibo.it 10 Jun '21

10 Jun '21

Hi, I have a problem using Chimera: I need to delete specific water molecules with a specific residue number, but this number is in common with residues that are useful (such as ligands or co-factors). For example, I type "del :546-893" in the command line in order to delete these water molecules, but I delete also the ligand and FAD and I don't want to. I've read the guide about atom specification, but still I don't know how to do it. Hope someone can help me, thank you. Francesca

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Re: [Chimera-users] [ChimeraX] #4232: RFE: make ViewDockX understand SwissDock output
by Elaine Meng 07 Jun '21

07 Jun '21

Hi Michael, I edited out the details of your files below in case you wanted to keep that private, but am CC-ing the chimera users list recommended for asking questions. Since the Swissdock server only keeps the files for a while, I understand you had to save them locally and now you are trying to modify the Chimera web-data files to use the local files. However, I think you can simplify and no longer use a web-data file, but simply a Chimera command file (see below), since the python stuff was just retrieving the files. In that case you would just insert the local file pathnames into the commands that open them. Just name the plain text file containing the commands something.com and open it with Chimera. The command file (plain text) would contain something like this, of course substituting your actual file locations for "[pathname-...]": open [pathname-of-pdb-file] viewdock [pathname-of-docked-ligands-file] color byatom #0 ribbon #0 repr stick :LIG ~disp element.H hbonds intramodel false lineWidth 5 color green Other than the opening of files, you wouldn't necessarily have to use those same commands, you could customize as desired. Further, you could just type in the commands into the command line one by one instead of making a command file, if that's easier. Chimera command files: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/indexcommand.html#cmdfile> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Jun 7, 2021, at 9:04 AM, Michael Weber <weberm(a)posteo.de> wrote: > > Dear Elaine, > thank you for your quick response. > > I have a question: when now trying to use Chimera instead of ChimeraX to analyze my SwissDock output files I noted that the files may only be analyzed as long as the entire data set related to that docking experiment is still available online on the SwissDock website. Fortunately, I had downloaded the entire data sets and stored them locally. > SwissDock delivers some sort of script in which Chimera commands and the required input file locations are stored as follows: > > <?xml version="1.0"?> > <ChimeraPuppet type="std_webdata"> > <web_files> > <file name="target.pdb" format="text" loc="http://www.swissdock.ch/files/tmp/[...other stuff...]/target.pdb" /> > </web_files> > <commands> > <py_cmd> > import urllib > import tempfile > from chimera import runCommand > tmpDirectory = tempfile.mkdtemp() > urllib.urlretrieve ("http://www.swissdock.ch/files/tmp/[...other stuff...]/clusters.dock4.pdb", "%s/clusters.dock4.pdb"%tmpDirectory) > runCommand("viewdock %s/clusters.dock4.pdb \"Dock 4, 5 or 6\""%tmpDirectory) > </py_cmd> > <mid_cmd>color byatom #0</mid_cmd> > <mid_cmd>ribbon #0</mid_cmd> > <mid_cmd>repr stick :LIG</mid_cmd> > <mid_cmd>~disp element.H</mid_cmd> > <mid_cmd>hbonds intramodel false lineWidth 5 color green</mid_cmd> > </commands> > </ChimeraPuppet> > > I thought I might cure the situation by replacing the web locations by the local hard drive file locations, so I modified it as follows: > [... edited out...] > Of course it does not work properly because I don't know what exactly the syntax looks like for solving my problem when working with local files. > I hope it is not asked too much, but could you help me how to fix this? > > Best regards, > Michael.

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command line clustering (how to select a subSection?)
by Laura Morris 04 Jun '21

04 Jun '21

Recently I've been clustering in Chimera but running into memory limitations on my system. I'd like to do the clustering on a computer with more RAM, but I need to be able to do this using only the command line. I found an old post (http://plato.cgl.ucsf.edu/pipermail/chimera-users/2010-May/005166.html) that includes an example script to do the clustering, but I don't know how to change the subSection to the residues and atoms I want. Here's the portion of relevant code: def main(): import chimera modelList = chimera.openModels.list(modelTypes=[chimera.Molecule]) subSelection = None # Change this to CAs or heavy atoms clusterInfo = _cluster(modelList, subSelection) saveReps(clusterInfo, "reps.pdb") # Change file name if needed The "Change this to CAs or heavy atoms" is exactly what I want to do, but I have no idea how to do it. If this were command line in Chimera, I'd use something like "select #0:3-55@CA". I know there's a "runCommand" function that can be included (using "from chimera import runCommand"). Is this used in some way to set subSelection, and if so, how? Any help is appreciated. Regards, Laura ----- Laura C. Morris Scientific Computing Professional Edison & Prestegard Labs Complex Carbohydrate Research Center 706-542-6286 (lab 1075)

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command question
by Yanhe Zhao 01 Jun '21

01 Jun '21

Good afternoon Elaine and users, I have two questions as to Chimera using as below: 1, how can I plane through and rotate volume at same time? For example how to add rotate options to command "volume #2 planes x,0,42,1; wait 43;"? 2, How I can merge volumes (for example 3 volumes) with their own threshold was kept? Thanks and best, Yanhe

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saving segmented copy of a map
by M.S. Islam 01 Jun '21

01 Jun '21

Hi I was just wondering, is there any way that I can save segmented copy of a map so that I don't have to do segmentation, followed by colouring different segments of the segmented map again and again. Thanks a lot in advance. Saif

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