May 2016 - Chimera-users - RBVI Mailing Lists

Alter both clipping planes at same time?
by Oliver Clarke 05 May '16

05 May '16

Hi, is there any way to alter both global clipping planes at the same time? This is handy to move the current viewable section, without altering its thickness. At the moment I use an alias for this: # move both clip planes hither or yon. # Usage: zslab x # Move hither and yon clip planes towards (positive) or away (negative) alias ^zslab clip hither $1; clip yon $1 This works fine, except when the clip planes are close together - in that case, I get an error stating that I'm trying to move the near clip plane behind the far clip plane. It would be nice to have an option to move both planes at once - e.g. maybe changing the syntax of clip so either hither, yon, or both can be specified in the same command would be possible? Cheers, Oliver.

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ImportError: No module named Chimera
by Eiros Zamora, Juan 04 May '16

04 May '16

Hi, I’m running a per-frame script to display the time in a MD movie. I used to run it without problems until I downloaded the new Mac OS X 64-bit 1.11 version. (I erased the old app, also tried to re-download the old version with no success). More specifically, I load the MD movie, and in the command line I write: 2dlabels create timer text "0 ns" color white ypos .9 xpos .9 size 50 then I open a per-frame script with the following commands: from Chimera import runCommand runCommand("2dlabels change timer text '%.1f ns'" % (mdInfo['frame']*0.02)) and get the error: Problem in per-frame script: ImportError: No module named Chimera I’ve googled it and found this reply: [Chimera-users] How to install chimera as a python module http://www.cgl.ucsf.edu/pipermail/chimera-users/2014-July/010120.html I’ve tried setting the $CHIMERA_PATH environment variable to /Applications/Chimera.app/Contents/Resources/share but I still run into the same problem. Now, I don’t want to run the script directly from the command line, as it’s a per-frame script I have to run after I load the MD movie and create the 2dlabel object. Anything obvious I’m missing here? Cheers Juan

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how to move the model and save as mrc
by rongjian li 04 May '16

04 May '16

Hi, I am trying to move the model/protein in some MRC file and save it as a new MRC file. I know how to do it in Windows by clicking the mouse, but I have lots of such operations expected. So I am wondering how could I realize this in Linux such that it can be done automatically. Thank you very much. Best, Rongjian

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Multiple Docking Using Chimera
by SOBAHY, TURKI MOHAMMED 02 May '16

02 May '16

Hello, I have a protein of interest that I need to perform molecular docking on by multiple ligands (~1000,000). The protein is in PDB file format, while ligands are in a SDF file format. Initially, the ligands were divided into multiple SDF files (mini) for hardware sake. Then, a python script was developed to handle the docking of each mini SDF file against the protein of interest. This works nicely, however docking scores (tables) have no ligands IDs associated to distinguish each score. So, basically I have scoring tables without any key IDs!! Kindly, I want to know if you have encountered the same problem and what approach you took to solve this. Thanks,? ______________________________ Turki Sobahy Research Associate Research Center (J-04) King Faisal Specialist Hospital & Research Center (Gen.Org.)-Jeddah Branch PO Box 40047, Jeddah 21499, Saudi Arabia Tel# +966 667 7777 ext. 66736| MCD# 40716 Mobile# +966 505837027 email tsobahy(a)kfshrc.edu.sa<mailto:ESan-Diego@kfshrc.edu.sa>

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Solicitud Información
by luz Martinez 02 May '16

02 May '16

Cordial Saludo Soy estudiante de licenciatura en Química de la UNIVERSIDAD PEDAGOGICA NACIONAL. Colombia, Cordialmente solicito información acerca del modelo matemático general que el programa UCSF Chimera utiliza, lo anterior con el fin llevar a cabo una investigación en el espacio académico de Química Computacional que curso. Agradezco la atención y pronta respuesta Luz Angela Martinez M. Estudiante Decimo semestre

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Thank you and a suggestion
by Mohamed Elrobh 01 May '16

01 May '16

Dear UCSF Chimera, Just wish to say big thank you for your program. If you kindly allowed me to ask if there is a possibility to make a live webinar tutorial on Mohamed Elrobh, Ph.D., Assistant Professor, Room 2A 66 B5, Department of Biochemistry, College of Science, King Saud University, PO Box 2455, Riyadh 11451, Saudi Arabia Phone +966 114675944, Fax +966 114675791, Mobile +966 502072937 Email melrobh(a)ksu.edu.sa<mailto:melrobh@ksu.edu.sa> Site http://fac.ksu.edu.sa/melrobh<http://faculty.ksu.edu.sa/elrobh> ________________________________ Disclaimer: This communication is intended for the above named person and is confidential and / or legally privileged. Any opinion(s) expressed in this communication are not necessarily those of KSU (King Saud University). If it has come to you in error you must take no action based upon it, nor must you print it, copy it, forward it, or show it to anyone. Please delete and destroy the e-mail and any attachments and inform the sender immediately. Thank you. KSU is not responsible for the political, religious, racial or partisan opinion in any correspondence conducted by its domain users. Therefore, any such opinion expressed, whether explicitly or implicitly, in any said correspondence is not to be interpreted as that of KSU. KSU may monitor all incoming and outgoing e-mails in line with KSU business practice. Although KSU has taken steps to ensure that e-mails and attachments are free from any virus, we advise that, in keeping with best business practice, the recipient must ensure they are actually virus free.

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Chimera-users May 2016