April 2021 - Chimera-users - RBVI Mailing Lists

Need help- Why there is network connection
by Siddhartha Pradhan (Contractor) 13 Apr '21

13 Apr '21

Hi, Before we install any software in our system within Gilead organization, we do the software security assessment. During our assessment for " UCSF Chimera v1.15", we found below external network connection is being made. 1. Connection to 169.230.27.29 on tcp/80 (www.cgl.ucsf.edu) * Why the network connection is being made and what is the reason behind it? * Is there any sorts of data transfer is being happened from the user system? * Is there any settings in the application to disable the network connections? * If users can use the software to export/import data. Is there any cloud service associated with this? It would be of great help if you can kindly give a clarity for the above network connection ASAP. Regards, Siddhartha

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combine models
by Francesco Pietra 11 Apr '21

11 Apr '21

Hi (1) I am faced by the coordinates for a nucleics/protein assembly being given in several bundle.pdb, while I need a sequential, continuous pdb file that comprises all nucleotides and proteins, not made of models (2) If I load all the bundles to chimera, I see all expected ligands around the small molecule. (3) With all models selected, copy/combine (adopting default first model as reference and allowing renaming chains) generates a new model. The new model laks some proteins that should lie near the ligand, as described at (2). I feel that I am missing something. Thanks for advice francesco pietra

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greeting and acknowledgement
by kajihara 09 Apr '21

09 Apr '21

Dear Prof. Ferrin, Dear stuff of Chimera, I am prof Yasuhiro Kajihara, Department of chemistry, Osaka University. Last April, Corona pandemic suddenly attack us, and our university closed in-person style classes. I needed to do online class of biochemistry. I recommended students to download UCSF Chimera for understanding protein structure and behavior. The Chimera soft wear was great help for us under the terrible Corona Pandemic and all students enjoy to deal with Chimera. They got unbelievable knowledge through the Chimera. I could not find a suitable word to express my thank. I thank you again for your great support and kindness to deliver it as free. Within a week 80 students will start download chimera. So, I need to send greeting e-mail to give my thanks. Sincerely Yasuhiro Kajihara, Ph. D. Department of Chemistry Osaka University Machikaneyama, 1-1, Toyonaka, 560-0043 Japan kajihara(a)chem.sci.osaka-u.ac.jp

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Where does Chimera copy command save images?
by Martti Tolvanen 09 Apr '21

09 Apr '21

I have tried to use the command copy on command line to save images, with a goal to do that in a script. The messages of rendering a high-res image and image saved come up, but the file is nowhere to be found. My guess is that the default save location is in the Chimera program folder, which would not be permitted, but Chimera just doesn't see it as a failed attempt. I do have a workaround of including the full path in a filename, but I'm just curious where the file would be going by default, and whether there is some command to change the working folder by a command. FYI it's Chimera 1.15 in Windows 10. Martti Tolvanen University Lecturer in Bioinformatics U of Turku, Finland

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Query about adding charge to ligand
by Nirban Dey 19MSM0098 08 Apr '21

08 Apr '21

Hello, I am a Masters student of VIT University India. I am using chimera to prepare my ligand. In the add charge option I noticed that if my ligand has negative or positive charge and I try to add AM1-BCC it gives error but I can add Gasteiger charge. Even if I set charge to +0 for the ligands that have charge like -1 or +1 and try to add AM1-BCC it gives error. I want to know what is the reason that Gasteiger charge can be added but AM1-BCC cannot be added..Kindly help me in this regard. Thanking You Nirban

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Re: [Chimera-users] Chimera-users Where does Chimera copy command save images?
by Susan 08 Apr '21

08 Apr '21

Hi there honey! I'm a 30 years old lonely housewife looking for an affair. I'm ready to try anything You can see my photos, you can see them right here <http://gallery.prince-ss.com?n=frfya&s=687474703a2f2f646174696e6773722e636f…> On Thu, Apr 8, 2021, at 5:41 PM, Chimera wrote: >Hi Martti, >I don't know the answer, but another thing you can do is use the Chimera cd command to change the working directory so that later in the same session, you no longer have to specify it in the filenames of files to open or save. (Alas, there is no Chimera pwd command to tell you what it thinks is the current working directory, however.) > > >I hope this helps, >Elaine >----- >Elaine C. Meng, Ph.D. >UCSF Chimera(X) team >Depa >

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rna model
by Divita Mathur, Contractor Code 6910, FN 06 Apr '21

06 Apr '21

Hello Chimera community I am trying to run the “rna model sequence #0” code but it is returning the following error: IndexError: list index out of range File “…path/RNALayout/rna_layout.py”, line 393, in place_residues rprev = rlist[0] See reply log for Python traceback. Anything elementary that I am missing? My fasta file is very simple and it is stored in the Documents folder. Regards, -- Divita Mathur, PhD Research Assistant Professor George Mason University & Center for Bio/Molecular Science and Engineering Naval Research Laboratory (202) 767-0687 (Office)

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ENQUIRY
by ogochukwu ngozi 05 Apr '21

05 Apr '21

Dear Concerned,I am a PHD student from University Putra Malaysia. This is my first time using Chimera, please I need your assistance. I want to use chimera to calculate RMSD values, could you direct me on steps to take please? Thanks as I await your kind reply.Ogochukwu Nwaefulu

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Re: [Chimera-users] ResProp Python code
by Elaine Meng 05 Apr '21

05 Apr '21

Dear Chittari Jaya Shree, I can't answer about python, but maybe you didn't know about the related feature that you can simply assign names to whatever you want. There is no need to use the ResProp tool if this is all going to be in a script anyway. For example, command: alias neutral :ile,val,leu,phe,cys,met,ala,gly,thr,ser,trp,tyr,pro,gln,asn ... will then let you use "neutral" in other commands, e.g. select neutral "alias" command <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/alias.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Apr 5, 2021, at 4:54 AM, Jayashree Chittari <jayashreechittari27(a)gmail.com> wrote: > > Respected sir/ma'am > > Greetings for the day! > I want to make a new category named as neutral in which I would assign some amino acids to this category. So, in GUI we know that it could be done through tools-->structural analysis--> ResProp. > > My question is how to do the similar process in python, like how to assign certain amino acids to a new category and then perform the selection("select neutral")? > > Here is the attached ss of Residue category definition. I want to use this process in python where the new category contains assigned amino acids. > > Kindly help me in this issue, it would be very grateful if you suggest the code. > thank you, > > Regards > Chittari Jaya Shree > > <Capture.PNG>

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translation along x,y and z
by Ashok Nayak 01 Apr '21

01 Apr '21

HI Elaine, I want to know the rotation and translation components along x,y and z separately from the rotation matrix obtained from chimera reply log upon fitting a model into a map. Will it be possible to know? Matrix rotation and translation 1.00000000 -0.00000000 -0.00000000 1.83458738 -0.00000000 1.00000000 -0.00000000 1.15016978 -0.00000000 -0.00000000 1.00000000 -0.53835221 Axis 0.00000000 0.00000000 1.00000000 Axis point 0.00000000 0.00000000 0.00000000 Rotation angle (degrees) 0.00000000 Shift along axis -0.53835221 thanks, Ashok

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Chimera-users April 2021