- Chimera-dev - RBVI Mailing Lists

Finding Coordinates of Maps
by Maximilian Julian Pokutta 04 Mar '24

04 Mar '24

Dear Chimera Dev Team, I have a chimera session with the ~500 maps overlayed onto a tomogram saved, and I would like to get their coordinates in relation to the tomogram on which they are overlayed. I am unsure how to get started on this and wanted to know if you had any pointers as to where to start. Best, Max

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Seeking Assistance with PyCharm Debugging Configuration
by himalgodage2759＠gmail.com 19 Feb '24

19 Feb '24

Dear ChimeraX Dev Team, I'm Himal Godage, and I am currently in the process of developing a bundle for ChimeraX software. I have been thoroughly following the provided documentation, successfully completing the steps related to setting up a ChimeraX development environment, obtaining the code, and compiling ChimeraX. However, I have encountered a challenge in the IDEs, Debugging, and Profiling section, specifically within PyCharm. Following the provided steps, I am instructed to: 1. Create a new Run/Debug Configuration. 2. Set the script path field to point at a module. 3. Set the module to “chimerax.core”. 4. Set the Python interpreter to ChimeraX’s internal Python. 5. Uncheck “Add content roots to PYTHONPATH”. 6. Uncheck “Add source roots to PYTHONPATH”. While attempting to follow these instructions, I encountered difficulty in locating the "chimerax.core" module. Unfortunately, the provided directory structure or module seems to be difficult to find in my current project. However there is a module named core in the following path. ChimeraX > src > bundles > core I am reaching out to seek your guidance on resolving this issue. Could you please provide insights on how I can locate or create the necessary "chimerax.core" module or suggest an alternative approach to address this problem? Thank you in advance for your time and support. Best regards, Himal Godage himalgodage2759(a)gmail.com

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Using Chimera in teaching
by Simon Wheeler 01 Feb '24

01 Feb '24

Dear Chimera people, I would like to use Chimera to teach some classes on an MSc course at my university and so would like to install the software on about 40 PCs. I just want to make sure that this is okay, and in particular how I would register the software. Please can you offer some guidance? Thanks very much. Best wishes, Simon Dr Simon Wheeler Lecturer in Pharmaceutical Chemistry, De Montfort University, Leicester, LE1 9BH Chemical Probes for Lysosomal Biology<https://royalsociety.org/science-events-and-lectures/2024/09/lysosomal-prob…> is a two-day conference bringing together lysosomal biologists and analytical chemists who have an interest in making sensors to interrogate the functions of this organelle. Click on the link for more details and to register your interest. [cid:image001.png@01DA54F3.C489C400]

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Web server inquiry
by Paula Jofily De Lima Rangel 26 Oct '23

26 Oct '23

Dear Chimera developers, I am Paula, a second-year PhD student at the University of Waterloo. I have recently developed a python program which performs automatic exhaustive mutagenesis of protein-ligand complexes using Chimera at the backend. My supervisor and I believe that the community could benefit from such a tool, so we intend to publish the code as a free and open source pipeline, with a permissive license. In addition, we believe that making it available as a web server would be especially useful. Therefore, we would like to ask your permission to run UCSF Chimera in a webserver hosted by our University. We will never distribute Chimera itself, and users would be instructed to register their own installation and always cite it whenever they use our server. Thank you for your time and consideration. Kind regards, Paula

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None
by None 26 May '23

26 May '23

Chimera User's Guide, the coloring of the MSMS surface using red, blue and white is described: "The Molecular Surface option allows coloring by electrostatic potential at the molecular surface (as in the figure above). Positive potentials range from white to blue, and negative potentials range from white to red. Potentials at or above the cutoff value are fully blue, and potentials at or below the negative of the cutoff value are fully red. The white area is transparent in MSMS surfaces, opaque in Grasp surfaces." The Chimera help menu has a User's guide entry that will show this stuff in a web browser. As you note, the areas of low potential really look gray, and dark gray not white. This is because they are set to be a very transparent white and the black background of the Chimera window shows through. To see this you can go to Settings/Preferences category Background and change the background color to white. That makes the low potential areas look white, but you probably don't want a white background. Eric Pettersen has added color buttons to the DelphiViewer user interface so you can change the red, blue, and white colors, including the transparency, and this will be in the next release. What you want is probably to make the white less transparent. You can do that in your current Chimera 1602 by editting a file. Look at /usr/local/chimera/share/DelphiViewer/MSMSTexturer.py near line 78 you'll find red = chimera.MaterialColor(1, 0, 0, 0.9, None) white = chimera.MaterialColor(1, 1, 1, 0.1, None) blue = chimera.MaterialColor(0, 0, 1, 0.9, None) This is setting the colors, red, white, blue, and transparency values each on a scale of 0 to 1. For the transparency 0 means completely transparent and 1 means completely opaque. So if you change these lines to red = chimera.MaterialColor(1, 0, 0, 0.9, None) # white = chimera.MaterialColor(1, 1, 1, 0.1, None) white = chimera.MaterialColor(1, 1, 1, 0.9, None) blue = chimera.MaterialColor(0, 0, 1, 0.9, None) and restart Chimera, you'll get white low potential regions. Here the "#" is the comment character in the Python language. I can ask Eric if the unreleased DelphiViewer with the color buttons on the user interface will work in Chimera 1602, and try to get that to you so you don't need to edit the file. Tell me if you want that. You say the MSMS surface looks incomplete. Can you tell me a specific PDB file and atom to look near to see the problem? The MSMS probe radius is set to 1.4A. You can see this by using Controllers/Model Panel, click on the line for the MSMS surface, and press the Attributes button. Normally you can edit the probe radius and press enter and it will automatically update the surface. But when I tried this with Delphi coloring I got an error and had to close the MSMS surface to get the graphics window to display anything again. If I change the probe radius before doing the Delphi coloring the surface is recalculated with no error. Tom > From: "Wade Nasholds" <vesuvius(a)omantel.net.om> > To: "Thomas Goddard" <goddard(a)cgl.ucsf.edu> > Subject: DelPhi in Chimera > Date: Fri, 14 Feb 2003 21:08:41 +0400 > > Hello Tom, > Thanks for your previous email. Certainly helps. > I got build 1602 of Chimera (thanks) and have tried it with some DelPhi .phi files > that I've generated. > I've been able to render MSMS surfaces showing electrostatic potentials successfully. > This is great news > because that's what I've been aiming to do! The potential extremes are shown in red > & blue but the intermediate > potential shows as shades of light grey to dark grey rather than the expected white > (neutral). Also, the molecular surface seems incomplete > in certain spots. I don't think it is a matter of DelPhi parameter settings, as I've > tried different ones but to no avail. Although it still may > be due to DelPhi settings still unknown to me as I'm still learning how to use it. > Might it be something to do with Chimera? I've altered the kT/e settings in DelPhi > viewer but it hasn't resolved the problem. > > Is the default surface probe (water) set at 1.4A in the MSMS feature of Chimera? > > Thanks again for your time. > Wade

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None
by None 26 May '23

26 May '23

"Note: Stereo is only available on Quadro cards, and is not supported in TwinView. Currently, stereo operation may not be completely stable on the original Quadro chip and left-right flipping may be erratic. This issue will be resolved in a future release." So it should work on our lastest Quadro 4 board, but might have problems on the ELSA Gloria IIs we bought. Greg

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Queries about operational command of chimera
by 吴明松 15 May '23

15 May '23

Dear Chimera developer, I would like to perform the same operation on multiple files and I know that this can be done using a loop. However, I am not sure how to write the corresponding command or script. Therefore, could you please help me by writing a script that can perform the following operation? I have installed the 64-bit version of Chimera Headless Linux on my Windows subsystem. Thank you very much for your help! ################################### operation: File-> open -> abc.pdb Select-> structure->ligand Actions-> delete File->save PDB->rec_noH.PDB Actions->Surface->show Tools ->structure editing->write dms->rec.ms Actions->Surface->hide Tools ->structure editing->Dock prep->rec_charged.mol2 ##select the parameter of Unspecified(determined by method)   File-> open -> abc.pdb Select-> structure->ligand Select-> invert (all models) Actions-> delete File->save mol2->ligand_site.mol2 ################################### Sincerely, Mingsong Wu mingsong_wu(a)foxmail.com

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question
by Ouertani Awatef 16 Mar '23

16 Mar '23

Dear all Good morning Please i would like to know : 1) how to make serine and threonine dehydration using chimera 2) how to make a cysteine-cysteine bridge using chimera Many thanks

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Fwd: RBVI web update results
by Eric Pettersen 22 Feb '23

22 Feb '23

For whoever is responsible for the "createPub" script... > Begin forwarded message: > > From: root <root(a)cgl.ucsf.EDU> > Subject: RBVI web update results > Date: February 22, 2023 at 4:04:54 AM PST > To: pett(a)cgl.ucsf.edu > > Traceback (most recent call last): > File "/usr/local/bin/createPub", line 188, in <module> > main() > File "/usr/local/bin/createPub", line 46, in main > htmlList = formatIds(idList, url) > File "/usr/local/bin/createPub", line 99, in formatIds > output.extend(bufferPid(url, idBuffer, flush=True)) > File "/usr/local/bin/createPub", line 109, in bufferPid > data = formatPubmedId(idBuffer, url) > File "/usr/local/bin/createPub", line 124, in formatPubmedId > esr = eSummaryResult.eSummaryResult(data) > File "/usr/local/lib/python2.7/site-packages/ncbi_eutils/eSummaryResult.py", line 43, in __init__ > raise ExpatError > xml.parsers.expat.ExpatError

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How to make script to run chimera command like add H and charged for multiple file
by Broto Santoso 15 Jan '23

15 Jan '23

Dear Chimera Staff, I want to run some chimera commands (such as add hydrogen and add charge) via python script for multiple files and save them as mol2 or pdb. I have read some examples, but still know nothing. Would you like to give me more about the script, how to make it easily? Thank you Best regards, -- *Broto Santoso* Laboratorium Kimia Farmasi Fakultas Farmasi UMS mobile: +6282136414379 (*no call, sms only*) My Youtube Channel <https://www.youtube.com/channel/UCCiJ8VZ1Vd3rVtywWkm4GyQ>

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