November 2021 - Chimera-users - RBVI Mailing Lists

Question about save images
by Chang, Jufang 29 Apr '24

29 Apr '24

Hi, there, I used Chimera for a very short period of time. When I just started using Chimera I was able to save image by going to "file" and "save image" to save the image on the display window. For some reason, this stopped working. Now, after I did the same thing, the image I saved has complete blackness (attached). I wonder whether I might get be able to get help from you. I also tried using command line to save image. The result is the same. The exact procedure I used are: Go to "Presets", choose "publication 1" , then go to "File" and "save image" I used window system. Thank you J ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Selecting and listing all residues in a specific area
by Eunice Gwee 29 Jan '22

29 Jan '22

To whom this may concern, I have been using the Autodock Vina function on Chimera for my studies and I was wondering if it is possible to list the residues in the selected area of the protein used in docking. Thank you. With regards, Eunice

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UCSF software cannot be opened normally
by 免孑 02 Dec '21

02 Dec '21

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Minimization on complex
by Francesca Magarotto - francesca.magarotto2＠studio.unibo.it 29 Nov '21

29 Nov '21

Hi, I need an advice regarding minimization of complexes. I've performed a virtual screening and I've selected some molecules of interest. Now, I've looked for the possibile interactions in the binding site and I would like to perform a minimization moving only the hydrogen atoms in the binding site. However, I have to create a new file pdb complex formed by my protein and one molecule from VS results. So, I opened the pdb file of the protein and the mol2 file of the molecule from the VS: now, do I need to save a pdb file of the complex and how to save it? I need the hydrogens to move according to the ligand inside the protein and I don't know if it's possibile with both the type of saving (is it better individual MOLECULE sections or combined MOLECULE section?). Moreover, I don't know if (for this kind of purpose) it's better first to save the complex in pdb file and then to use dockprep and minimization or use dockprep and minimization and only after saving the file of the complex. My main aim is to see if some hydrogens of the residues in the binding site move their places according to the presence of this ligand. Hope someone can help me, thanks.

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Get Minimization Energy
by Leonard Zhao 26 Nov '21

26 Nov '21

Hello, I am running a Python script to perform multiple structure minimizations and I need to extract to final potential energy from each minimization. I see that the potential energy is usually reported in the Reply Log, but when IDLE is open, it is instead redirected to IDLE. Is there any way to redirect it back to the Reply Log so I can more easily extract it in my script, or is there some other method to easily extract the energy value programmatically? Thanks, Leonard Zhao

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question regarding UCSF Chimera FindHBond feature
by Aditi Laddha 25 Nov '21

25 Nov '21

Hello, I have been using the FindHBond feature of Chimera for finding hydrogen bonds between water molecules and the polypeptide chains. I need to use some specific distance and angle criteria to find H-bonds, so I wanted to ask what is the default distance (D....A) and angle criteria (D-H....A) used in the software to find out the H-bonds, -- Regards, Aditi Laddha PhD Scholar Indian Institute of Technology, Kanpur, Uttar Pradesh 208016

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how to rectify error No MMTK name for atom
by Smriti Singh 2018RBT01 24 Nov '21

24 Nov '21

hello administrator, I am trying to minimize the Nucleotide sequence (DNA aptamer) through chimera. While performing energy minimisation steps, Chimera error "No MMTK name for atom 'HO5' in standard residue 'DA' showed. Please let me know how to rectify this issue. With warm regards Smriti Singh Research Scholar Department of Biotechnology MNNIT Allahabad

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Color volume series by per voxel variance?
by Oliver Clarke 24 Nov '21

24 Nov '21

Hi all, Is there any way in either Chimera or X to calculate the per voxel variance of a volume series, and then use that to color the individual voxels in each frame? When one has a series of volumes showing a subtle conformational change - lets say identified using cryoDRGN or 3D variability analysis in cryoSPARC - it would be nice to be able to visually highlight on the map the region that is changing the most, in some kind of quantitatively sound way. Often local changes are visually apparent when looking at the maps and rotating them around, but don't necessarily stand out in a movie of the whole volume. Coloring the series of maps (which are all on the same grid) by the variance of the density value at each voxel might be one way to visualize this. Is this possible? Cheers Oli

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Chimera compatibility with Window 11
by HK Haris 23 Nov '21

23 Nov '21

Hi, Please confirm can I download the following version of Chimera on my laptop which is operating on Windows 11. Microsoft Windows 64-bit chimera-1.15-win64.exe <https://www.cgl.ucsf.edu/chimera/cgi-bin/secure/chimera-get.py?file=win64/c…> Size: 152310162 bytes MD5: 6a68ab33f35a298059b9ef89f6372cfc Dec 18, 2020 Instructions <https://www.cgl.ucsf.edu/chimera/data/downloads/1.15/win64.html> Documentation <https://www.cgl.ucsf.edu/chimera/data/downloads/1.15/docs/> Runs on Windows 7 or later. *Best Regards,Dr. HIRA KHALID* Associate Professor Chemistry Forman Christian College University (A Chartered University) Lahore, Pakistan.54600 Ph: 042-99231581-88 x: 562 www.fccollege.edu.pk ........................ HEC APPROVED Supervisor Advisor ACS Punjab Associate member RSC Member & Ambassador Chemistry ACS Member AOCS Life-time CSP Member IUPAC Young Fellow

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FAD Topology/Parameter Files
by Zehra GÜNEŞ 22 Nov '21

22 Nov '21

Dear all, I am working on a research protein that contains FAD. I have tried to prepare it for simulation but unfortunately I have neither trajectory nor parameter file of FAD. Would it be possible to share with me these files if you have? Thanks in advance, Zehra Güneş

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Chimera-users November 2021