August 2023 - ChimeraX-users - RBVI Mailing Lists

re error with Movie recorder utility
by Anna Lohning 17 Aug '23

17 Aug '23

Hi I have the freeware version installed and trying to make a movie using the Tools/Utilities/Movie recorder window. At this stage, I seem to only have the command line available for commands one at a time. Anyway, under the Tools/Utilities, the only options there currently are Register Updates Be grateful for some clarification as I cant seem to find anyone having this issue. Many thanks Kind regards Anna Dr Anna Elizabeth Lohning Associate Professor - Biochemistry Faculty of Health Science & Medicine Bond University ROBINA 4229 (07) 5595 4779 alohning(a)bond.edu.au<mailto:alohning@bond.edu.au>

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Getting number of residues from a PDB contain only a fragment
by huybk81＠gmail.com 16 Aug '23

16 Aug '23

Hi, I used this Python code to get the number of residues: model = run(session, 'open %s' % input_model)[0] print(model.chains[0].num_residues) It works when the input_model is a complete pdb file. However, when the input_model only contain part of the structure of the full pdb but retains the full sequence information, the code above always return the num_residues of the full structure, not the input_model only. Is there any way to get this done? Best, Huy

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colouring by entity
by Manon Demulder 15 Aug '23

15 Aug '23

Hi I have a model that consists of a sheet made out of repeats of a dimer. Currently I have a .mmcif file with the monomers in each dimer being labelled either 1 or 2. I would like to give monomer 1 and 2 a different color in my sheet. Is it possible in ChimeraX to recolour the different monomers by their entity 'name'? Thanks in advance! Best Manon ------------------------------------------------------------ Manon DEMULDER PhD | Post-doctoral researcher University of Basel | Biozentrum | Ben ENGEL lab Spitalstrasse 41 | 4056 Basel | Switzerland manon.demulder(a)unibas.ch | www.biozentrum.unibas.ch<http://www.biozentrum.unibas.ch>

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AreaSAS Function in ChimeraX
by Andy Nguy 14 Aug '23

14 Aug '23

Hello, I was wondering if there is a AreaSAS function for ChimeraX. To my knowledge, there was such a function in Chimera under "Render by Attribute". If not, is there a way to identify all solvent-accessible residues for a protein of interest? Thanks! -- Andy.

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Problem with saving files through command line
by Vorländer,Matthias Kopano 14 Aug '23

14 Aug '23

Dear Developers, I have found a strange behavior when saving files through the chimeraX command line. Essentially, file naming does not seem to be properly sensitive to capitalization. For example, when I am trying to save a file called “chain_A.pdb” and then another file called “chain_a.pdb”, “chain_A.pdb” will be overwritten with the contents of “chain_a.pdb”. It also does not matter if I am saving a pdb file or a log file. If “chain_A.pdb” does not exist, then “chain_a.pdb” will be correctly saved with as a lowercase a. Details: version 1.6.1 (2023-05-09) OS: MacOS Catalina Version 10.15.7 Would be great if this could be fixed : ) Many thanks in advance, Matthias

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Library Missing in Debian v-12
by Stephen P. Molnar 14 Aug '23

14 Aug '23

I have just downloaded ucsf-chimerax_1.6.1ubuntu22.04_amd64.deb for installation on my Debian-12 platform. Unfortunately, the missing dependency libffi7 is not part of the distributiojn. Please Advise. Thanks in advance. ucsf-chimeax-- Stephen P. Molnar, Ph.D. https://insilicochemistry.net (614)312-7528 (c) Skype: smolnar1

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Opacity of atoms
by Haaris Ahsan Safdari 13 Aug '23

13 Aug '23

Hi ChimeraX team, I am working on a protein that clashes with RNA. Hence, to show those, I selected atoms of proteins (sphere representation) which are less or equal to 3.5Å from RNA and then colored them red. Through this criteria, some atoms of protein which do not clash with RNA, I keep them as lime colour. All of this works fine. Now, I wanted to show the clash more clearly since RNA segments pierces through many atoms of protein, so I wanted to make protein atoms (which is now a combination of red for clashing atoms and lime for non-clashing atoms) transparent. However, as soon as I make my protein more transparent (by changing opacity), all atoms of my protein turn red and I lose the green ones which I dont want. I just wanted to know if there is any workaround for this (to retain green while making everything more transparent) or if it is just a bug? Best regards, Haaris Ahsan Safdari

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Fwd: how to fix this.... it is windows machine.
by Eric Pettersen 11 Aug '23

11 Aug '23

> Begin forwarded message: > > From: Krishnan Raman <RKrishnan(a)BIOCRYST.com> > Subject: how to fix this.... it is windows machine. > Date: August 11, 2023 at 12:20:16 PM PDT > To: "chimerax-users-owner(a)cgl.ucsf.edu" <chimerax-users-owner(a)cgl.ucsf.edu> > > > > Krishnan Raman > Executive Director, Structural Biology > BioCryst Pharmaceuticals > > > > > CONFIDENTIALITY NOTICE > > This email, including any attachments, may contain confidential or legally privileged information that is intended only for the individual or entity to whom it is addressed. If you are not the intended recipient, please be advised that any dissemination, distribution or copying of this email and any attachment is strictly prohibited. If you have received this email in error, please reply to the sender so that BioCryst Pharmaceuticals, Inc. can take corrective measures and then permanently delete this email and any attachment, including any printed copies. Thank you. >

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Regarding Volume Morph Issue
by Chen, Shin-Fu 11 Aug '23

11 Aug '23

Hello, I hope this message finds you well. I am currently working on creating a movie using the "volume morph" command based on ten sets of mrc files. I have encountered an issue that I would appreciate your assistance with. Prior to applying the "volume morph" command, I have utilized the "color near atoms" option to assign colors to the visualization. However, after executing the "volume morph" command, the previously assigned colors are reset to a default single color. I am reaching out to seek guidance on resolving this issue. Your insights and advice would be greatly appreciated. Thank you for your attention to this matter, and I eagerly await your response. Best regards, Shin-Fu Shin-Fu Chen, Ph.D. Postdoctoral Fellow Department of Biochemistry and Molecular Biology McGovern Medical School University of Texas Health Science Center Houston 6431 Fannin St | MSB 6.326 | Houston, Texas 77030

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Re: [Chimera-users] making composite map using vop maximum command
by Elaine Meng 10 Aug '23

10 Aug '23

Hi, In ChimeraX it is documented as "volume maximum" (even though I believe that "vop maximum" like in the older program Chimera could be used). Also if you want to ask about ChimeraX specifically, there is a different email address, chimerax-users(a)cgl.ucsf.edu -- I CC'd it here so you don't need to do anything this time. Here is the ChimeraX "volume maximum" help link: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#maximum> For example, if your maps are #2 and #3, you can create a new map containing the maxima of their two values with ChimeraX command: vol max #2,3 ... but there are many additional options that could also be included in that command, so you should check the help link above to see if you want to use any of them. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Aug 7, 2023, at 2:20 PM, ytakagi--- via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hi > I want to make a composite map using two locally refined maps. I tried Phenix but did not work well. So, I like to do it by Chimera. Apparently, a composite map can be made using Chimera's vop maximum command. But I could not find the instruction of how to do it. Can you tell me how to do it? > Thanks

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