June 2016 - Chimera-users - RBVI Mailing Lists

Chimera is featured on LabWorm this week!
by Alon V 15 Jun '16

15 Jun '16

Dear people of Chimera, I'm Alon, a co-founder of LabWorm.com , a discovery platform that exposes top research tools with the goal of promoting a more open, collaborative and cutting edge science. Our community members have recently submitted Chimera to LabWorm. Since we thought our community could greatly benefit from getting to know a resource for powerful molecular visualization such as Chimera, we decided to feature it on our main feed under “New this week” here . Featured tools are voted on by the community and the top 5 voted tools appear in our weekly newsletter. I invite you to join our community. Once you register an account(s), I'll also be able to designate that account(s) as official creator/representative of Chimera , just reply to this e-mail with your account(s) name(s). Feel free to contact me with any thoughts or questions. Best wishes, Alon Vitenshtein Co-founder | LabWorm.com | @TheLabWorm

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RR distance plot export
by Toshiki Nakashige 14 Jun '16

14 Jun '16

Hello, I am creating distance difference plots and was interested in exporting the plots. I want to generate two plots comparing different chains, and since the maximum and minimum difference values are different for each plot, I'm not able to have both plots on the same color scale. Is there a way to export the figure as a table of numbers such that I can create a color scale in a different program? I only see the icon to save the figure as an image and am not sure if there is an export as table option. Thank you, Toshiki

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Paper viruses
by David Bhella 14 Jun '16

14 Jun '16

Hi, I have been trying to recreate the paper viruses shown on ViperDB and on your own site here: http://www.cgl.ucsf.edu/chimera/data/kids-day-apr2008/papervirus.html How did you keep the structure within the confines of the triangular facets? Is this possible within the flatten-icosahedron command, or was there some additional manual processing involved? Thanks, Dr David Bhella MRC-University of Glasgow Centre for Virus Research Sir Michael Stoker Building Garscube Campus 464 Bearsden Road Glasgow G61 1QH Scotland (UK) Telephone: 0141-330-3685 Skype: d.bhella Virus structure group on Facebook: https://www.facebook.com/CVRstructure Molecular Machines - Images from Virus Research: http://www.molecularmachines.org.uk CVR website: http://www.cvr.ac.uk CVR on Facebook: https://www.facebook.com/centreforvirusresearch

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How to check flexibility of a protein
by shazia sabir 14 Jun '16

14 Jun '16

Can we check flexibility of a protein in chimera? Can we see if protein is affected after a mutation of only single amino acid? Are there some parameters that shows protein become more rigid or flexible after mutation? Regards, Shazia. Sent from my iPhone

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Re: [Chimera-users] Save bond-distance label-position
by Eric Pettersen 13 Jun '16

13 Jun '16

Hi Maarten, I hope you wound up having something better to do on Sunday, because the code I committed wasn’t quite right. I’ve corrected the code and committed it to the release candidate as well now. —Eric Eric Pettersen UCSF Computer Graphics Lab > On Jun 10, 2016, at 10:17 AM, Maarten Schledorn <m.schledorn(a)gmail.com> wrote: > > Dear Eric, > It is not urgent. I knew in advance that they would not be saved so today I just positioned them and exported my images and video without closing the session. I'm happy to hear that they should be saveable soon! I'll give it a try on Sunday (: > Thanks again, > Maarten > > > On Friday, 10 June 2016, Eric Pettersen <pett(a)cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu>> wrote: > Hi Maarten, > This is a bug. Label offsets are being saved for bonds, but not pseudobonds (e.g. distances). I have committed changes to the code to save/restore the offsets, but as I'm working from home today it's awkward for me to test the changes. If you are feeling brave you can try tomorrow's daily build and see if the changes work. Otherwise I will test them myself Monday and ensure they work, and then add them to the release candidate as well. > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > > On Jun 10, 2016, at 4:28 AM, Maarten Schledorn wrote: > > > Dear reader, > > > > The distance measurement tool outputs a distance 'label' that by default is on the center of the line connecting the two atoms involved. In my structure I have about twenty of these, and I have manually dragged all distance values to empty spots in the image. However, if I save and re-open the session, the labels are back at their default position. I have tried <savepos>, and also <scene save>, but to no avail. Is there a way to save the bond-distance label-positions? > > > > Many thanks in advance, > > with kind regards, > > Maarten > > _______________________________________________ > > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <javascript:;> > > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users> >

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configuring stereoscopic view in RHEL-7.x
by abhisek Mondal 13 Jun '16

13 Jun '16

Hi, I'm using Chimera - 1.10 on a RHEL-7.x operating system (64-bit) with 128 GB of DDR3 RAM, 2.3 GHz Intel Xeon processor, Nvidia Quadro K5200, ASUS VG278 monitor (3D compatible). I have successfully configured Coot to run in stereoscopic view in the same machine but Chimera is giving me a hard time regarding the same. Any suggestions regarding this issue will be highly appreciated. Thank you. -- Abhisek Mondal *Research Fellow* *Structural Biology and Bioinformatics Division* *CSIR-Indian Institute of Chemical Biology* *Kolkata 700032* *INDIA*

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Re: [Chimera-users] Splitting an pdb with multiple proteins
by Eric Pettersen 13 Jun '16

13 Jun '16

Hi Jochen, Support for chain descriptions coming from mmCIF files (rather than PDB files) was only added after the 1.10.2 release. Please try the current 1.11 release candidate and see how that works. --Eric Eric Pettersen UCSF Computer Graphics Lab On Jun 10, 2016, at 1:36 AM, Jochen Baßler wrote: > Dear Elaine, Eric, > > Thanks a lot for your fast replay. > I imported 3jct and 5hau to test your suggestions, but the reply log just contained : > > [MMLIB:WARNING] monomer description not found in zipfile for '4SU' > [MMLIB:WARNING] monomer description not found in zipfile for '5MC' > > How can I activate the status message? > With the mouse I can see the chain number near the mouse pointer, but there is no information below at the main window. > > (I am running chimera version 1.10.2) > > Best wishes > > Jochen > > > From: Eric Pettersen <pett(a)cgl.ucsf.edu> > Date: Friday, 10June, 2016 1:51 AM > To: "chimera-users(a)cgl.ucsf.edu BB" <chimera-users(a)cgl.ucsf.edu> > Cc: J B <jochen.bassler(a)bzh.uni-heidelberg.de> > Subject: Re: [Chimera-users] Splitting an pdb with multiple proteins > > It is also listed in the reply log as the structure is opened. > > —Eric > > Eric Pettersen > UCSF Computer Graphics Lab > > >> On Jun 9, 2016, at 4:49 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: >> >> Hi Jochen, >> This information is already imported, and when you mouse over the chain, it is shown in the “status message” area across the bottom of the Chimera window. >> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/chimerawindow.html> >> >> I tested just now, and the information is retained and can be shown in the same way after “split” is used. However, it is not automatically used as the model names. >> I hope this helps, >> Elaine >> ---------- >> Elaine C. Meng, Ph.D. >> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab >> Department of Pharmaceutical Chemistry >> University of California, San Francisco >> >> >>> On Jun 9, 2016, at 4:05 AM, Jochen Baßler <jochen.bassler(a)bzh.uni-heidelberg.de> wrote: >>> >>> Hi, >>> >>> I´m frequently looking at pdb´s that contain multiple chains, like ribosomes or preribosomes (e.g. Pdb 3JCT). >>> Is there a way to import the information from the pdb database, which tells you the name of the chains? >>> Chain A = rpl2 >>> Chain B = Rpl4 etc. >>> Cool would be to split the pdb into multiple models that have the name from the pdb database. >>> (It is quite annoying to have a pdb with nearly 60 different chains and you have to spend half a day to rename the chains or to create individual models, before analyzing the structure) >>> >>> Thanks for suggestions and solutions >>> >>> Best wishes >>> >>> Jochen >>> >> >> _______________________________________________ >> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu >> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >> >

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pdb coordinates and their fonts in article
by Vasantha Kumar 10 Jun '16

10 Jun '16

Dear Chimera users I have a trivial question related to pdb coordinates in text format. For a small molecule I would like to report pdb coordinates (12 column) in an article. Regular .text (to pdf and illustrator ) file fonts are horrible, Is there is way to keep same space between columns and change the fonts size and style that respects pdb format. Therefore I want know is there any additional option in chimera to export coordinates? in a nice way so that if someone copy these coordinates from the article they should be open in chimera with out further editing. Have a good weekend!! thanks in advance.. Vince

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Save bond-distance label-position
by Maarten Schledorn 10 Jun '16

10 Jun '16

Dear reader, The distance measurement tool outputs a distance 'label' that by default is on the center of the line connecting the two atoms involved. In my structure I have about twenty of these, and I have manually dragged all distance values to empty spots in the image. However, if I save and re-open the session, the labels are back at their default position. I have tried <savepos>, and also <scene save>, but to no avail. Is there a way to save the bond-distance label-positions? Many thanks in advance, with kind regards, Maarten

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Splitting an pdb with multiple proteins
by Jochen Baßler 09 Jun '16

09 Jun '16

Hi, I´m frequently looking at pdb´s that contain multiple chains, like ribosomes or preribosomes (e.g. Pdb 3JCT). Is there a way to import the information from the pdb database, which tells you the name of the chains? Chain A = rpl2 Chain B = Rpl4 etc. Cool would be to split the pdb into multiple models that have the name from the pdb database. (It is quite annoying to have a pdb with nearly 60 different chains and you have to spend half a day to rename the chains or to create individual models, before analyzing the structure) Thanks for suggestions and solutions Best wishes Jochen

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Chimera-users June 2016