July 2015 - Chimera-users - RBVI Mailing Lists

Measure translation of two domains?
by Oliver Clarke 07 Jul '15

07 Jul '15

Hi all, I’m puzzling how to measure the translation of two domains in Chimera, in a situation where there is small but non-zero translation. I expected I could do this by first using match to superimpose the two selections, then using measure rotation to obtain the rotation (if any) and translation. This has worked fine for me in measuring rotation of domains. However, on a purely translational test case, this gives confusing results. I have attached two structures of 1bl8, one of which has been displaced from the other manually by 20 Å. If I match one to the other, it successfully superimposes the two structures. If I then use measure rotation to try to recover the translation, I get a message telling me that the rotation angle is near zero (which is not surprising), but when I check the reply log, the listed translation along the axis is only 1.7Å (see screenshot attached), rather than the 20Å I expect. What am I doing wrong here? Is there another command I ought to be using? Or am I misinterpreting the output? Cheers, Oliver.

2 1

question
by A G Szabo 07 Jul '15

07 Jul '15

I am pleased to inform you that I have been using aspects of Chimera that permit me to prepare images of proteins deposited in the pdb. It was a pleasant surprise to find that the learning curve was not as steep as I thought it might be. Mind you, there are many aspects of Chimera that I have not yet attempted to use. Now I wish to do something that may not be possible to do with Chimera. And I am not sure where to look in the tutorials. I have a ribbon diagram of a protein-RNA complex, PDB 4p3e, two proteins, SRP 19 and SRP68, bound to a segment of 7SL RNA. I can also obtain the structure of another protein SRP54 which also bind to this complex. However, the structure of pdb 4p3e with SRP54 is not available. I know where SRP54 should bind to the RNA, and I know which domain of SRP54 binds to the RNA. How can I somehow combine the two files, one for SRP54 and the other 4p3e and locate SRP54 onto the 4p3e structure? (not sure it is possible) Of course crystallographers know how to achieve this structural combination. I don't have a clue. I checked the tutorial list and the closest I seemed to come was the Merge command. However, the tutorial did not seem to deal with what I wanted to do. Thank you in advance for your assistance. Arthur G. Szabo Ph.D. Professor Emeritus, Chemistry Wilfrid Laurier University Waterloo, Canada.

2 4

Question
by Damjanovic Marko 07 Jul '15

07 Jul '15

To whom it may concern, I am trying to solve a problem that is more of mathematical nature, and I would be very grateful if I could get any advice or pointers on how it may be possible to do this (in Chimera or some other program I am not aware of). I have a molecule that is more or less of cylindrical shape (quite simple shape). I would need a way to surround this molecule with a certain number of layers of solvent molecules that fit around the surface of a cylinder (preferably 1 layer and then going up gradually). The solvent molecules should be packed around the central molecule efficiently (closest packing). An alternative way to approach this would be to take a sphere made out of solvent molecules, put in the centre of the sphere the one cylindrical molecule what is of interest, and let the big sphere accommodate the new molecule. Also, for the sake of simplicity, the solvent molecules can be approximated as small spheres as well (their exact shape is not that relevant). When this is done, all I would need is to get this file in a format like cif, mol or gjf. I underline here that I am looking for a relatively crude model. Could anyone please advise me on how to do something like this? Thanks in advance and best wishes, Damjanovic Marko

3 3

chimera extensions & dialog location
by Dougherty, Matthew T 06 Jul '15

06 Jul '15

1) How can I reload an extension when chimera is running? At the present, after I modify python code I restart chimera for the s/w changes to take effect. Is there a way through idle, etc, that I can cause user code modifications to load without restarting chimera? 2) How can I position the location of IDLE using python? I have IDLE on autostart. In a user extension I have a button, when pressed it organizes the various dialogs, placing them in specific locations. When I try to do something with IDLE, running dialogs.activeDialogs() does not show IDLE in the list. Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ===========================================================================

2 1

change B factor
by McCafferty, Caitlyn (NIH/NEI) [F] 06 Jul '15

06 Jul '15

Hi, Is there a feature in Chimera that allows you to change the B-factor of the Amino Acids. I have a txt file with the values that I would like to replace the current B-factors with. Thank you, Caitie

2 1

Undisplay pseudo bonds (missing segments) in pipes-and-planks representation?
by Oliver Clarke 03 Jul '15

03 Jul '15

Hi all, just wondering if there is an option I am missing to undisplay pseudobonds when using pipes-and-planks? At present chimera seems to represent missing segments in pipes-and-planks as a continuation of the chain rather than a break, which is a little confusing, e.g. check the following pair of snapshots (chain break in green section corresponds to missing 10aa loop): https://www.dropbox.com/s/cbwar1i197kt3ep/Screenshot%202015-07-03%2010.09.5… <https://www.dropbox.com/s/cbwar1i197kt3ep/Screenshot%202015-07-03%2010.09.5…> https://www.dropbox.com/s/we058qjv3ibwjmn/Screenshot%202015-07-03%2010.10.0… <https://www.dropbox.com/s/we058qjv3ibwjmn/Screenshot%202015-07-03%2010.10.0…> Also in general it would be nice if cylindrical representations of helices were more integrated into chimera, perhaps with their own style adjustments (e.g. allowing for curved cylinders), as for large structures they provide much less visual clutter, but I guess that is probably something for Chimera 2. Cheers, Oliver.

2 2

Cross eyed stereo pair generated by default
by Oliver Clarke 02 Jul '15

02 Jul '15

Hi all, I’ve noticed that when I save a stereo pair (using File/Save Image/Image Type/stereo pair), the resultant stereo pair is suitable for cross-eyed viewing. This is great for me, as I can’t do wall eyed stereo, but the default for many journals is to provide a wall-eyed stereo pair. Of course it is easy enough to convert by swapping the two halves of the pair, but for the sake of convenience, would it be possible to list stereo pair (cross eye) and stereo pair (wall eye) as two separate options in this dialogue? Cheers, Oliver.

3 8

Re: [Chimera-users] Chimera-users Digest, Vol 147, Issue 4
by Oliver Clarke 02 Jul '15

02 Jul '15

Thanks Greg! To clarify, I wasn't actually intending these for use with a viewer of any sort - just to provide in a paper for use as a stereo pair, viewed by either diverging or crossing one's eyes to superimpose the two halves of the pair. Some people can easily view wall-eyed pairs, while others (myself included) can only view cross-eyed pairs, so it would be nice to have the option of generating either. Cheers, Oliver. On Thu, Jul 2, 2015 at 3:00 PM, <chimera-users-request(a)cgl.ucsf.edu> wrote: > Send Chimera-users mailing list submissions to > chimera-users(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > or, via email, send a message with subject or body 'help' to > chimera-users-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimera-users-owner(a)cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-users digest..." > > > Today's Topics: > > 1. Re: on beta strand assignmet by chimera (Elaine Meng) > 2. Cross eyed stereo pair generated by default (Oliver Clarke) > 3. Re: Cross eyed stereo pair generated by default (Greg Couch) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 2 Jul 2015 09:55:55 -0700 > From: Elaine Meng <meng(a)cgl.ucsf.edu> > To: Smith Liu <smith_liu123(a)163.com> > Cc: chimera-users(a)cgl.ucsf.edu > Subject: Re: [Chimera-users] on beta strand assignmet by chimera > Message-ID: <E1E1B5D3-B0A5-4849-88D2-237944AFFA48(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=utf-8 > > Dear Smith, > If the PDB files came from the Protein Data Bank repository, generally the > proteins already have secondary structure assigned in HELIX and SHEET > records. If so, Chimera just uses those assignments. > < > http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html#se… > > > > If the PDB file of a peptide/protein doesn?t have HELIX and SHEET records > in it, then it runs a method ?ksdssp? described here: > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/ksdssp.html> > > If you don?t like the results for some reason, you could try re-running > the ?ksdssp? command (or the ?compute SS? function in the Model Panel) with > different (nondefault) parameters, or just manually assign residues as > helix or strand however you like with the ?setattr? command, as shown in > the lower part of this previous post: > < > http://plato.cgl.ucsf.edu/pipermail/chimera-users/2014-January/009574.html > > > > 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 Jul 2, 2015, at 6:09 AM, Smith Liu <smith_liu123(a)163.com> wrote: > > > > Dear All, > > > > I have a protein, which contains fragment aa 239-251. The protein has > been fitted its map with 2 different (minor difference) resolution, and > thus I have 2 PDB. For PDB 1 (the first resolution), the H-bonds inside aa > 239-251 include: > > #2 Gly 245.A N-Asn 242.A O 2.708A > > #2 Asn 242.A N-Tyr 246.A O 3.120 A > > #2 Val 248.A N-Val 240.A O 3.120 A > > #2 GLN 251.A N-Ser 238.A 0 3.033 A > > > > For PDB 2 (the second resolution), the H-bonds inside aa 239-251 include: > > #0 Gly 245.A N-Asn 242.A O 2.715A > > #0 Asn 242.A N-Tyr 246.A O 3.1206 A > > #o Val 248.A N-Val 240.A O 2.858 A > > #0 GLN 251.A N-Ser 238.A 0 3.074 A > > > > Naked eye check found the H-bonds in PDB 1 were almost the same H-bonds > in PDB 2. > > > > However for PDB 2, aa23-242 and aa 247-251 form 2 strands, but for PDB > 1, it was a un-disconnected loop for aa 239-251. > > > > Will you please explain how chimer assign beta strand? > > > > Best regards. > > > > Smith > > > > > > ------------------------------ > > Message: 2 > Date: Thu, 2 Jul 2015 14:20:01 -0400 > From: Oliver Clarke <olibclarke(a)gmail.com> > To: Mailing List <chimera-users(a)cgl.ucsf.edu> > Subject: [Chimera-users] Cross eyed stereo pair generated by default > Message-ID: <B5D941AF-2692-4E71-8D5A-2A9C8D1610E2(a)gmail.com> > Content-Type: text/plain; charset=utf-8 > > Hi all, > > I?ve noticed that when I save a stereo pair (using File/Save Image/Image > Type/stereo pair), the resultant stereo pair is suitable for cross-eyed > viewing. > > This is great for me, as I can?t do wall eyed stereo, but the default for > many journals is to provide a wall-eyed stereo pair. > > Of course it is easy enough to convert by swapping the two halves of the > pair, but for the sake of convenience, would it be possible to list stereo > pair (cross eye) and stereo pair (wall eye) as two separate options in this > dialogue? > > Cheers, > Oliver. > > > ------------------------------ > > Message: 3 > Date: Thu, 02 Jul 2015 11:39:26 -0700 > From: Greg Couch <gregc(a)cgl.ucsf.edu> > To: chimera-users(a)cgl.ucsf.edu > Subject: Re: [Chimera-users] Cross eyed stereo pair generated by > default > Message-ID: <5595855E.4020903(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=utf-8; format=flowed > > I'll look into it. > > FYI, cross-eyed stereo is the standard for stereo PNG and stereo JPEG > files. There is a buglet in stereo image saving -- the .png files > should be renamed to have a .pns suffix, and the stereo JPEG images > should have a .jps suffix. However there aren't many viewers other than > the one that comes with NVIDIA's 3D Vision setup. > > -- Greg > > On 07/02/2015 11:20 AM, Oliver Clarke wrote: > > Hi all, > > > > I?ve noticed that when I save a stereo pair (using File/Save Image/Image > Type/stereo pair), the resultant stereo pair is suitable for cross-eyed > viewing. > > > > This is great for me, as I can?t do wall eyed stereo, but the default > for many journals is to provide a wall-eyed stereo pair. > > > > Of course it is easy enough to convert by swapping the two halves of the > pair, but for the sake of convenience, would it be possible to list stereo > pair (cross eye) and stereo pair (wall eye) as two separate options in this > dialogue? > > > > Cheers, > > Oliver. > > _______________________________________________ > > Chimera-users mailing list > > Chimera-users(a)cgl.ucsf.edu > > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > > > > ------------------------------ > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > End of Chimera-users Digest, Vol 147, Issue 4 > ********************************************* >

1 0

on beta strand assignmet by chimera
by Smith Liu 02 Jul '15

02 Jul '15

Dear All, I have a protein, which contains fragment aa 239-251. The protein has been fitted its map with 2 different (minor difference) resolution, and thus I have 2 PDB. For PDB 1 (the first resolution), the H-bonds inside aa 239-251 include: #2 Gly 245.A N-Asn 242.A O 2.708A #2 Asn 242.A N-Tyr 246.A O 3.120 A #2 Val 248.A N-Val 240.A O 3.120 A #2 GLN 251.A N-Ser 238.A 0 3.033 A For PDB 2 (the second resolution), the H-bonds inside aa 239-251 include: #0 Gly 245.A N-Asn 242.A O 2.715A #0 Asn 242.A N-Tyr 246.A O 3.1206 A #o Val 248.A N-Val 240.A O 2.858 A #0 GLN 251.A N-Ser 238.A 0 3.074 A Naked eye check found the H-bonds in PDB 1 were almost the same H-bonds in PDB 2. However for PDB 2, aa23-242 and aa 247-251 form 2 strands, but for PDB 1, it was a un-disconnected loop for aa 239-251. Will you please explain how chimer assign beta strand? Best regards. Smith

2 1

gzip error while starting REST server on Windows
by Mungo Carstairs (Staff) 02 Jul '15

02 Jul '15

I'm testing Jalview starting Chimera (1.10.1) with RESTServer on a Windows 7 machine without gzip installed. On starting the Chimera process: new ProcessBuilder().start("chimera.exe", "--start", "RESTServer") I get two lines of response: Cannot execute 'gzip': no automatic decompression of .Z files REST server on host 127.0.0.1 port nnnnn which is ok - I can get the REST port number I need and carry on. Am I safe to ignore the other message? I can't see what file (I assume part of the Chimera installation) it is arising from. Thanks, Mungo Mungo Carstairs Jalview Computational Scientist The Barton Group Division of Computational Biology College of Life Sciences University of Dundee, Dundee, Scotland, UK. www.jalview.org<http://www.jalview.org/> www.compbio.dundee.ac.uk<http://www.compbio.dundee.ac.uk/> The University of Dundee is a registered Scottish Charity, No: SC015096

2 1

Chimera-users July 2015