November 2015 - Chimera-users - RBVI Mailing Lists

Chimera 2 release date
by Markus Heller 13 Nov '15

13 Nov '15

Hello, Just curious, what's the anticipated release date for Chimera 2? Couldn't find it on the homepage ... Thanks Markus

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Built-in residue specific annotations in mmCIF?
by Oliver Clarke 13 Nov '15

13 Nov '15

Hi all, As discussed on the ccp4bb (https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ccp4bb;2223469c.1511 <https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ccp4bb;2223469c.1511>), the mmCIF format incorporates an atom_sites_foornote record (http://mmcif.wwpdb.org/dictionaries/mmcif_nmr-star.dic/Categories/atom_site…) which allows for the direct association of specific comments/annotations with particular atoms/residues. As part of expanding mmCIF support in Chimera2, would it be possible to consider incorporating the capacity to read, write, and display these records as labels or notes? This could be a great way of incorporating built-in-annotations in a structure pertaining to specific features that could potentially be readable by other software such as Coot and pymol. Cheers, Oliver.

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Re: [Chimera-users] compounds
by Elaine Meng 09 Nov '15

09 Nov '15

Dear Dwey, You can use “Join Models” to join any structures that are open as two separate models (from two separate input files). You just couldn’t use the “peptide” option in that tool if they are not peptides; you would have to use the “other bond” option. See the Join Models part of the Build Structure tool for details: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.h…> You are more likely to find answers to questions in the User’s Guide than in the chimera-users archive. You can search the User’s Guide with menu: Help… Search Documentation. If that doesn’t help, then emailing the forum (CC’d here) is recommended unless you are including private data. 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 Nov 9, 2015, at 2:05 PM, MPI <mpi566(a)gmail.com> wrote: > > Dear Elaine > Thanks for kindly answering my questions in Chimera forum. > > I have a question related to compounds and I appreciate your > valuable oppions. > > Let's say I have compound A and compund B. Both have strucctures. > > I would like to use a moiety (part) of compound A and a moeity > (part) of compound B. I wonder if Chimera can combine the desired > moeities of compound A and compound B to generate a new compound C. > > Another simpler version. Can Cimera merge compound A and > compound B into compound D ? > > I checked Chimera list but I found that Chimera provides a > function of joining models NOT for "compounds/drugs" but rather for > "Proteins". I also see you made comments in the past. I wonder if > you can provide insights into "compounds" or some hints to allow me > working on compounds in Chimera. > Many thanks, > Dwey

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obj file origin
by Erin Cutts 08 Nov '15

08 Nov '15

I am trying to use the .obj file generated as a surface mesh. Where the chimera outputs it as a list of vertices (points in 3D), a list of nomals (which I ignore) and a list of faces defined by 3 vertex reference numbers, it is super easy to import this into any mesh handling software. The problem is it seems to reset the orgin (the 0,0,0 point) to some mysterious location. As I am trying to compare this to electrostatics stored in a grid mesh format, where the orgin is specified, it would be nice if I could find out where the .obj has translated the axis coordinates too... The problem could also be caused by Chimera loading the molecule with a translation. All this gets very hard to deal with and trace...Any ideas that doesn't lead to me getting lost in cartesian space?

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3D dashed pseudobond styles?
by Oliver Clarke 07 Nov '15

07 Nov '15

Hi all, Feature request - more 3D psuedobond styles (for missing segments and metal coordination) would be nice. Specifically, small spheres (3D equivalent of dotted line) and cylinders with either rounded or flat ends (3D equivalent of dashed lines) would be very helpful. Often when used in combination with 3X3 or 4X4 supersampling, pseudobonds drawn in wire representation become too thin to see, whereas this is not the case for bonds or other 3D elements of the structure. Normally this doesn’t matter, because I can just redraw these bonds in a vector graphics program, but for stereo figures this doesn’t work. There is already one such option (representing pseudo bonds as sticks), but this looks weird - dashing or dotting is I think desirable to avoid confusion with regular bonds. Also, is there any way to add a custom pseudo bond (not a distance, no label) between a single pair of selected atoms? Similar to the dist command? This would be very helpful, for example, when trying to highlight a handful of specific interactions of a ligand with active site residues. One more while I’m thinking of it - a bit out there and certainly not for chimera 1 - it would be great to have a way of arranging 3D labels for residues such that they are displaced from the structure (perhaps arranged in a circle on the x-y plane), but with lines or arrows connecting them back to the residues they are labeling - this would be particularly great for generating labeled stereo figures, which is otherwise hard to do. Cheers, Oliver.

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resmap
by R.I.Koning＠lumc.nl 05 Nov '15

05 Nov '15

I want to use the colors representing resolution in Resmap to color the surface of my map. From what I understand from the documentation the script that automatically runs after Resmap is finished and “… color the surface of your input map with the results of ResMap…”. This last thing does not happen. Though this script seems to run (I see a slice depicting the remap (in 2D) moving back and forth in chimera somehow only a map with 1 slice opens in Chimera afterwards and I cannot use the resolution color coding for my surface. Should some sort of 3D file be generated that can be used to do this via Surface color or should the coloring be on the surface map by default? Both is not possible now. Best regards, Roman

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Using pip/easy install in Python 2.7.8 included in Chimera
by Ahir Pushpanath 05 Nov '15

05 Nov '15

Dear Chimera Team, As I specifically want to use the python included with chimera as the main python distribution available on my system, I am limited to using the python version shipped with it, as a standard. This is no problem for me, however, I am struggling to get pip /easy install working with the inbuilt python, namely because of errors between "urllib3" and python versions below 2.7.10. So, I keep getting HTTPS errors. Is there any way to use pip and easy install properly with the inbuilt Chimera Python? I did see a section called "import python modules into Chimera", but it appears as though that requires an additional python distribution to be present on the system? Please do let me know. Ahir If the reader of this email is not the intended recipient(s), please be advised that any dissemination, distribution or copying of this information is strictly prohibited. Johnson Matthey Plc has its main place of business at 5th Floor, 25 Farringdon Street, London (020 7269 8400). Johnson Matthey Public Limited Company Registered Office: 5th Floor, 25 Farringdon Street, London EC4A 4AB Registered in England No 33774 Whilst Johnson Matthey aims to keep its network free from viruses you should note that we are unable to scan certain emails, particularly if any part is encrypted or password-protected, and accordingly you are strongly advised to check this email and any attachments for viruses. The company shall not accept any liability with regard to computer viruses transferred by way of email. Please note that your communication may be monitored in accordance with Johnson Matthey internal policy documentation.

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Append PDB file to all individual PDB chains
by Carl Brown 04 Nov '15

04 Nov '15

To Whom This May Concern: In previous discussions, you explained how you could append two PDB files through the "join models" function: Discussion: <http://www.cgl.ucsf.edu/pipermail/chimera-users/2011-April/006245.html> Build Structure: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.ht…> I would like attach a second PDB file to an initial one as well. However, my primary PDB file is a tetramer, made up of four identical chains. I would like to attach the second PDB to each of the four chains at the C-terminus. Is this possible? If so, how would I go about this? My concern is that using the "join models" function, it will only append the second PDB file once to the whole structure instead of to each individual chain. Cheers, Carl

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Open .pse file in Chimera?
by Desiree Benefield 04 Nov '15

04 Nov '15

Dear all, I have a .pse file generated with MacPyMOL that I would like to try to dock into a EM density map using Chimera. It would appear that this is not possible. Can you offer any advice or alternative approaches to try? With many thanks, Dez

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Silhouettes and depth cueing
by Oliver Clarke 02 Nov '15

02 Nov '15

Hi all, I’ve noticed that the intensity/color of silhouettes does not vary with depth cueing the way everything else does - normally this is fine, except when one is showing a slab of a structure - fragments of secondary structural elements which would otherwise blend into the background tend to become overly emphasized by the presence of silhouettes. The obvious solution to this for now is to turn off silhouettes when making these kinds of figures, but I quite like the effect that silhouettes provide, so I would rather not do so if there is an alternative. Perhaps in Chimera 2 it may be worth considering applying a depth dependent factor to the silhouette color (so it fades into the background color as it approaches the yon clipping plane)? Cheers, Oliver.

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