[Chimera-users] Regarding the UNDO issue raised by Luca
Boaz Shaanan
bshaanan at bgu.ac.il
Thu Nov 28 06:27:22 PST 2019
Hi,
Is not possible to install an automatic 'save session' at intervals determined by the user just as done in an MS word session? This at least may rescue the last operations. Following my own Chimera 'disasters' of this kind, I actually save session quite frequently when it becomes heavily loaded, particularly prior to a major new operation. My 2p.
Happy and warm Thanksgiving.
Boaz
Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel
E-mail: bshaanan at bgu.ac.il
Phone: 972-8-647-2220
Fax: 972-8-647-2992 or 972-8-646-1710
________________________________________
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Subject: Chimera-users Digest, Vol 199, Issue 25
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Today's Topics:
1. secondary structure restraints and crosslink restraints
(Fr?nze M?ller)
2. Undo option? (Luca Pellegrini)
3. Re: Undo option? (Elaine Meng)
4. Re: secondary structure restraints and crosslink restraints
(Elaine Meng)
5. Re: Auto-associate define attribute/render by attribute
(Elaine Meng)
----------------------------------------------------------------------
Message: 1
Date: Wed, 27 Nov 2019 13:50:32 +0100
From: Fr?nze M?ller <fraenze.mueller at biologie.uni-freiburg.de>
To: chimera-users at cgl.ucsf.edu
Subject: [Chimera-users] secondary structure restraints and crosslink
restraints
Message-ID:
<cde7ad0e-503b-b0cc-5466-006d64019f5a at biologie.uni-freiburg.de>
Content-Type: text/plain; charset="utf-8"; Format="flowed"
Dear Chimera developers,
I would like to perform homology modelling using Modeller in Chimera. At
the moment I am using just distance restraints formatted like in the
Chimera documentation (res1 res2 dist stdev). This file only contains
crosslinking data. Is there a way to also include secondary structure
restraints, that can serve as additional information during homology
modelling? Or can I provide some were another file including this
information separate from the crosslink information?
Best wishes and Thanks for your help,
--
*Fr?nze M?ller*
Postdoctoral Researcher
*Biochemistry and Functional Proteomics, Warscheid Lab*
University of Freiburg|Sch?nzlestr. 1|79104 Freiburg|Germany
Phone +49 761 203 2681
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Message: 2
Date: Wed, 27 Nov 2019 15:27:08 +0000
From: Luca Pellegrini <lp212 at cam.ac.uk>
To: chimera-users at cgl.ucsf.edu
Subject: [Chimera-users] Undo option?
Message-ID: <EF35376C-EB8A-4235-998D-CE315333F593 at cam.ac.uk>
Content-Type: text/plain; charset=utf-8
I was wondering if there are any plans for an Undo option? I just managed to wipe a detailed view of an active site with lots of side chains, by selecting one more amino acid on the ribbon drawing and then picking by mistake ?show only? rather than ?show? (slip of the finger).
ps: I found an old post on this in 2004, explaining that there is no such option, but perhaps the Chimera authors are open to changing their mind? After all, we are using Chimera to make ever more complex drawings.
Best wishes,
Luca
Luca Pellegrini, PhD
Department of Biochemistry
University of Cambridge
Cambridge CB2 1GA
United Kingdom
lp212 at cam.ac.uk
tel.: 0044 1223 760469
https://www.bioc.cam.ac.uk/pellegrini-group/pellegrini-group
@PellegriniLab
------------------------------
Message: 3
Date: Wed, 27 Nov 2019 12:32:44 -0800
From: Elaine Meng <meng at cgl.ucsf.edu>
To: Luca Pellegrini <lp212 at cam.ac.uk>
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] Undo option?
Message-ID: <870DFA7C-C511-4C00-8052-E14E9F4798D0 at cgl.ucsf.edu>
Content-Type: text/plain; charset=utf-8
Hi Luca,
We have all done similar things? very sorry! Despite its importance and usefulness, it is a big task to add undo support, and we are now devoting resources to ChimeraX development rather than Chimera.
We are working on undo for ChimeraX. It is somewhat limited, but we intend for most common display, style, and coloring changes to be undoable. Current ?undo? description in ChimeraX:
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/undo.html
Best,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco
> On Nov 27, 2019, at 7:27 AM, Luca Pellegrini <lp212 at cam.ac.uk> wrote:
>
> I was wondering if there are any plans for an Undo option? I just managed to wipe a detailed view of an active site with lots of side chains, by selecting one more amino acid on the ribbon drawing and then picking by mistake ?show only? rather than ?show? (slip of the finger).
>
> ps: I found an old post on this in 2004, explaining that there is no such option, but perhaps the Chimera authors are open to changing their mind? After all, we are using Chimera to make ever more complex drawings.
>
> Best wishes,
> Luca
------------------------------
Message: 4
Date: Wed, 27 Nov 2019 12:42:18 -0800
From: Elaine Meng <meng at cgl.ucsf.edu>
To: Fr?nze M?ller <fraenze.mueller at biologie.uni-freiburg.de>
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] secondary structure restraints and
crosslink restraints
Message-ID: <99AC7120-A7CA-4A0F-9F83-1D8102CE3684 at cgl.ucsf.edu>
Content-Type: text/plain; charset=utf-8
Dear Fr?nze M?ller,
The Modeller interface in Chimera was meant to be simple, which means easy to use, but also not including many things that are possible when using Modeller directly. The Modeller interface in Chimera just allows specifying template structure(s) and optionally, the distance restraints you mention. There must be some secondary structure knowledge used at least indirectly via the template secondary structure, but I do not have a detailed understanding of how that works? you?d have to look in the Modeller documentation. There is no option for additional files/types of restraints in the interface from Chimera, however.
All the options in our interface to Modeller are described in the User Guide:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/modeller.html>
Best,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco
> On Nov 27, 2019, at 4:50 AM, Fr?nze M?ller <fraenze.mueller at biologie.uni-freiburg.de> wrote:
>
> Dear Chimera developers,
> I would like to perform homology modelling using Modeller in Chimera. At the moment I am using just distance restraints formatted like in the Chimera documentation (res1 res2 dist stdev). This file only contains crosslinking data. Is there a way to also include secondary structure restraints, that can serve as additional information during homology modelling? Or can I provide some were another file including this information separate from the crosslink information?
>
> Best wishes and Thanks for your help,
> --
> Fr?nze M?ller
> Postdoctoral Researcher
>
------------------------------
Message: 5
Date: Wed, 27 Nov 2019 13:07:27 -0800
From: Elaine Meng <meng at cgl.ucsf.edu>
To: "Healey, Joseph" <J.Healey.1 at warwick.ac.uk>
Cc: "chimera-users at cgl.ucsf.edu BB" <chimera-users at cgl.ucsf.edu>
Subject: Re: [Chimera-users] Auto-associate define attribute/render by
attribute
Message-ID: <B13E40B0-11D7-4CB6-90C1-8C8516BD8D6D at cgl.ucsf.edu>
Content-Type: text/plain; charset="utf-8"
Hi Joe,
Those chains are two different sequences.
Pvc12 is chains P,Q,R,S,T,U with >900 positions in the sequence
Pvc4 is chains V,W,X,Y,Z,a with 410 positions in the sequence
So I can load the headers from your file for the former sequences (I tried chain T) but not the latter, because your file specifies up to position 436.
Python is beyond my skill set, though? somebody else would have to advise on that.
An aside: I note that it was much easier to tell which chains are the same sequence as each other in ChimeraX, which is also a lot faster on big structures like this. Unfortunately we don?t yet have it reading custom header files or making the headers into attributes, or else I would suggest using ChimeraX instead. Below is a screenshot from opening 6j0n in ChimeraX and clicking the ?Pvc12? and ?Pvc4? links in the Chain Description table that automatically appears when the file is opened.
Best,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco
> On Nov 27, 2019, at 1:43 AM, Healey, Joseph <J.Healey.1 at warwick.ac.uk> wrote:
>
> Hi Elaine,
>
> Thank you for clarifying, I had missed the option for any atom-spec (I was following one of the examples but there didn't appear to be one addressing chains). As you say, this still requires some a priori knowledge of 'what's what' in the structures though. An added complication is that the structures are grouped in to a single model, and need to be split to be treated as different models (though I suppose in practice this makes little difference as its either a case of specifying a chain or a model).
>
> Consequently, this is why I was hoping that sequence-based auto-assignment could be possible. The sequence/alignment headers looks like they have potential, but this leads me to another 2 questions:
>
> - So far, it is complaining that the numeric values I'm using are less than one or greater than the alignment length. The data appears to possibly be longer than the structure (but is shorter than the corresponding gene sequence) so I assume some residues are not present in the mature structure. However, it complains about Position 402 of the file, which should still be in the structure displayed as far as I can tell.According to the docs, numeric values that fall outside [0, 1] should be converted for the histogram, but retained as attributes, so I don't think the numeric values are an issue. Any idea why Chimera is complaining? I've attached the header file I'm using. The model in question is PDB 6j0n (chains T, U, V, W, X, Y).
>
> - Secondly, what would be the equivalent python/chimera command interface for loading header files such that I can render them by these attributes (the latter of which I'm already au fait with).
>
> Thanks again,
>
> Joe
>
>
>> On Nov 26, 2019, at 7:40 AM, Healey, Joseph <J.Healey.1 at warwick.ac.uk> wrote:
>>
>> Hi Chimera team,
>> I?m working on a script to automatically render proteins in a complex by attributes (in this case, a number of scores obtained from different immunogenicity prediction algorithms). I currently have the script outputting attribute files as intended, but ideally I?d like to define the same attributes across all the chains of the model, which are made up of a number of different proteins.
>>
>> Is there any way for me to define the attribute file, or utilise some functionality to auto-associate an attribute file with all of the chains which have the correct sequence (similarly to how the sequence alignment input works at the moment?). Currently the attribute file is only using ?numbered? coordinates (:1, :2, :3?etc) , rather than the actual sequence.
>>
>> Since there?s no chain information in the attribute files, I?m not sure how I can go about connecting it to the right structure, other than manually at the moment?
>> Many thanks,
>> Joe
>
>
>
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