[Chimera-users] Distance tool: Line thickness of the number (of angstroms) in the picture

Boaz Shaanan bshaanan at bgu.ac.il
Sat Oct 21 04:31:13 PDT 2017


Hi,

The number that shows up after creating a distance is very thin and can hardly be seen. I couldn't find how to make it thicker (I did change the actual line thickness in the menu). I also tried in the preference menu that you pointed to a user a while ago but it didn't work for me. How can I change it? This is on the Windows 64b nightly build from 17 October. Thanks.
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  Skype: boaz.shaanan
Fax:   972-8-647-2992 or 972-8-646-1710





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Today's Topics:

   1. Re: Trouble with Volume surface and active model not aligned
      (Elaine Meng)
   2. Re: Selecting residues in chains defined by segname
      (Francesco Pietra)
   3. Re: Selecting residues in chains defined by segname (Elaine Meng)
   4. Re: Trouble with Volume surface and active model not aligned
      (Phan Trieu Truong)


----------------------------------------------------------------------

Message: 1
Date: Fri, 20 Oct 2017 13:41:34 -0700
From: Elaine Meng <meng at cgl.ucsf.edu>
To: Phan Trieu Truong <truongp at uga.edu>
Cc: "chimera-users at cgl.ucsf.edu" <chimera-users at cgl.ucsf.edu>
Subject: Re: [Chimera-users] Trouble with Volume surface and active
        model not aligned
Message-ID: <5596D972-35F9-4643-8CDB-6F7D4DE590FD at cgl.ucsf.edu>
Content-Type: text/plain; charset=utf-8

Hi Phan,
I?m not sure what happened either, since your images show the ?A? (active for motion) boxes in the Model Panel are checked for both the molecule and the orbitals, meaning that using the mouse should move both of them together.

You could try command:
reset
? to put them back together.

If that doesn?t work, you may have to start over by quitting and reopening the files.  However, if you didn?t uncheck the ?A? boxes or the ?Active models? boxes below the Command Line, mouse movements should always move them both together.  Maybe you accidentally had one of the A(ctive) boxes unchecked and moved the other model.  In that case, reset will work.
I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco




> On Oct 20, 2017, at 8:57 AM, Phan Trieu Truong <truongp at uga.edu> wrote:
>
> Hi,
>
> I have been using Chimera to visualize MO orbital on molecules from ORCA calculations. I have been able to visualize the MO orbitals as a surface volume from cube files. However, I just found out that when I try to reorient the molecule with the surface volume, they are no longer aligned. I don't know what I did to cause this. Any help is much appreciated.
>
> Attached is the picture of the molecules before and after I tried to reorient the molecule with the surface volume.
>
> Thank you,
> Phan
> <Before and after reorientation.jpg.png>_______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users




------------------------------

Message: 2
Date: Fri, 20 Oct 2017 23:37:32 +0200
From: Francesco Pietra <chiendarret at gmail.com>
To: Eric Pettersen <pett at cgl.ucsf.edu>
Cc: chimera <chimera-users at cgl.ucsf.edu>
Subject: Re: [Chimera-users] Selecting residues in chains defined by
        segname
Message-ID:
        <CAEv0nmsDA8dd+hQ8H_t9uK8-LntPucKQ7UiiqVybva3XWdBgjA at mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

A pity, in my view. As more and more complex proteins are being examined
(thanks to faster clusters), working without segname would be practically
impossible in  the frame of today pdb files. For example, how visualizing
the trajectory of a particular ligand in a 24-chain protein assembly? I can
do that with vmd, but at the price of a less clear-cut trajectory and
poorer graphics.
But I understand that there may be different viewpoints.
Cheers
francesco

On Fri, Oct 20, 2017 at 8:36 PM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:

> Realistically no.  Too many other priorities.  The gap will eventually get
> filled in in ChimeraX, but even that will be awhile.
>
> ?Eric
>
> On Oct 19, 2017, at 1:24 PM, Francesco Pietra <chiendarret at gmail.com>
> wrote:
>
> Hi Eric:
>
> Any plan to fill this gap?
>
> thanks
>
> francesco
>
> On Thu, Oct 19, 2017 at 7:59 PM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:
>
>> Hi Francseco,
>> Unfortunately, segment IDs are not preserved by the trajectory reader.
>>
>> ?Eric
>>
>> Eric Pettersen
>> UCSF Computer Graphics Lab
>>
>>
>> On Oct 19, 2017, at 9:53 AM, Francesco Pietra <chiendarret at gmail.com>
>> wrote:
>>
>> Hi Elaine:
>> While, as I wrote, the commands for segname did work fine with .psf/.pdb
>> namd files,
>> in contrast, with .psf/.dcd files (movie)
>>
>> select @/pdbSegment=C1
>>
>> selects all chains of the protein assembly, including ligands. The same
>> occurs with
>>
>> select @/pdbSegment=O2C1
>>
>> where O2C1 is the segname of the molecule dioxygen associated with chain.
>>
>> This occurs both on my desktop and on a large-memory nextscale cluster on
>> remote visualization (the latter is the actual interest)
>>
>> Do you know of any remedy?
>>
>> thanks a lot
>>
>> francesco
>> ---------- Forwarded message ----------
>> From: Francesco Pietra <chiendarret at gmail.com>
>> Date: Mon, Oct 16, 2017 at 7:12 PM
>> Subject: Re: [Chimera-users] Selecting residues in chains defined by
>> segname
>> To: UCSF Chimera Mailing List <chimera-users at cgl.ucsf.edu>
>>
>>
>> Hi Elaine:
>>
>> Great!
>>
>> thank you
>> francesco
>>
>> On Mon, Oct 16, 2017 at 5:58 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>>
>>> Hi Francesco,
>>> The symbol for intersection is ?&? ... in other words, you could use
>>>
>>> select :17 & @/pdbSegment=A1
>>>
>>> Intersection and union symbols are explained here:
>>> <http://www.rbvi.ucsf.edu/home/meng/docs/UsersGuide/midas/at
>>> om_spec.html#combinations>
>>>
>>> I hope this helps,
>>> Elaine
>>>
>>> > On Oct 16, 2017, at 12:29 AM, Francesco Pietra <chiendarret at gmail.com>
>>> wrote:
>>> >
>>> > Hi Elaine:
>>> > That works fine. However, I was unable to extend your suggestions to
>>> pick up a specific residue within a specific chain. Neither "select :17
>>> @/pdbSegment=A1" nor "select @/pdbSegment=A1 :17" are valid commands
>>> (obviously expected).
>>> >
>>> > On the other hand, with such complex situations, it is Xplor, with its
>>> segname features, that helps.
>>> >
>>> > Should you need a pdb fine with segname, I could attach a simple one,
>>> with a single chain.
>>> >
>>> > On Sun, Oct 15, 2017 at 8:04 PM, Elaine Meng <meng at cgl.ucsf.edu>
>>> wrote:
>>> > Hi Francesco,
>>> > Although I don?t have an example file with segnames to try myself, I?m
>>> told you can specify by the atom attribute pdbSegment, e.g.
>>> >
>>> > select @/pdbSegment=A1
>>> > color red @/pdbSegment=F3
>>> >
>>> > I hope this helps,
>>> > Elaine
>>> >
>>> > > On Oct 15, 2017, at 10:40 AM, Francesco Pietra <
>>> chiendarret at gmail.com> wrote:
>>> > >
>>> > > Hi Elaine:
>>> > >
>>> > > I am referring to Oct 28, 2005, at 9:50 AM, Eric Gillitzer wrote:
>>> > >  and your answer:
>>> > >
>>> > > command: select :45.a-d > or > command: select :45.* > > Or, to
>>> select residue 45 in just chains A and D: > > command: select :45.a,45.d
>>> > >
>>> > > I have a more complex case, where chains are defined by segname,
>>> > > for example
>>> > >
>>> > > A1 A2 A3 A4 A5 etc
>>> > >
>>> > > while the standard PDB definition is "A" for all them.
>>> > >
>>> > > The same for standard "B", "C" etc.
>>> > >
>>> > > As I want to display a movie of ligand pathways, where the ligand
>>> > > moves from, say, "A1" to, say, "F3", I want in the first instance
>>> > > become able to select particular residues in particular chains,
>>> > > as defined by their segname.
>>> > >
>>> > > Could you imagine a simple way not requiring selection by atom
>>> numbers?
>>> > > Thanks
>>> > > francesco pietra
>>> >
>>> >
>>> > _______________________________________________
>>> > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
>>> > Manage subscription: http://plato.cgl.ucsf.edu/mail
>>> man/listinfo/chimera-users
>>>
>>>
>>
>> _______________________________________________
>> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
>> Manage subscription: http://plato.cgl.ucsf.edu/mail
>> man/listinfo/chimera-users
>>
>>
>>
>
>
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------------------------------

Message: 3
Date: Fri, 20 Oct 2017 14:49:57 -0700
From: Elaine Meng <meng at cgl.ucsf.edu>
To: Francesco Pietra <chiendarret at gmail.com>
Cc: chimera <chimera-users at cgl.ucsf.edu>
Subject: Re: [Chimera-users] Selecting residues in chains defined by
        segname
Message-ID: <9F9FC1BD-E897-4F94-9F27-B8B1C2C7A3F0 at cgl.ucsf.edu>
Content-Type: text/plain; charset=utf-8

Hi Francesco,
Is it not possible to specify the ligand without using the segname?   You can use residue number, chain number, residue name?  are you saying that there is more than one residue in the same chain with both the same name and the same number?
Elaine

> On Oct 20, 2017, at 2:37 PM, Francesco Pietra <chiendarret at gmail.com> wrote:
>
> A pity, in my view. As more and more complex proteins are being examined (thanks to faster clusters), working without segname would be practically impossible in  the frame of today pdb files. For example, how visualizing the trajectory of a particular ligand in a 24-chain protein assembly? I can do that with vmd, but at the price of a less clear-cut trajectory and poorer graphics.
> But I understand that there may be different viewpoints.
> Cheers
> francesco
>
> On Fri, Oct 20, 2017 at 8:36 PM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:
> Realistically no.  Too many other priorities.  The gap will eventually get filled in in ChimeraX, but even that will be awhile.
>
> ?Eric
>
>> On Oct 19, 2017, at 1:24 PM, Francesco Pietra <chiendarret at gmail.com> wrote:
>>
>> Hi Eric:
>>
>> Any plan to fill this gap?
>>
>> thanks
>>
>> francesco
>>
>> On Thu, Oct 19, 2017 at 7:59 PM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:
>> Hi Francseco,
>>      Unfortunately, segment IDs are not preserved by the trajectory reader.
>>
>> ?Eric
>>
>>      Eric Pettersen
>>      UCSF Computer Graphics Lab
>>
>>
>>> On Oct 19, 2017, at 9:53 AM, Francesco Pietra <chiendarret at gmail.com> wrote:
>>>
>>> Hi Elaine:
>>> While, as I wrote, the commands for segname did work fine with .psf/.pdb namd files,
>>> in contrast, with .psf/.dcd files (movie)
>>>
>>> select @/pdbSegment=C1
>>>
>>> selects all chains of the protein assembly, including ligands. The same occurs with
>>>
>>> select @/pdbSegment=O2C1
>>>
>>> where O2C1 is the segname of the molecule dioxygen associated with chain.
>>>
>>> This occurs both on my desktop and on a large-memory nextscale cluster on remote visualization (the latter is the actual interest)
>>>
>>> Do you know of any remedy?
>>>
>>> thanks a lot
>>>
>>> francesco
>>> ---------- Forwarded message ----------
>>> From: Francesco Pietra <chiendarret at gmail.com>
>>> Date: Mon, Oct 16, 2017 at 7:12 PM
>>> Subject: Re: [Chimera-users] Selecting residues in chains defined by segname
>>> To: UCSF Chimera Mailing List <chimera-users at cgl.ucsf.edu>
>>>
>>>
>>> Hi Elaine:
>>>
>>> Great!
>>>
>>> thank you
>>> francesco
>>>
>>> On Mon, Oct 16, 2017 at 5:58 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>>> Hi Francesco,
>>> The symbol for intersection is ?&? ... in other words, you could use
>>>
>>> select :17 & @/pdbSegment=A1
>>>
>>> Intersection and union symbols are explained here:
>>> <http://www.rbvi.ucsf.edu/home/meng/docs/UsersGuide/midas/atom_spec.html#combinations>
>>>
>>> I hope this helps,
>>> Elaine




------------------------------

Message: 4
Date: Fri, 20 Oct 2017 21:05:37 +0000
From: Phan Trieu Truong <truongp at uga.edu>
To: chimera <chimera-users at cgl.ucsf.edu>
Subject: Re: [Chimera-users] Trouble with Volume surface and active
        model not aligned
Message-ID:
        <SN4PR0201MB3616BC42A32496EDB8B242EBB6430 at SN4PR0201MB3616.namprd02.prod.outlook.com>

Content-Type: text/plain; charset="windows-1252"

Hi Elaine,


I have tried the "reset" command. It works. Thank you very much!


Phan

________________________________
From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: Friday, October 20, 2017 4:41:34 PM
To: Phan Trieu Truong
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] Trouble with Volume surface and active model not aligned

Hi Phan,
I?m not sure what happened either, since your images show the ?A? (active for motion) boxes in the Model Panel are checked for both the molecule and the orbitals, meaning that using the mouse should move both of them together.

You could try command:
reset
? to put them back together.

If that doesn?t work, you may have to start over by quitting and reopening the files.  However, if you didn?t uncheck the ?A? boxes or the ?Active models? boxes below the Command Line, mouse movements should always move them both together.  Maybe you accidentally had one of the A(ctive) boxes unchecked and moved the other model.  In that case, reset will work.
I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco




> On Oct 20, 2017, at 8:57 AM, Phan Trieu Truong <truongp at uga.edu> wrote:
>
> Hi,
>
> I have been using Chimera to visualize MO orbital on molecules from ORCA calculations. I have been able to visualize the MO orbitals as a surface volume from cube files. However, I just found out that when I try to reorient the molecule with the surface volume, they are no longer aligned. I don't know what I did to cause this. Any help is much appreciated.
>
> Attached is the picture of the molecules before and after I tried to reorient the molecule with the surface volume.
>
> Thank you,
> Phan
> <Before and after reorientation.jpg.png>_______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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