[Chimera-users] Gap between C=O mainchain bond and supersmooth ribbon
Dr. Jean-Didier Maréchal
jeandidier.marechal at gmail.com
Fri Mar 6 02:41:12 PST 2009
Dear all,
I want to represent the C=O bond that chelates an ion in my structure and
the rest of the prot in ribbon (supersmooth). I don't want the carbon
explicitly represented but yes the bond and the oxygen with a ball and stick
representation. Following a previous post, I have two copies of my model.
One is represented in ribbon. In the other one, I have the oxygen in bs and
for the bond I did "bonddisplay always #1:22 at C,O". It does pretty much what
I want but I see that in many cases I have a empty gap between the end of
the bond and the ribbon. Something I don't want. Is there a way to remove
this gap? Or should I always represent the carbon also (something I find
less esthetic that the other option).
All the best,
JD
-----Mensaje original-----
De: chimera-users-bounces at cgl.ucsf.edu
[mailto:chimera-users-bounces at cgl.ucsf.edu] En nombre de
chimera-users-request at cgl.ucsf.edu
Enviado el: viernes, 06 de marzo de 2009 5:16
Para: chimera-users at cgl.ucsf.edu
Asunto: Chimera-users Digest, Vol 71, Issue 6
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Today's Topics:
1. (no subject) (Du, Sean)
2. Re: (no subject) (Elaine Meng)
3. Re: (no subject) (Eric Pettersen)
4. Re: Issue with surface modelling using Chimera (Elaine Meng)
5. saving a rotated map (Scott Stagg)
6. Re: saving a rotated map (Gabriel Lander)
----------------------------------------------------------------------
Message: 1
Date: Thu, 5 Mar 2009 14:08:39 -0800
From: "Du, Sean" <Sean.Du at maxygen.com>
Subject: [Chimera-users] (no subject)
To: <chimera-users at cgl.ucsf.edu>
Message-ID:
<3A581C9EE7D7DF43ACE4FAA43592FAEC07B3542B at rc-ga-mail-1.mxygn.com>
Content-Type: text/plain; charset="us-ascii"
Dear Chimera developers and sophisticated users,
I have trouble to show the surfaces of serveral crystal structures,
including 1rzk and 2b4c. Whenever I select: Action/Surface/Show, I would
get pop-up error window and the following message in my Reply Log:
C:\Program Files\Chimera\bin\mscalc.exe 1.400000 2.000000 0
Surface calculation failed, mscalc returned code 5
C:\Program Files\Chimera\bin\mscalc.exe 1.400000 2.000000 0
Surface calculation failed, mscalc returned code 5
Since I don't have problem with other pdb files, such as 3dnn, I wonder
if this problem is simply associated with some particular pdb files? If
anyone out there knows a few tricks to overcome this, I'd really
appreciate it.
Many thanks in advance,
Sean
----------------------------------------------
Sean Du, Ph.D.
Senior Scientist, Project Leader
Maxygen, Inc.
515 Galveston Drive
Redwood City, CA 94063
Office: (650) 298-5380
Cell: (510) 366-3586
-----------------------------------------------
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Message: 2
Date: Thu, 5 Mar 2009 16:34:11 -0800
From: Elaine Meng <meng at cgl.ucsf.edu>
Subject: Re: [Chimera-users] (no subject)
To: "Du, Sean" <Sean.Du at maxygen.com>
Cc: chimera-users at cgl.ucsf.edu
Message-ID: <6EEB308A-2329-4F61-8E92-91348D21BA06 at cgl.ucsf.edu>
Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
Dear Sean,
Unfortunately it is a very common problem relating to numerical
failure of the MSMS code on certain structures, and is listed in our
known bugs. We have been working on our own code to replace MSMS, but
it is not available yet. There are many possible things to try to
avoid the problem, but it is very trial-and-error and different for
each structure.
It is helpful when reporting a problem to say what version of Chimera
you are using, since there have been some improvements throughout time
(although not eliminating the problem completely). It might help to
get a newer version of Chimera, or it might not.
Please see these previous posts for more information and workaround
suggestions:
<http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-September/003096.html
>
<http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-March/002417.html>
<http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-August/
002954.html>
I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
http://www.cgl.ucsf.edu/home/meng/index.html
On Mar 5, 2009, at 2:08 PM, Du, Sean wrote:
> Dear Chimera developers and sophisticated users,
>
> I have trouble to show the surfaces of serveral crystal structures,
> including 1rzk and 2b4c. Whenever I select: Action/Surface/Show, I
> would get pop-up error window and the following message in my Reply
> Log:
>
> C:\Program Files\Chimera\bin\mscalc.exe 1.400000 2.000000 0
> Surface calculation failed, mscalc returned code 5
> C:\Program Files\Chimera\bin\mscalc.exe 1.400000 2.000000 0
> Surface calculation failed, mscalc returned code 5
>
> Since I don't have problem with other pdb files, such as 3dnn, I
> wonder if this problem is simply associated with some particular pdb
> files? If anyone out there knows a few tricks to overcome this, I'd
> really appreciate it.
>
> Many thanks in advance,
>
> Sean
>
>
------------------------------
Message: 3
Date: Thu, 5 Mar 2009 16:51:02 -0800
From: Eric Pettersen <pett at cgl.ucsf.edu>
Subject: Re: [Chimera-users] (no subject)
To: "Du, Sean" <Sean.Du at maxygen.com>
Cc: "chimera-users at cgl.ucsf.edu BB" <chimera-users at cgl.ucsf.edu>
Message-ID: <634220BC-4C50-4639-8D86-59719265517F at cgl.ucsf.edu>
Content-Type: text/plain; charset="us-ascii"
Hi Sean,
I find that these structures surface on my Mac, but do fail on the
Windows machine I tried. There is a workaround I recently found that
isn't mentioned in the messages Elaine listed and that is to split the
model into separate models on a per-chain basis and then surface those
models. This works for both the structures your mentioned, but of
course might be awkward to work with depending on what you intend to
do after surfacing. Anyway, to do the splitting/surfacing open the
command line (Favorites->Command Line) and type:
split
surf
We intend to replace our current surfacing library (MSMS) with our
own custom library in our next release, but that won't be until the
middle of this year.
--Eric
Eric Pettersen
UCSF Computer Graphics Lab
http://www.cgl.ucsf.edu
On Mar 5, 2009, at 4:34 PM, Elaine Meng wrote:
> Dear Sean,
> Unfortunately it is a very common problem relating to numerical
> failure of the MSMS code on certain structures, and is listed in our
> known bugs. We have been working on our own code to replace MSMS, but
> it is not available yet. There are many possible things to try to
> avoid the problem, but it is very trial-and-error and different for
> each structure.
>
> It is helpful when reporting a problem to say what version of Chimera
> you are using, since there have been some improvements throughout time
> (although not eliminating the problem completely). It might help to
> get a newer version of Chimera, or it might not.
>
> Please see these previous posts for more information and workaround
> suggestions:
>
>
<http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-September/003096.html
>>
> <http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-March/002417.html
> >
> <http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-August/
> 002954.html>
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> http://www.cgl.ucsf.edu/home/meng/index.html
>
>
>
> On Mar 5, 2009, at 2:08 PM, Du, Sean wrote:
>
>> Dear Chimera developers and sophisticated users,
>>
>> I have trouble to show the surfaces of serveral crystal structures,
>> including 1rzk and 2b4c. Whenever I select: Action/Surface/Show, I
>> would get pop-up error window and the following message in my Reply
>> Log:
>>
>> C:\Program Files\Chimera\bin\mscalc.exe 1.400000 2.000000 0
>> Surface calculation failed, mscalc returned code 5
>> C:\Program Files\Chimera\bin\mscalc.exe 1.400000 2.000000 0
>> Surface calculation failed, mscalc returned code 5
>>
>> Since I don't have problem with other pdb files, such as 3dnn, I
>> wonder if this problem is simply associated with some particular pdb
>> files? If anyone out there knows a few tricks to overcome this, I'd
>> really appreciate it.
>>
>> Many thanks in advance,
>>
>> Sean
>>
>>
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
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Message: 4
Date: Thu, 5 Mar 2009 16:52:12 -0800
From: Elaine Meng <meng at cgl.ucsf.edu>
Subject: Re: [Chimera-users] Issue with surface modelling using
Chimera
To: Leiah Luoma <lluoma at ualberta.ca>
Cc: chimera-users at cgl.ucsf.edu
Message-ID: <06674585-12C3-4409-AE8F-098507154F17 at cgl.ucsf.edu>
Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
Dear Leiah,
It is hard to tell without looking at your data file. However, here
is my best guess: maybe your file has long "bonds" that shouldn't be
there at all (maybe there should be TER lines in your file, or maybe
it has incorrect CONECT lines). When you show the surface it doesn't
enclose the lines because there are no atoms there. However, I can't
get this to happen in Chimera in my tests, so maybe your file is
incorrect in some way that makes it different from my missing segment
test case 1www (taken from the PDB, so it has correct format).
Best,
Elaine
-----
Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
http://www.cgl.ucsf.edu/home/meng/index.html
On Mar 5, 2009, at 2:03 PM, Leiah Luoma wrote:
> Hi there,
>
> I'm in the middle of using Chimera to analyze my protein model and
> want to look at the predicted surface. I cannot get it to show the
> whole surface: a few tracts of ribbon structure pepper the model.
>
> I selected all from the drop down menu, and waited until the whole
> model was highlighted, and then set it to show surface. When I
> select the regions which are not showing up, and try to surface
> model them individually, it does not work either.
>
> Is there any solution, or some reason why this would happen? The
> tracts are between 2 and 5 amino acids long. Attached is an image
> (jpg) of the problem I'm describing.
>
> Thanks for your help in advance,
>
> Leiah Luoma
------------------------------
Message: 5
Date: Thu, 5 Mar 2009 22:34:05 -0500
From: Scott Stagg <sstagg at fsu.edu>
Subject: [Chimera-users] saving a rotated map
To: chimera-users at cgl.ucsf.edu
Message-ID: <F9F24C77-4591-444B-9D5F-2F36BEB48C5C at fsu.edu>
Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed
Hello all,
I would like to save a rotated density map after using the fit
map in map feature, but I can't figure out how to save the
transformed map. Does anyone have any suggestions?
Thanks,
Scott
--
This message has been scanned for viruses and
dangerous content by MailScanner, and is
believed to be clean.
------------------------------
Message: 6
Date: Thu, 5 Mar 2009 20:15:30 -0800
From: Gabriel Lander <glander at scripps.edu>
Subject: Re: [Chimera-users] saving a rotated map
To: Scott Stagg <sstagg at fsu.edu>
Cc: chimera-users at cgl.ucsf.edu
Message-ID: <B3D23906-7252-4625-9F8A-C3761C9D6B84 at scripps.edu>
Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
Hi Scott,
This question has been coming up an awful lot in lab lately, Tom
showed me how to do this a while back -
Say you open 2 maps - #0 and #1
you fit map #1 into map #0, and then in the command line type:
"resample #1 onGrid #0"
it will save the density #1 onto the same grid space as #0.
-gabe
On Mar 5, 2009, at 7:34 PM, Scott Stagg wrote:
> Hello all,
> I would like to save a rotated density map after using the fit
> map in map feature, but I can't figure out how to save the
> transformed map. Does anyone have any suggestions?
>
> Thanks,
> Scott
>
> --
> This message has been scanned for viruses and
> dangerous content by MailScanner, and is
> believed to be clean.
>
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
>
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