[Chimera-users] Fwd: Re: Density display with CHIMERA

[F.Xavier Gomis-Rüth]

Fantastic, Tom, it worked right away with the vop cover command!
Thanks a lot!
Best,
Xavier

On 13/4/16 11:12 PM, Tom Goddard wrote:
> Hi Xavier,
>
>   Chimera positions the map according to the header values in the CCP4 
> file.  Perhaps the alignment is correct but the map does not cover the 
> PDB model.  Coot will use the crystal unit cell size to replicate the 
> map to cover the atomic model but Chimera does not do that.  You can 
> make a new map that covers the atomic coordinates in Chimera using the 
> “vop cover” command, for example, "vop cover #0 atombox #1” where #0 
> is the original map and #1 is the atomic model.
>
>   If this isn’t the problem and really the atomic model does not match 
> the density then you might try Chimera command “volume #0 dumpheader 
> true” to get the CCP4 header values.  The nrstart, ncstart, nzstart 
> values control the map alignment and other values give the unit cell 
> size and cell angles.  Send me all those header values and maybe I’ll 
> have an idea why Chimera and Coot give different alignment.
>
> Tom
>
>
>> On Apr 13, 2016, at 9:58 AM, F.Xavier Gomis-Rüth <fxgr at ibmb.csic.es 
>> <mailto:fxgr at ibmb.csic.es>> wrote:
>>
>> Dear Elaine,
>> thanks a lot for your prompt answer and sorry for not using the . The 
>> coordinates are regular PDB coordinates coming from a crystallographic
>> refinement program such as PHENIX, BUSTER/TNT, REFMAC5, and the map 
>> file was likewise generated by these
>> programs. It's the regular pair of coordinates and map one uses to 
>> perform subsequent model building with COOT and, in this program, 
>> everything
>> is fine as to the matching of coordinates and map. In this case, 
>> should I really change the origin of the map?
>> Best wishes,
>> Xavier
>>
>>
>> -------- Forwarded Message --------
>> Subject: 	Re: Density display with CHIMERA
>> Date: 	Wed, 13 Apr 2016 09:52:07 -0700
>> From: 	Elaine Meng
>> Reply-To: 	Chimera User Forum <chimera-users at cgl.ucsf.edu>
>>
>> 	
>> CC: 	Chimera User Forum <chimera-users at cgl.ucsf.edu>
>>
>>
>>
>> On Apr 13, 2016, at 9:27 AM, F.Xavier Gomis-Rüth  wrote:
>>
>> > Dear Elaine,
>> > I am encountering problems while trying to display a fragment of a structure from a PDB file superimposed
>> > with its Fourier map. When I load the latter, it is presented displaced from the model and I cannot get it centered
>> > onto it. All other features (contouring, mesh/solid style, etc.) work fine, it's just that atoms and density do not superimpose.
>> > I've tried it with different space groups, just for the case it was a problem in a particular library, but without success.
>> > I am working on a Mac, I don´t know if there is a problem, and I am using CCP4 maps.
>> > Any suggestions would be very welcomed!
>> > Best wishes,
>> > Xavier
>> > --
>> > <fxgr_signanew.jpg>
>>
>> Dear Xavier,
>> I don’t know where or from what program these files came frome, so it is hard to say why the coordinates don’t match up.  In some cases the map file does not include information that aligns its coordinates with the corresponding atomic structure, or maybe the map file header does have this information but it is not in a format understood by Chimera.
>>
>> You can change the offset of the map in Chimera, if you know what it should be.  After opening the map, in the Volume Viewer dialog choose Features… Coordinates, and in the resulting options you can change origin index, spacing, etc.  However, I don’t know how to figure out what values are needed, if you don’t already have that information.  The options are explained here:
>>
>> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/framevolumeviewer.html>
>> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#coordinates>
>>
>> It is generally recommended to send Chimera questions tochimera-users at cgl.ucsf.edu   (CC’d here), especially in certain areas where others know more than I do.  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
>>
>>
>>
>>
>>
>>
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