[Chimera-users] Binding pocket surface command script not working

Fri Mar 28 12:14:38 PDT 2014

Hi Markus,

This error occurs when the two specified surfaces have no points within the specified distance range. This is a bug -- it should just report the contact area as zero in that case. I've fixed that in tonight’s daily build.

	http://plato.cgl.ucsf.edu/trac/chimera/ticket/12966

But there is a second problem, since your commands work on Mac with 64-bit Chimera 1.8.1. The trouble is almost surely that the surface calculation for one of the two sets of atoms failed on 64-bit Windows. Unfortunately the 3rd part surface calculation code we use (MSMS) often fails. Some ideas about how to try to get surfaces are here

	http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html

although often nothing works. The surface calculation fails especially often in 64-bit Windows Chimera. You might try 32-bit Windows Chimera. Our next generation Chimera will have surface calculation that always works, but is not expected out for at least 6 months.

	Tom

On Mar 28, 2014, at 11:23 AM, Markus Heller <mheller at cdrd.ca> wrote:

> Hi Elaine,
>  
> Thanks for your reply.  I just filed a bug report on this, as per Tom’s request.
>  
> I should also mention that I did get some result with your version, but not what I expected: essentially a couple of surface blobs, but nothing like your figure.
>  
> Anyhow, this seems to be a genuine bug, so I’ll just hang tight and wait for a fix.
>  
> Cheers
> Markus
>  
> From: Elaine Meng [mailto:meng at cgl.ucsf.edu] 
> Sent: Thursday, March 27, 2014 2:39 PM
> To: Markus Heller
> Cc: chimera-users at cgl.ucsf.edu
> Subject: Re: [Chimera-users] Binding pocket surface command script not working
>  
> Hi Markus,
> It is a mystery to me… I tried it in both 1.8.1 and the current pre-1.9 daily build and didn't get the error.  I'd say go ahead and submit a report… we can always close it if it's not reproducible.
>  
> However, the result I got was somewhat ugly because there were several holes in the pocket.  I then tried a larger cutoff, as in the folowing:
>  
> open 2v5z
> delete :.b
> split atoms :sag
> surface
> measure contactArea #0.2 #0.1 4 slab -.1,0 color tan
> measure contactArea #0.2 #0.1 3.99 slab -.11,-.01 color cornflowerblue
> ~surf #0
> ~disp; ~ribbon; disp :sag
> sop hideDust #1,2 size 1 metric sizeRank
>  
> which I think got rid of as many of the holes as reasonably possible, but there were still a couple of ugly places that might be surface calculation artifacts:  where the blue shows through the tan near the middle of the attached image, and the little funnel on the upper right.  There is a small opening through the funnel, so I'm not sure whether it's an artifact or the actual shape of the pocket. This general process would be expected to make a better-looking figure for pockets with fewer openings.
>  
> This pocket could alternatively be considered one large pocket containing both the SAG and FAD.  For example, in a separate Chimera session I tried:
>  
> open castp:2v5z
>  
> which reports the two largest pockets as the SAG/FAD pockets of the A and B chains, respectively.  If you are using the "measure contactArea" approach to get the appearance of different inside and outside pocket colors as shown in the image gallery figure, it could be done for this collective pocket with "split atoms :sag,fad" (well, assuming you didn't get that mysterious error again!).  Sorry for the weirdness,
> Elaine
> ----------
> Elaine C. Meng, Ph.D. 
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> <image001.png>
> 
> On Mar 27, 2014, at 1:05 PM, Markus Heller <mheller at cdrd.ca> wrote:
> 
> Hello,
>  
> I’m trying to reproduce the Binding Pocket Surface image from the Gallery with a different pdb file.
>  
> I can successfully reproduce with the pdb used in the example (2zcp), but not with 2v5z.  Running latest Chimera.
>  
> Steps to reproduce:
>  
> open 2v5z
> delete :.b
> split atoms :sag
> surface
> measure contactArea #0.2 #0.1 3 slab -.1,0 color tan
>  
> gives an error:
>  
> error: Array must be 2-dimensional, got 1-dimensional
>  
>  
>   File "C:\Program Files\Chimera 1.8.1\share\MeasureVolume\__init__.py", line 60, in surface_area
>     area = surface_area(varray, tarray)
>  
> See reply log for Python traceback.
>  
> Why, and would it be helpful to file a bug report?
>  
> Thanks and Cheers
> Markus
>  
> --
> Markus Heller, Ph.D.
> NMR Scientist
> CDRD - The Centre for Drug Research and Development
> 2405 Wesbrook Mall, Fourth Floor | Vancouver, BC  V6T 1Z3 | Main: (604) 827-1147
> Direct: (604) 827-1122 | F: (604) 827-1299 | E: mheller at cdrd.ca | www.cdrd.ca
> <image007.png>
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