[Chimera-users] PDB not opening

Elaine Meng meng at cgl.ucsf.edu
Wed Jun 24 10:33:41 PDT 2015

Hi Yaikhomba,
For your question 2:

Cap coloring should work exactly as described in the bfactor tutorial, where you first color the atoms by the property of interest (bfactor, conservation, hydrophobicity...), then use color zone to make the surface match nearby atoms.  It sounds like you didn’t color the *atoms* by conservation or hydrophobicity before using color zone.


The atoms could have been colored with the rangecolor command or the Render by Attribute dialog.  As you said, Color Zone will apply to the whole surface, but it will match the atom coloring.  

If you really only want to use the zoning on the cap part, there is an ugly workaround, but the differences in coloring will be rather subtle.  The ugly workaround is to do rangecolor (or Render dialog) twice.  First use it to color the atoms (coloring ribbons, surface too is OK), then instead of Color Zone dialog, use command “scolor zone” with “autoUpdate false” to color the whole surface by zone to the protein atoms, then rangecolor (or Render dialog) again to recolor the non-cap part of the surface.

I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jun 24, 2015, at 1:03 AM, YAikhombA Mutum <yaikhomba.mutum at students.iiserpune.ac.in> wrote:

> Hi
> 1. I'm not able to fetch pdb's from Chimera by the command 'open 121p'. It just says 'opened 121p' in the reply log while it display a blank black screen. There are no active models displayed too (in the active models panel, there are no active tabs for models (0,1,2...)) despite the status in the reply log.
> The internet connections are ok (my browser is working fine). On checking the preferences (Favorites ---> preferences), everything seems fine (for instance in Category: Fetch (save fetched flie: True and use local files:True/False (I've tried both cases))). Even the category of web access seems ok.
> A day before I'd been able to fetch pdb's by just the command (open 1zik (say)). Now, the only way to retrieve it is to go to the rcsb website, download the pdb from a browser and then run it in chimera.
> Moreover, even if it (the pdb file) is already downloaded it doesn't run by entering the command (again the preferences are fine).
> How can I sort out this?
> 2. Is there a way to color the capped surface (the flat surface when you cut a protein virtually) based on sequence conservation color range. I tried the same way B factor surface capping is done as in the tutorials but the one for conservation doesn't work. It instead colors the 'whole' surface something else (Automatically uses default 'color by heteroatom' (red, tan and blue) not the colors I used for the sequence conservation).
> The same when I try to cap a surface based on hydrophobicity.
> Thanks in advance!
> Yaikhomba

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