Thomas,
Thanks for your quick reply. Just to show you the size of the input file, it
has 12854 atoms per model (including waters and protein hydrogens) and 94
models. Answering your questions:
> - Does the state indicator in the bottom right corner also max out, or does
> it show all models?
On the iMac that works, it shows 94 frames, but on all the other Macs, it shows
52, but frame 52 shows an incomplete dimer.
> - Does the "rebuild" command eventually show the partial/missing models?
No.
> - Does "set defer_builds_mode, 3" make a difference?
No, using it in two ways: (1) loading in the pdb file, then “set
defer_builds_mode, 3” or (2) start PyMol, set defer_builds_mode, 3, and then
load pdb file. In both cases, the state indicator still shows only 52 frames
(out of the 94), but in the latter, PyMol logs each model loaded up to 52.
One new piece of information is that merely stripping out all the hydrogen
atoms, which reduces the atoms per model significantly (file size now is ~102
MB rather than ~200 MB), circumvents the problem on these Macs. So the
question is why this quite sharp and consistent model limitation on these Macs.
Moreover, we are using PyMol not only to display the loop fluctuations from
model to model, but also to calculate the rms fluctuations in Å per residue.
When PyMol fails to load all the models, we get this error from the script we
use:
Traceback (most recent call last):
File "/Applications/MacPyMOL.app/Contents/pymol/modules/pymol/parser.py",
line 256, in parse
self.result=layer.kw[0](*layer.args, **layer.kw_args)
File "/Users/admin/Desktop/ens_tools_rev.py", line 252, in ens_rmsf
rmsf_coord[i_seq] += distance(xyz, mean_coords[i_seq])**2
IndexError: list index out of range
Hope this allows you to find the problem, but at least I have a work-around.
Thanks,
Michael
****************************************************************
R. Michael Garavito, Ph.D.
Professor of Biochemistry & Molecular Biology
603 Wilson Rd., Rm. 513
Michigan State University
East Lansing, MI 48824-1319
Office: (517) 355-9724 Lab: (517) 353-9125
FAX: (517) 353-9334 Email: rmgarav...@gmail.com
****************************************************************
> On Jun 6, 2017, at 11:19 AM, Thomas Holder <thomas.hol...@schrodinger.com>
> wrote:
>
> Hi Michael,
>
> This is unexpected. Some quick questions:
>
> - Does the state indicator in the bottom right corner also max out, or does
> it show all models?
>
> - Does the "rebuild" command eventually show the partial/missing models?
>
> - Does "set defer_builds_mode, 3" make a difference?
> https://pymolwiki.org/index.php/Defer_builds_mode
>
> Thanks,
> Thomas
>
>> On Jun 6, 2017, at 4:26 PM, R. Michael Garavito <rmgarav...@gmail.com> wrote:
>>
>> We’ve been having some problems with Mac PyMol when dealing with PDB files
>> with 50+ models output from ensemble refinement. The pdb files are large
>> (up to 200 MB) and can contain up to 100 models. My iMac (OS 10.10.5, 4
>> GHz Intel Core i7, 32 GB ram, AMD Radeon R9 M290X 2048 MB) works fine with
>> these large files.
>>
>> However, some of our older Macs (e.g., Mac Pro with 24 GB ram and a quite
>> reasonable graphics board) fail to load in all the models, maxing out at 51
>> models/frames regardless of the number of models/frames in the PDB. We have
>> seen this on 3 different Macs. Frame 52 also shows a partial load: subunit
>> A looks fine, but subunitB has only a portion of the polypeptide loaded.
>> This problems occurs even with PyMol 1.8.6.0 on these Macs. As we need to
>> run scripts to calculate rms fluctuations and to make some figures, we need
>> to look at all the models. Any ideas? Has anyone seen this before?
>>
>> We are currently testing to see whether this occurs on linux machines.
>>
>> Thanks,
>>
>> Michael
>>
>> ****************************************************************
>> R. Michael Garavito, Ph.D.
>> Professor of Biochemistry & Molecular Biology
>> 603 Wilson Rd., Rm. 513
>> Michigan State University
>> East Lansing, MI 48824-1319
>> Office: (517) 355-9724 Lab: (517) 353-9125
>> FAX: (517) 353-9334 Email: rmgarav...@gmail.com
>> ****************************************************************
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
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