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<p>There are many problems with the given mmCIF file. The major
problem for ChimeraX is that in the atom_site table, all of the
chains are designated as the same entity, but they have different
sequences. It would be best if you fixed the program that
generated the mmCIF file to give each chain its own entity. It
would be even better if the entity, entity_poly, and
entity_poly_seq tables were given.<br>
</p>
<p><br>
</p>
<p>A secondary problem is that the struct_conn table is malformed.
The id is not unique. LINK is not a legal conn_type_id. The
mandatory ptrn[12]_label_* columns are missing. The
ptrn[12]_auth_* columns are given, but ptrn[12]_auth_atom_id's
have explicit spaces them that don't match the
atom_site.auth_atom_id's. And the ptrn[1]_symmetry fields are
bogus. Again, it would be best if you fixed the program that
generated the mmCIF file.</p>
<p><br>
</p>
<p>That said, while I am reluctant to put in fixes for bad data
because it slows down the mmCIF reader for everyone, I will see
what I can do for the atom_site table. The struct_conn table is
too messed up to workaround.<br>
</p>
<p><br>
</p>
<p> HTH,</p>
<p><br>
</p>
<p> Greg<br>
</p>
<p><br>
</p>
<div class="moz-cite-prefix">On 6/15/2020 10:21 AM, Anderson, Jacob
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:SN6PR07MB49288188BDABEF27FEEEEB5C9B9C0@SN6PR07MB4928.namprd07.prod.outlook.com">
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255, 255);">
Dear Dr. Pettersen,</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255,
255, 255);">
<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255,
255, 255);">
Thank you so much for your help. That helps me understand what
was causing the problem greatly! <span style="font-family:
Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;">Unfortunately
this is just one filament of a large microtubule complex which
we will have >100 chains (the reason we tried to move to
mmcif). </span></div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255,
255, 255);">
<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255,
255, 255);">
I wrote something to make it ATOM-ee so I could refine it in
coot/phenix. I will probably continue with that pipeline (dock
in chimerax, change to ATOM w/ python, refine in coot/phenix,
wash and repeat). Perhaps if I figure out the mmcif issue it
will be more OK.</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255,
255, 255);">
<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255,
255, 255);">
Thank you again for adding me to that thread!</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255,
255, 255);">
<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255,
255, 255);">
~jacob </div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255,
255, 255);">
<br>
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<div id="divRplyFwdMsg" dir="ltr"><font style="font-size:11pt"
face="Calibri, sans-serif" color="#000000"><b>From:</b> Eric
Pettersen <a class="moz-txt-link-rfc2396E" href="mailto:pett@cgl.ucsf.edu"><pett@cgl.ucsf.edu></a><br>
<b>Sent:</b> Monday, June 15, 2020 1:11 PM<br>
<b>To:</b> Anderson, Jacob
<a class="moz-txt-link-rfc2396E" href="mailto:jacob_r_anderson@hms.harvard.edu"><jacob_r_anderson@hms.harvard.edu></a><br>
<b>Cc:</b> <a class="moz-txt-link-abbreviated" href="mailto:chimerax-users@cgl.ucsf.edu">chimerax-users@cgl.ucsf.edu</a>
<a class="moz-txt-link-rfc2396E" href="mailto:chimerax-users@cgl.ucsf.edu"><chimerax-users@cgl.ucsf.edu></a><br>
<b>Subject:</b> Re: [chimerax-users] ChimeraX: mmcif
connectivity lost in some chains; OK in Coot</font>
<div> </div>
</div>
<div>
<div class="" style="word-wrap:break-word;
line-break:after-white-space">Hi Jacob,
<div class=""><span class="x_x_Apple-tab-span" style="white-space:pre"></span>I
can’t answer your first question (Greg Couch, our “mmCIF
guy”, is the expert there), but I can help with the second.
In the PDB standard there are 3 columns allocated to the
residue name, followed by a blank column and then one column
for the chain ID. Some programs steal that blank column for
a 4-character residue name (Amber) and some steal it for a
2-character chain ID. ChimeraX’s PDB code is based on code
from Chimera, and Chimera interfaced extensively with Amber
programs and therefore interprets that column as as the 4th
character of the residue name. So, when that file is read
in you get single-character chain IDs (which is fine in your
case since you only had ~10 chains that only differed in the
second character) and residue names like SERL and ALAL.
Obviously, those names are non-standard and therefore
ChimeraX writes them out in HETATM records.</div>
<div class=""><span class="x_x_Apple-tab-span" style="white-space:pre"></span>The
good news is that your problem is pretty easy to fix, at
least in this particular case: just throw away the fourth
character of the residue name. I have attached a simple
Python script that does just that, which you just use the
‘open’ command to run (<i class="">i.e.</i> “open res-fix.py”).</div>
<div class=""><br class="">
</div>
<div class="">
<div class="">--Eric</div>
<div class=""><br class="">
</div>
<div class=""><span class="x_x_Apple-tab-span" style="white-space:pre"></span>Eric
Pettersen</div>
<div class=""><span class="x_x_Apple-tab-span" style="white-space:pre"></span>UCSF
Computer Graphics Lab</div>
<div class=""><br class="">
</div>
</div>
</div>
<div class="" style="word-wrap:break-word;
line-break:after-white-space">
<div class="">
<div><br class="">
<blockquote type="cite" class="">
<div class="">On Jun 13, 2020, at 2:59 PM, Anderson,
Jacob <<a
href="mailto:jacob_r_anderson@hms.harvard.edu"
class="" moz-do-not-send="true">jacob_r_anderson@hms.harvard.edu</a>>
wrote:</div>
<br class="x_x_Apple-interchange-newline">
<div class="">
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As an addendum, in coot, I saved OK mmcif file as a
PDB (in zip as coot-mmcifTOpdb.pdb). Reviewing the
file, it looks OK. It also opens and docks OK in
ChimeraX with proper connectivity. However, upon
saving the pdb with its updated coordinates after
using the "Fit To Map" module, all the atoms have
been changed to HETATM (in zip
as it_to_map_PDB_savedinchimerax.pdb)</div>
<div class="" style="font-style:normal;
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<br class="">
</div>
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Might this be a bug? or possibly a product of saving
a cif file in coot to pdb? It was reproduced upon a
second try.</div>
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</div>
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Maybe to consolidate the problems:</div>
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</div>
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1) mmcif not connected in chimerax, but OK in coot</div>
<div class="" style="font-style:normal;
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letter-spacing:normal; text-align:start;
text-indent:0px; text-transform:none;
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font-family:Calibri,Arial,Helvetica,sans-serif;
font-size:12pt; background-color:rgb(255,255,255)">
[upon trying a workaround with an OK PDB file]</div>
<div class="" style="font-style:normal;
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2) A fit to map PDB, when saved with chimerax, has
all atoms changed to HETATM</div>
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<br class="">
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<font class="" face="Arial, sans-serif"><span
class="" style="font-size:12px"><b
class="">~jacob</b></span></font></div>
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<font class="" style="font-size:11pt" face="Calibri,
sans-serif"><b class="">From:</b><span
class="x_x_Apple-converted-space"> </span>Anderson,
Jacob<br class="">
<b class="">Sent:</b><span
class="x_x_Apple-converted-space"> </span>Saturday,
June 13, 2020 1:48 PM<br class="">
<b class="">To:</b><span
class="x_x_Apple-converted-space"> </span><a
href="mailto:chimerax-users@cgl.ucsf.edu"
class="" moz-do-not-send="true">chimerax-users@cgl.ucsf.edu</a><span
class="x_x_Apple-converted-space"> </span><<a
href="mailto:chimerax-users@cgl.ucsf.edu"
class="" moz-do-not-send="true">chimerax-users@cgl.ucsf.edu</a>><br
class="">
<b class="">Subject:</b><span
class="x_x_Apple-converted-space"> </span>ChimeraX:
mmcif connectivity lost in some chains; OK in Coot<span
class="x_x_Apple-converted-space"> </span></font>
<div class=""> </div>
</div>
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<div class=""
style="font-family:Calibri,Arial,Helvetica,sans-serif;
font-size:12pt; background-color:rgb(255,255,255)">
Dear ChimeraX team,</div>
<div class=""
style="font-family:Calibri,Arial,Helvetica,sans-serif;
font-size:12pt; background-color:rgb(255,255,255)">
<br class="">
</div>
<div class=""
style="font-family:Calibri,Arial,Helvetica,sans-serif;
font-size:12pt; background-color:rgb(255,255,255)">
Thank you very much for your work on this great
software. We use it daily, and without which it
would be extremely difficult to articulate our
science. </div>
<div class=""
style="font-family:Calibri,Arial,Helvetica,sans-serif;
font-size:12pt; background-color:rgb(255,255,255)">
<br class="">
</div>
<div class=""
style="font-family:Calibri,Arial,Helvetica,sans-serif;
font-size:12pt; background-color:rgb(255,255,255)">
I am touching base with a problem I am having
after migrating from a pdb --> mmcif format.<span
class=""
style="font-family:Calibri,Arial,Helvetica,sans-serif;
font-size:12pt">For context, I am running
ChimeraX on Ubuntu 20.04 using a fresh deb
install this morning:</span></div>
<div class=""
style="font-family:Calibri,Arial,Helvetica,sans-serif;
font-size:12pt; background-color:rgb(255,255,255)">
<br class="">
</div>
<div class=""
style="font-family:Calibri,Arial,Helvetica,sans-serif;
font-size:12pt; background-color:rgb(255,255,255)">
<span class=""> chimerax --version<br class="">
</span>
<div class="">UCSF ChimeraX version: 1.0
(2020-06-04)<br class="">
</div>
<div class="">© 2016-2020 Regents of the
University of California. All rights reserved.<br
class="">
</div>
<span class=""></span><br class="">
</div>
<div class=""
style="font-family:Calibri,Arial,Helvetica,sans-serif;
font-size:12pt; background-color:rgb(255,255,255)">
<br class="">
</div>
<div class=""
style="font-family:Calibri,Arial,Helvetica,sans-serif;
font-size:12pt; background-color:rgb(255,255,255)">
To be explicit, my problem is entirely
reproducible. Specifically, I have a file
(attached) that when opened in ccpem's Coot
v0.9-pre, has all the connectivity present.
However, when I switch to ChimeraX, the
connectivity of some chains are lost. A good
example of this contrast on chain connectivity
fidelity is chain LA and LB. (photo attached).</div>
<div class=""
style="font-family:Calibri,Arial,Helvetica,sans-serif;
font-size:12pt; background-color:rgb(255,255,255)">
<br class="">
</div>
<div class=""
style="font-family:Calibri,Arial,Helvetica,sans-serif;
font-size:12pt; background-color:rgb(255,255,255)">
I tried reading through the<span
class="x_x_Apple-converted-space"> </span><a
href="https://urldefense.proofpoint.com/v2/url?u=https-3A__www.rbvi.ucsf.edu_chimerax_docs_devel_bundles_mmcif_src_mmcif-5Fguidelines.html&d=DwMFaQ&c=WO-RGvefibhHBZq3fL85hQ&r=WAfw3qrUG1ShU2YpwE9tWl1TX9X2iVUkDLLxcqiRjEo&m=Vg4JgEdu2yfdqjQKWHvvz4CoIUTuDldwAMK6apyPSrA&s=iNw8sd1v4Q1zVr_9fm2k4XezIAR-Wec218Jy-ONABQY&e="
title="https://www.rbvi.ucsf.edu/chimerax/docs/devel/bundles/mmcif/src/mmcif_guidelines.html"
class="" moz-do-not-send="true">ChimeraX
documentation on this CIF format,</a> but it
remained not totally clear to me what is going
awry in some chains but not in others.</div>
<div class=""
style="font-family:Calibri,Arial,Helvetica,sans-serif;
font-size:12pt; background-color:rgb(255,255,255)">
<br class="">
</div>
<div class=""
style="font-family:Calibri,Arial,Helvetica,sans-serif;
font-size:12pt; background-color:rgb(255,255,255)">
If you might have any insight on how to overcome
this problem in chimerax, and allow all the chains
to remain their connectivity, I would very much
appreciate your thoughts/wisdom on the topic.</div>
<div class=""
style="font-family:Calibri,Arial,Helvetica,sans-serif;
font-size:12pt; background-color:rgb(255,255,255)">
<br class="">
</div>
<div class=""
style="font-family:Calibri,Arial,Helvetica,sans-serif;
font-size:12pt; background-color:rgb(255,255,255)">
~Jacob</div>
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<br class="">
</div>
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<span
id="x_x_cid:0f6782e1-eb79-43db-93e8-0f8f44417fb3"><image.png></span><br
class="">
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<span
id="x_x_cid:E2312170-76A5-4C93-A44A-200D3A6A3F81@cgl.ucsf.edu"><pdb_hetatm_files.zip></span><span
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<a href="mailto:ChimeraX-users@cgl.ucsf.edu" class=""
style="font-family:Helvetica; font-size:12px;
font-style:normal; font-variant-caps:normal;
font-weight:normal; letter-spacing:normal;
orphans:auto; text-align:start; text-indent:0px;
text-transform:none; white-space:normal;
widows:auto; word-spacing:0px"
moz-do-not-send="true">ChimeraX-users@cgl.ucsf.edu</a><br
class="" style="font-family:Helvetica;
font-size:12px; font-style:normal;
font-variant-caps:normal; font-weight:normal;
letter-spacing:normal; text-align:start;
text-indent:0px; text-transform:none;
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text-decoration:none">
<span class="" style="font-family:Helvetica;
font-size:12px; font-style:normal;
font-variant-caps:normal; font-weight:normal;
letter-spacing:normal; text-align:start;
text-indent:0px; text-transform:none;
white-space:normal; word-spacing:0px;
text-decoration:none; float:none;
display:inline!important">Manage subscription:</span><br
class="" style="font-family:Helvetica;
font-size:12px; font-style:normal;
font-variant-caps:normal; font-weight:normal;
letter-spacing:normal; text-align:start;
text-indent:0px; text-transform:none;
white-space:normal; word-spacing:0px;
text-decoration:none">
<a
href="https://urldefense.proofpoint.com/v2/url?u=https-3A__plato.cgl.ucsf.edu_mailman_listinfo_chimerax-2Dusers&d=DwMFaQ&c=WO-RGvefibhHBZq3fL85hQ&r=WAfw3qrUG1ShU2YpwE9tWl1TX9X2iVUkDLLxcqiRjEo&m=Vg4JgEdu2yfdqjQKWHvvz4CoIUTuDldwAMK6apyPSrA&s=TqPt2UK_I5TXkKmACbYqexgynVNPJ28_fsYTqyWza3w&e="
class="" style="font-family:Helvetica;
font-size:12px; font-style:normal;
font-variant-caps:normal; font-weight:normal;
letter-spacing:normal; orphans:auto;
text-align:start; text-indent:0px;
text-transform:none; white-space:normal;
widows:auto; word-spacing:0px"
moz-do-not-send="true">https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</a><br
class="" style="font-family:Helvetica;
font-size:12px; font-style:normal;
font-variant-caps:normal; font-weight:normal;
letter-spacing:normal; text-align:start;
text-indent:0px; text-transform:none;
white-space:normal; word-spacing:0px;
text-decoration:none">
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<pre class="moz-quote-pre" wrap="">_______________________________________________
ChimeraX-users mailing list
<a class="moz-txt-link-abbreviated" href="mailto:ChimeraX-users@cgl.ucsf.edu">ChimeraX-users@cgl.ucsf.edu</a>
Manage subscription:
<a class="moz-txt-link-freetext" href="https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users">https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</a>
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